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大麦DUF668家族基因鉴定及表达分析

大麦DUF668家族基因鉴定及表达分析

麦类作物学报 2024,44(2):158-168J o u r n a l o fT r i t i c e a eC r o ps d o i :10.7606/j.i s s n .1009-1041.2024.02.03网络出版时间:2023-12-13网络出版地址:h t t ps ://l i n k .c n k i .n e t /u r l i d /61.1359.s .20231212.1500.010大麦D U F 668家族基因鉴定及表达分析收稿日期:2023-01-23 修回日期:2023-07-04基金项目:国家自然科学基金面上项目(32272159);国家重点研发计划项目(2019Y F D 1005002-03-04)第一作者E -m a i l :799148942@q q .c o m (王月雪)通讯作者E -m a i l :z yh b o b @163.c o m (赵彦宏)王月雪1,母景娇1,王孜逸2,耿梓瀚1,倪守飞1,刘梦迪1,蔡倩2,赵彦宏1,王艳芳2(1.鲁东大学农学院,山东烟台264025;2.鲁东大学生命科学学院,山东烟台264025)摘 要:D U F 668家族基因对植物逆境胁迫响应有重要作用㊂为探讨大麦D U F 668家族基因的结构及表达模式,采用生物信息学的方法对大麦D U F 668基因结构㊁蛋白结构㊁系统进化树㊁共线性及表达模式进行了分析㊂结果显示,供试大麦中共鉴定出9个D U F 668基因,分布在5条染色体上㊂系统发育进化树将9个D U F 668基因分为三个亚组,第Ⅰ亚组包括H v D U F 668-01㊁H v D U F 668-02和H v D U F 668-09,内含子数量较多,均有11个内含子;第Ⅲ亚组包括H v D U F 668-04㊁H v D U F 668-05㊁H v D U F 668-07和H v D U F 668-08,内含子数0~3个,其中H v D U F 668-04与H v D U F 668-05没有内含子;第Ⅱ亚组包括H v D U F 668-03和H v D U F 668-06,内含子数量(9和7)介于第Ⅰ亚组和第Ⅲ亚组之间㊂蛋白保守基序分析表明,9个蛋白均含有D U F 668保守结构域的特征序列及D U F 3475保守结构域的特征序列(H v D U F 668-06除外);第Ⅰ亚组蛋白的M o t i f 数量(8~10个)比第Ⅱ㊁Ⅲ亚组(4~6个)多,且包含第Ⅱ㊁Ⅲ亚组中的所有M o t i f ㊂表达谱分析表明,不同D U F 668基因在不同组织和发育时期的表达量存在差异,H v D U F 668-09在颖果中的表达量随着颖果的发育而升高,而H v D U F 668-01和H v D U F 668-02则相反;H v D U F 668-01和H v D U F 668-02在花序中的表达量随着花序的发育而升高㊂q R T -P C R 结果显示,受黄矮病病毒侵染大麦幼苗与未受侵染幼苗相比,H v D U F 668-04㊁H v D U F 668-05和H v D U F 668-08表达量提高了100~180倍㊂关键词:大麦;D U F 668家族基因;生物信息学;逆境胁迫;表达模式分析中图分类号:S 512.3;S 330 文献标识码:A 文章编号:1009-1041(2024)02-0158-11I d e n t i f i c a t i o na n dE x p r e s s i o nP r o f i l e s o fD U F 668G e n eF a m i l y i nB a r l e yW A N GY u e x u e 1,M UJ i n g j i a o 1,W A N GZ i y i 2,G E N GZ i h a n 1,N I S h o u f e i 1,L I U M e n g d i 1,C A I Q i a n 2,Z H A OY a n h o n g 1,W A N GY a n f a n g2(1.C o l l e g e o fA g r i c u l t u r e ,L u d o n g U n i v e r s i t y ,Y a n t a i ,S h a n d o n g 264025,C h i n a ;2.C o l l e g e o fL i f e s c i e n c e ,L u d o n g U n i v e r s i t y,Y a n t a i ,S h a n d o n g 264025,C h i n a )A b s t r a c t :T h eD U F 668g e n e f a m i l yp l a y sa n i m p o r t a n t r o l e i n p l a n t s t r e s s r e s po n s e .I no r d e r t oe x -p l o r e t h e g e n e s t r u c t u r e a n d e x p r e s s i o n p a t t e r no f b a r l e y D U F 668g e n e f a m i l y ,w e a n a l yz e d t h e g e n e s t r u c t u r e ,p r o t e i n s t r u c t u r e ,p h y l o g e n e t i c t r e e ,c o l l i n e a r i t y a n d e x p r e s s i o n p a t t e r no f b a r l e y D U F 668g e n e f a m i l y b y bi o i n f o r m a t i c s .T h e r e s u l t s s h o w e d t h a t n i n eD U F 668g e n e sw e r e i d e n t i f i e d ,d i s t r i b u -t e do n f i v e c h r o m o s o m e s .T h e n i n eD U F 668g e n e sw e r e d i v i d e d i n t o t h r e e s u b g r o u p s b yp h y l o ge n e t i c t r e e .S u b g r o u p Ic o n t a i n ed H v D U F 668-01,H v D U F 668-02a n d H v D U F 668-09w i t h11i n t r o n s ,w h i le s u b g r o u p Ⅲco n t a i n e d H v D U F 669-04,H v D U F 668-05,H v D U F 668-07a n d H v D U F 668-08,w i t ht h e l e a s t i n t r o n s ,a m o n g w h i c h H v D U F 668-04a n d H v D U F 668-05h a dn o i n t r o n s ;s u b g r o u p Ⅱco n t a i n e d H v D U F 668-03a n d H v D U F 668-06,w i t h i n t r o n s b e t w e e n s u b g r o u p Ⅰa n d s u b g r o u p Ⅲ.P r o t e i n c o n -s e r v e dm o t i f a n a l y s i s s h o w e d t h a t a l l p r o t e i n s c o n t a i n e d t h e c h a r a c t e r i s t i c s e qu e n c e so fD U F 668c o n -s e r v e dd o m a i na n dD U F3475c o n s e r v e dd o m a i n(e x c e p t f o rH v D U F668-06).T h en u m b e ro fm o t i f i n s u b g r o u pⅠ(8-10)w a sm o r e t h a n t h a t i n s u b g r o u pⅡa n dⅢ(4-6),a n d t h em o t i f s o f s u b g r o u pⅡa n dⅢw e r e a l s o c o n t a i n e d i n s u b g r o u pⅠ.E x p r e s s i o n p r o f i l e a n a l y s i s s h o w e d t h a t t h e e x p r e s s i o no f d i f f e r e n tD U F668g e n e sw a s d i f f e r e n t i nd i f f e r e n t t i s s u e s a n dd e v e l o p m e n t a l s t a g e s.T h e e x p r e s s i o n o f H v D U F668-09i nc a r y o p s i si n c r e a s e d w i t ht h ed e v e l o p m e n to fc a r y o p s i s,w h i l et h ee x p r e s s i o no f H v D U F668-01a n d H v D U F668-02i n c r e a s e d w i t ht h ed e v e l o p m e n to f i n f l o r e s c e n c e.T h er e s u l t so f q R T-P C Rs h o w e d t h a t t h e e x p r e s s i o n l e v e l so f H v D U F668-04,H v D U F668-05a n d H v D U F668-08i n b a r l e y s e e d l i n g s i n f e c t e d b y y e l l o wd w a r f v i r u sw e r e i n c r e a s e d b y100-180t i m e s c o m p a r e dw i t h t h o s e o f s e e d l i n g sw i t h o u t y e l l o wd w a r f v i r u s i n f e c t i o n.K e y w o r d s:B a r l e y;D U F668g e n e f a m i l y;B i o i n f o r m a t i c s;S t r e s s;E x p r e s s i o n p r o f i l e a n a l y s i sD U F(d o m a i no fu n k n o w nf u n c t i o n)家族是一大类含有未知功能的超基因家族总称[1-2]㊂随着研究的深入,D U F家族的数量迅速增加,截至2021年,整个家族已扩展至D U F3598[3]㊂大部分D U F基因被认为与非生物胁迫有关[4-9]㊂D U F668是其中一类高度保守的植物特异性的转录因子[10],其特征是包含29个氨基酸的保守结构域,在植物抗逆与抗病的过程中发挥着重要作用[11]㊂该结构域最初在拟南芥中发现,位于拟南芥P S I蛋白的C-末端,P S I蛋白具有促进植物生长的作用[12]㊂Z h o n g等[10]研究了拟南芥和8种禾本科代表作物(103个)的D U F668家族基因,发现其对抗旱和生物防御至关重要㊂Z h a o等[11]研究结果显示,D U F668家族基因可增加棉花抗逆性㊂D U F668家族蛋白的重要特征是其中一个亚组包含A v r9/C f-9;C f-9是一种通过识别A v r 多肽而产生特种抗性的蛋白质,而两者相互识别成为C f/A v r互作体系中的一种[10,13]㊂A v r9/C f-9对病原体入侵的识别被作为分析植物防御反应信号通路的典型模型系统[14]㊂研究显示,A v r9/ C f-9有助于水稻提高对伤口及稻瘟病的防御能力[10],有助于棉花提高抗寒性及抗黄萎病的能力[10-11]㊂大麦是世界第四大重要的谷物,也是世界上最早驯化作物之一,不仅是重要的粮食和饲料作物,也是有价值的二倍体模式谷物[15]㊂大麦生长发育过程中面临着很多逆境胁迫[15-18]及病虫害[19-21],而有关D U F668家族在大麦中的进化㊁功能和分类尚未得到系统研究㊂本研究拟系统鉴定大麦D U F668家族的成员,并利用生物信息学的方法对鉴定到的成员进行染色体分布㊁基因结构㊁顺式作用元件等分析,以揭示其可能的生物学功能,为大麦抗逆育种提供参考㊂1材料与方法1.1大麦D U F668家族成员的鉴定及定位从E n s e m b l P l a n t数据库(h t t p://p l a n t s.e n-s e m b l.o r g/i n d e x.h t m l)和U n i P r o t数据库(h t-t p s://w w w.u n i p r o t.o r g/)中下载大麦蛋白序列㊂从P f a m数据库(h t t p://p f a m.x f a m.o r g/)获取D U F668蛋白特征文件(P F05003)㊂利用HMM E R3软件(h t t p://w w w.h mm e r.o r g/)扫描大麦蛋白序列并预测候选的D U F668蛋白;通过S MA R T软件(h t t p://s m a r t.e m b l-h e i d e l-b e r g.d e/)对候选的D U F668蛋白进行鉴定㊂从P h y t o z o m e数据库(h t t p s://p h y t o z o m e. j g i.d o e.g o v/p z/p o r t a l.h t m l)获取大麦D U F668基因在染色体上的位置信息,通过MG2C软件(h t t p://m g2c.i a s k.i n/m g2c_v2.1/)绘制染色体位置图;利用C e l l-P l o c2.0(h t t p://w w w.c s b i o. s j t u.e d u.c n/b i o i n f/C e l l-P L o c-2/)进行蛋白亚细胞定位㊂1.2蛋白结构及基因结构分析利用P r o t P a r a m(h t t p s://w e b.e x p a s y.o r g/ p r o t p a r a m/)预测蛋白的基本理化性质;通过S O P MA(h t t p s://n p s a-p r a b i.i b c p.f r/c g i-b i n/ n p s a_a u t o m a t.p l?p a g e=n p s a_s o p m a.h t m l)预测蛋白的二级结构;使用S W I S S-MO D E L(h t-t p s://s w i s s m o d e l.e x p a s y.o r g/i n t e r a c t i v e)预测蛋白的三级结构;通过T MHMM工具(h t t p s:// s e r v i c e s.h e a l t h t e c h.d t u.d k/s e r v i c e.p h p?T M-HMM-2.0)预测蛋白跨膜结构域㊂利用G S D S(h t t p://g s d s.c b i.p k u e d u.c n/)绘制基因结构图;利用M E M E(h t t p://m e m e s u-i t e.o r g/t o o l s/m e m e)绘制蛋白保守基序图(M o-t i f最大数值设定为10),利用G E N E D O C软件进㊃951㊃第2期王月雪等:大麦D U F668家族基因鉴定及表达分析行保守序列分析㊂1.3顺式作用元件、进化与共线性分析使用P l a n t C A R E(h t t p://b i o i n f o r m a t i c s. p s b.u g e n t.b e/w e b t o o l s/p l a n t c a r e/h t m l/)预测基因启动区域的顺式作用元件并绘制其分布图谱㊂利用M E G A-X软件[22]进行D U F668蛋白的多序列比对,并采用邻接法(N e i g h b o r-j o i n i n g, N J)构建系统发育进化树㊂利用T B t o o l s[23]分别对大麦与玉米㊁大麦与水稻之间的D U F668基因进行共线性分析㊂1.4大麦D U F668基因在不同组织的表达分析从E x p r e s s i o nA l t a s数据库(h t t p s://w w w.e b i.a c.u k/g x a/e x p e r i m e n t s)下载大麦R N A-S e q 转录组数据(E-MT A B-2809),该套数据包含了大麦的根㊁花序1c m㊁花序5c m㊁节间㊁颖果15d㊁颖果5d㊁幼苗和胚芽共8个组织的基因表达信息;从该转录组数据中获取大麦D U F668基因的F P-KM值,并使用T B t o o l s软件绘制大麦D U F668基因的表达热图㊂1.5大麦D U F668基因在不同胁迫下的表达分析试验材料为抗大麦黄矮病品种M o r e x和感病品种A t l a s68㊂将大麦M o r e x种子平铺于平板上浸湿的纱布表面,保持纱布湿润,待种子萌发露白后转移至水培盒进行温室培养,温室条件为昼26ħ/夜23ħ,光照周期为16h光照/8h黑暗;用霍格兰营养液配置100μm o l㊃L-1M e J A㊁100μm o l㊃L-1P E G6000,以营养液为对照;将温室培养7d的大麦分别移至750m L上述溶液中,其中营养液培养分为两组,一组暗处理,一组正常温室培养;不同处理12h㊁24h㊁48h后,取幼苗地上部30m g,于-80ħ保存待用㊂每个处理3次重复㊂将大麦A t l a s68种子分两组播种于花盆中,并放置在温室培养,温室条件同上;大麦出苗15d 后,用不少于20只携带黄矮病毒的蚜虫对其中一组幼苗进行侵染,用同样数量的无毒蚜虫接在另一组大麦幼苗上,作为对照组;蚜虫取食2d后灭蚜,灭蚜后第6天取其地上部分叶片30m g,3次重复,并于-80ħ保存备用㊂用R N Ai s o l a t e rT o t a lR N A E x t r a c t i o nR e-a g e n t(R401-01,诺唯赞)参照使用说明书提取不同处理大麦叶片(-80ħ保存)总R N A㊂使用超微量核酸蛋白测定仪(D e N o v i x,D S-11)测定R N A提取浓度㊂利用试剂盒H i S c r i p tI I1s t S t r a n dc D N A S y n t h e s i s K i t(+g D N A w i p e r)(R212-02,诺唯赞)参照说明书合成c D N A㊂利用P r i m e r3在线软件(h t t p s://p r i m e r3.u t.e e/)设计大麦D U F668基因的q R T-P C R引物,以H v A c t i n基因作为内参,引物由上海生工生物工程有限公司合成㊂使用实时荧光定量试剂盒B i o E a s y M a s t e rM i xS Y B R G r e e n(艾科瑞)参照说明书在A B I7500荧光定量P C R仪中进行基因扩增;扩增条件为95ħ15s,60ħ15s,72ħ30s,39个循环;每个样品3次重复㊂采用2-ΔΔC t 方法计算基因的相对表达量㊂2结果与分析2.1大麦D U F668家族成员的鉴定结果及分析利用HMM E R从大麦中鉴定到9个D U F668基因,其长度为1187~11490b p,对应的C D S长度为888~2007b p;根据其在染色体上的位置分别命名为H v D U F668-01~ H v D U F668-09(表1)㊂9个基因不均匀地分布在大麦的5条染色体上(图1),在C h r5H上最多(4个),在C h r2H和C h r6H上没有检测到;H v D U F668基因在染色体上分布较为分散,没有成簇分布现象㊂这与水稻和棉花的D U F668基因在染色体上的分布特征类似[10-11]㊂9个大麦D U F668蛋白质长度为475~680a a,相对分子量为34.1~74.2k D,等电点(p I)为7.4~9.0,亲水指数(G R A V Y)均为负数,表明大麦D U F668蛋白均为亲水性碱性蛋白(p I>7),但亲水程度有差异(表2)㊂大部分蛋白的二级结构表现为α-螺旋>无规则卷曲>β-折叠>β-转角,只有H v D U F668-06蛋白的二级结构表现为α-螺旋>无规则卷曲>β-转角>β-折叠;9个蛋白的α-螺旋和无规则卷曲占比之和均大于90%㊂H v D U F668蛋白的三级结构呈现出一定的规律性,同一亚组有较大的相似性,不同亚组间有一定差别(图2)㊂跨膜结构域预测结果显示,9个H v D U F668蛋白均不含跨膜结构域,暗示H v D U F668蛋白合成后不会经历跨膜运输㊂亚细胞定位预测结果显示,9个蛋白均定位于细胞核中㊂2.2基因结构及蛋白保守基序分析根据进化树,9个H v D U F668基因被划分为3个亚组,第Ⅰ亚组包括H v D U F668-01㊁H v D U F-668-02和H v D U F668-09共3个基因,其内含子数量较多,均有11个;第Ⅱ亚组包含H v D U F668-03㊃061㊃麦类作物学报第44卷和H v D U F 668-06基因,分别有9和7个内含子;第Ⅲ亚组包含H v D U F 668-04㊁H v D U F 668-05㊁H v D U F -668-07和H v D U F 668-08共4个基因,内含子数依次为0㊁0㊁2和3(图3)㊂由此可看出,不同亚组间的H v D U F 668基因内含子数存在明显差异㊂这与棉花D U F 668家族基因类似[11]㊂第Ⅰ亚组H v D U F 668表1 大麦D U F 668基因的染色体定位及序列信息T a b l e 1 C h r o m o s o m a l l o c a l i z a t i o no f b a r l e y DU F 668g e n e s 基因名G e n e n a m e基因I DG e n e I D位置P o s i t i o n长度L e n g t h /b pC D S /b p 亚组S u b g r o u pH v D U F 668401H O R V U 1H r 1G 074410C h r 1H :507969852~507980221:+6561938ⅠH v D U F 668-02H O R V U 3H r 1G 082170C h r 3H :598203067~598214558:-6802007ⅠH v D U F 668-03H O R V U 4H r 1G 018430C h r 4H :84574590~84578912:-6751992ⅡH v D U F 668-04H O R V U 4H r 1G 060260C h r 4H :505089218~505091246:-4751404ⅢH v D U F 668-05H O R V U 5H r 1G 041250C h r 5H :311355148~311357153:+5551638ⅢH v D U F 668-06H O R V U 5H r 1G 077430C h r 5H :553244801~553250995:-3021569ⅡH v D U F 668-07H O R V U 5H r 1G 112000C h r 5H :637875117~637876304:+563888ⅢH v D U F 668-08H O R V U 5H r 1G 124940C h r 5H :667585479~667589994:+4961461ⅢH v D U F 668-09H O R V U 7H r 1G 116880C h r 7H :644288248~644294274:+6331869Ⅰ+:前导链;-:滞后链㊂+:L e a d i n g s t r a n d ;-:L a g g i n g st r a n d .表2 大麦D U F 668蛋白的基本理化性质T a b l e 2 S e q u e n c e f e a t u r e s a n d p h y s i c o c h e m i c a l p r o p e r t i e s o f t h eD U F 668p r o t e i n s i nb a r l e y蛋白名称P r o t e i nn a m e蛋白I DP r o t e i n I D 长度L e n g t h /a a 分子量MW /k D 等电点P I 亲水指数G R A V Y α-螺旋α-h e l i x β-折叠β-s h e e t β-转角β-a n g l e 卷曲C o i l定位L o c a t i o n H v D U F 668-01M 0Y V S 164572.47.4-0.5250.54.502.842.2N u c l e u sH v D U F 668-02A 0A 287L Y 8651774.19.2-0.6850.34.792.442.5N u c l e u s H v D U F 668-03A 0A 287N F 5666374.29.3-0.5548.77.394.239.7N u c l e u s H v D U F 668-04F 2C Z T 146751.49.9-0.3362.33.002.432.3N u c l e u s H v D U F 668-05A 0A 287RW 7235959.79.6-0.2656.04.771.737.6N u c l e u s H v D U F 668-06A 0A 287RW 0530234.18.5-0.2968.20.662.728.5N u c l e u s H v D U F 668-07A 0A 287RW 2536461.68.5-0.2753.87.102.336.8N u c l e u s H v D U F 668-08M 0X 41251752.110.6-0.2663.26.161.429.2N u c l e u s H v D U F 668-09A 0A 287X X Z 762269.78.7-0.7051.14.662.342.0N u c l e us 图1 大麦H v D U F 668在染色体上的位置F i g .1 C h r o m o s o m e l o c a t i o n s o f b a r l e y Hv D U F 668g e n s ㊃161㊃第2期王月雪等:大麦D U F 668家族基因鉴定及表达分析图2 9个大麦D U F 668蛋白的三级结构图F i g .2 T e r t i a r ys t r u c t u r e s o f t h e n i n e D U F 668p r o t e i n s i nb a r l e y基因较长,其中H v D U F 668-02最长(大于11k b );第Ⅲ亚组的基因较短,其中H v D U F 668-07最短(介于1k b ~2k b )㊂9个H v D U F 668基因内含子的长度差别较大,第Ⅲ亚组基因的内含子较短㊂内含子数量越多,基因形成剪接体的潜在能力越高,推测第Ⅰ亚组H v D U F 668基因形成剪接体的能力强于其它两个亚组㊂蛋白保守基序分析结果(图4)显示,9个H v D U F 668蛋白中共鉴定出10个保守的M o t i f ㊂所有成员均包含M o t i f 1与M o t i f 5,其中M o t i f 1包含D U F 668家族的典型特征保守结构域(29个氨基酸),M o t i f 5则包含D U F 3475家族保守结构域;推测这两个M o t i f 对大麦H v D U F 668的功能至关重要㊂第Ⅰ亚组的H v D U F 668蛋白(H v D U F 668-01㊁H v D U F 668-02㊁H v D U F 668-09)都包含10个M o t i f,且具有相同的排列顺序㊂第Ⅲ亚组H v D U F 668蛋白共包含6个M o t i f ,其中5个M o t i f (M o t i f 1㊁M o t i f 6㊁M o t i f 3㊁M o t i f 5和M o t i f 7)是该亚组所有蛋白共有的,且排列顺序基本一致;M o t i f 2仅在H v D U F 668-07和H v D U F 668-05检测到㊂第Ⅱ亚组的H v D U F 668-03蛋白具有8个M o t i f ,而H v D U F 668-06蛋白则具有最少的M o t i f (4个)㊂总的来看,3个亚组均含有M o t i f 4㊁M o t i f2㊁M o t i f 6和M o t i f 1;不同亚组间的M o t i f 组成存在差异,推测同一亚组大麦H v D U F 668蛋白具有相似功能,不同亚组的H v D U F 668则存在功能差异㊂2.3 进化分析及共线性分析将拟南芥(A r a b i d o ps i st h a l i a n a )㊁亚洲棉(G o s s y p i u ma r b o r e u m )㊁玉米(Z e a m a ys )㊁水稻(O r y z a s a t i v a )㊁野生稻(O r y z ar u f i p o g p o n )㊁二穗短柄草(B r a c h y p o d i u m d i s t a c h yo n )和大麦(H o r d e u mv u l ga r e )的D U F 668蛋白序列(共83条)进行比对,并构建系统进化树(图5)㊂结果发现,83条蛋白被分为3个亚族(Ⅰ亚族㊁Ⅱ亚族㊁Ⅲ亚族)㊂其中,第Ⅱ亚族仅存在于单子叶植物,推测这一亚族是单子叶植物单独分化而来,或者在进化过程中双子叶植物丢失了这一亚族;第Ⅰ亚族与第Ⅲ亚族均含有单㊁双子叶植物,推测其起源于共同祖先,且D U F 668是高度保守的基因家族㊂大麦9个D U F 668蛋白中有7个相邻分支均是二穗短柄草,说明相比其它物种,大麦与二穗短柄草的亲缘关系更近㊂共线性分析结果(图6)显示,大麦与水稻D U F 668基因有6对共线性基因对,大麦与玉米D U F 668基因有3对共线性基因对,大麦与拟南芥没有共线性基因对㊂这说明大麦与同属于单子叶禾本科的水稻的亲缘关系比属于双子叶植物的拟南芥更近;大麦与水稻的亲缘关系近于玉米㊂共线性基因对往往具有相同或高度相似的功能,推测大麦与水稻之间的6对共线性D U F 668基因具有相似功能㊂图3 大麦D U F 668基因结构分析F i g .3G e n e s t r u c t u r e a n a l y s i s o f b a r l e y DU F 668㊃261㊃麦 类 作 物 学 报 第44卷图4 大麦D U F 668蛋白保守结构域与蛋白基序分析F i g .4 A n a l y s i s o f t h e c o n s e r v e dd o m a i n s a n dm o t i f s o fD U F 668i nb a r l ey图5 D U F 668家族基因的多物种进化树F i g .5 P h y l o g e n e t i c t r e e o fD U F 668g e n e f a m i l y i nm u l t i -s pe c i e s 图6 大麦与水稻和玉米D U F 668家族基因的共线性分析F i g .6 C o l l i n e a r i t y a n a l y s i sD U F 668g e n e f a m i l y i nb a r l e y ,r i c e a n d s o yb e a n ㊃361㊃第2期王月雪等:大麦D U F 668家族基因鉴定及表达分析2.4 大麦D U F 668基因顺式作用元件分析利用P l a n t C A R E 软件从大麦H v D U F 688基因上游的启动区(起始密码子上2000b p)进行顺式作用元件预测分析,结果发现,9个大麦H v D U F 668基因的上游启动区中共存在266个顺式作用元件㊂根据功能将其分为4种类型:植物生长,胁迫响应,植物激素响应和光响应(表3和图7)㊂其中,参与植物激素响应的顺式作用元件数量最多,主要包括茉莉酸甲酯㊁脱落酸㊁生长素㊁赤霉素和水杨酸等响应元件;其次是光响应顺式作用元件,包括A A A 基序(光响应元件)和A E -b o x(光响应模块的一部分)等;植物生长类中鉴定出C A T -b o x (分生组织表达)和O 2位点(参与玉米醇溶蛋白代谢调节)等多个作用元件;胁迫响应原件有M B A ㊁C C A A T -b o x 等㊂4个类型中,激素响应元件和光响应元件的数量较大,分别为99和86个,推测H v D U F 668在大麦对激素响应中发挥重要的作用,并且其基因的转录可能受光周期的调控;逆境胁迫的响应元件含有57个,暗示该家族基因在大麦面对逆境胁迫时发挥了重要的作用;植物生长的响应元件数量最少(37个),证明该家族基因在大麦的生长过程中也有一定的作用㊂表3 H v D U F 668基因的顺式作用元件T a b l e 3 C l a s s i f i c a t i o no f c i s -a c t i n g r e g u l a t o r y e l e m e n t s i nb a r l e y Hv D U F 668g e n e s 类型T y pe 顺式作用元件C i s -e l e m e n t光响应元件L i g h t r e s p o n s e e l e m e n t A C E ㊁S p1㊁A T C T -m o t i f ㊁G -b o x ㊁B o x4㊁G T 1-m o t i f ㊁T C T -m o t i f ㊁A E -b o x ㊁A A A C -m o t i f ㊁A T 1-m o t i f ㊁G A -m o t i f ㊁T C C C -m o t i f ㊁B o x Ⅱ㊁c h s -C MA 2a 和G A T A -m o t i f激素响应元件H o r m o n e r e s po n s e e l e m e n t A B R E ㊁A T -A B R E ㊁G A R E -m o t i f ㊁P -b o x ㊁C G T C A -m o t i f ㊁T G A C G -m o t i f ㊁T G A -e l e m e n t㊁A u x R R -c o r e 和T C A -e l e m e n t 植物生长响应元件P l a n tG r o w t he l e m e n tO 2-s i t e ㊁C A T -b o x ㊁R Y -e l e m e n t ㊁G C N 4-m o t i f ㊁M S A -l i k e ㊁c i r c a d i a n ㊁A -b o x 和H D -Z i p 1胁迫响应元件S t r e s s r e s po n s e e l e m e n t M B A ㊁C C A A T -b o x ㊁W b o x ㊁WU N -m o t i f ㊁G C -m o t i f ㊁A R E ㊁L T R 和T C -r i c h r e pe a ts 图7 大麦D U F 668家族基因的顺式作用元件分析F i g .7 A n a l y s i s o f c i s -a c t i n g e l e m e n t s o f b a r l e y D U F 668g e n e f a m i l y2.5 大麦D U F 668家族基因在不同组织中的表达分析研究基因的时空表达模式有助于了解基因潜在的功能[24]㊂对大麦D U F 668基因在8个不同组织中的表达量进行分析,结果(图8)显示,H v D U F 668-01与H v D U F 668-02基因在这8个组织中均有非常高的表达量,暗示这2个基因对大麦生长发育有重要的作用;H v D U F 668-07基因在这8个组织中表达量极低,甚至不表达;H v D U F 668-09㊁H v D U F 668-04与H v D U F 668-06基因在某些特定组织中表达量处于中等水平;H v D U F 668-03㊁H v D U F 668-05和H v D U F 668-08基因在这8个组织中表达量都相对较低㊂H v D U F 668-04㊁H v D U F 668-06和H v D U F 668-09基因在幼苗㊁根和节间的表达量明显高于其在花序与颖果等组织中的表达量;H v D U F 668-03基因则在颖果中的表达量明显高于其他组织,而且随着颖果的发育而增加;H v D U F 668-02和H v D U F 668-09基因在颖果中的表达量则是随着颖果的发育而降低㊂总的来看,H v D U F 668基因的表达具有明显的组织特异性,而且在不同的发育阶段其表达量也不同㊂除H v D U F 668-07基因外,其余8个基因在大麦被分析组织中都有表达,这进一步证实了H v D U F 668基因在大麦的生长发育等方面发挥着特定作用㊂㊃461㊃麦 类 作 物 学 报 第44卷图8 大麦H v D U F 668基因在不同组织中的表达量F i g .8 E x p r e s s i o no f b a r l e y Hv D U F 668g e n e s i nd i f f e r e n t t i s s u e s 2.6 大麦D U F 668家族基因在不同胁迫下的表达分析为了探索H v D U F 668基因在不同胁迫下的表达模式,用1种激素(M e J A )㊁2种环境胁迫(干旱㊁暗处理)以及1种生物胁迫(大麦黄矮病毒侵染)对大麦幼苗进行了处理,利用q R T -P C R 分析处理后不同时间H v D U F 668基因的相对表达量,引物序列如表4㊂结果(图9)显示,与C K 相比,胁迫处理12h 的大麦叶片中,有6个H v D U F 668基因表达发生显著变化;有3个H v D U F 668基因在病毒侵染后与未侵染相比表达显著增强㊂对照C K 中,随着时间推移,H v D U F 668-01㊁H v D U F 668-02和H v D U F 668-05的相对表达量先升高后降低,H v D U F 668-08的相对表达量先降低后升高,H v D U F 668-04的相对表达量降低,H v D U F 668-09的相对表达量升高㊂经M e J A 处理后,随着时间推移,H v D U F 668-01和H v D U F 668-09表达量先上升后降低,在24h 时表达量最高;H v D U F 668-02和H v D U F 668-05表达量先下降后上升;H v D U F 668-04和H v D U F 668-08表达量逐步上升,H v D U F 668-08表达量变化显著,48h 时较C K 增加40倍㊂推测该基因在激素表4 q R T -P C R 分析所用引物T a b l e 4 P r i m e r s u s e d i nR T -q P C Ra n a l ys i s 基因名称G e n en a m e上游引物(5'-3')F o r w a r d pr i m e r 下游引物(5'-3')R e v e r s e p r i m e rH v A c t i n C C A C G A G A C G A C C T A C A A C C A C T G A G C A C G A T G T T T C C H v D U F 668-01A G G C A T G A C A G A C A C A G C A G C A G A C C A T C A A G C C T G T C A A H v D U F 668-02A A G G C T C A T C A T G G T T T T G G G A T G C T G A A G C G A T A C G A C A H v D U F 668-04T A C G C G A A C G T G A T C T T G T C T C C T C T C A A C C T C T C C C T C A H v D U F 668-05G T G G A T G C T C G A A A G A G G T C A C T G G A A T C C T C G T T G T T G G H v D U F 668-08A G C A G G A C G T G A A G A A C C T C C C T C C A T C G A C A T G G A C T T T H v D U F 668-09T T G T A C C A T G G A C T G C C A G AC C A T G T C A C T C C C G A A G T T T㊃561㊃第2期王月雪等:大麦D U F 668家族基因鉴定及表达分析误差线表示标准误差;图柱上方*和**表示处理与C K间的相对表达量差异在0.05和0.01水平显著㊂T h e e r r o r b a r r e p r e s e n t s t h e s t a n d a r d e r r o r;*a n d**a b o v e c o l u m n sm e a n s i g n i f i c a n t d i f f e r e n c e b e t w e e n t r e a t m e n t sw i t hC Ka t 0.05a n d0.01l e v e l s,r e s p e c t i v e l y.图9不同胁迫下9个基因相对表达量分析F i g.9E x p r e s s i o n p r o f i l e a n a l y s i s o f t h e n i n e H v D U F668g e n e s i nb a r l e y u n d e r d i f f e r e n t s t r e s s e s响应中起着至关重要的作用㊂经P E G6000处理后,随着时间推移, H v D U F668-02表达量先降低后升高,H v D U F668-04呈上升趋势,但在48h表达量大幅度升高;H v D U F668-01和H v D U F668-08表达量逐渐上升,H v D U F668-08在48h时表达量最高;㊃661㊃麦类作物学报第44卷H v D U F668-09表达量先升高后降低,在24h表达量最高,较C K高10倍㊂推测这2个基因与干旱胁迫有关㊂经暗处理后,随着时间推移,H v D U F668-02和H v D U F668-05表达量呈降低趋势,H v D U F668-04的表达量在48h开始上升;H v D U F668-01与H v D U F668-08表达量升高,H v D U F668-01在24 h表达量最高,H v D U F668-08在12h时表达量较C K高30倍左右,推断该基因对光响应敏感程度较高,在光反应中可能起着关键的作用㊂前人研究发现,含有A v r9/C f-9的水稻具有抗病性[10]㊂系统进化分析中,发现H v D U F668-04㊁H v D U F668-05和H v D U F668-08与水稻含有A v r9/C f-9的基因同属于第Ⅲ亚族㊂因此对这3个H v D U F668基因进行黄矮病毒侵染,结果发现,H v D U F668-04㊁H v D U F668-05和H v D U F668-08表达量发生了显著变化,表达量较C K高100~180倍㊂说明这3个基因在大麦遭受黄矮病侵染时发挥重要作用,可能介导大麦的生物防御反应㊂3讨论D U F家族最初是一类功能未知的超基因家族,随着研究的深入,部分功能被发掘㊂本研究在全基因组和蛋白数据库的基础上,利用两种预测工具(HMME R㊁S MA R T)共同预测并鉴定出了9个大麦H v D U F668基因,这比单一软件预测结果会更可靠,但可能漏掉非典型大麦D U F668蛋白,是本研究的缺点㊂本研究基因结构分析发现,第Ⅲ亚组中的H v D U F668-04和H v D U F668-05基因没有内含子,第Ⅰ亚组最多,为11个,第Ⅱ亚组分别有7个和9个,这与水稻与棉花中基因结构相似[10-11]㊂对蛋白基序分析后发现,除大麦H v D U F668-06蛋白外,其他8个蛋白均含有2个高度保守的D U F668和D U F3475结构域,这与前人研究相似[10-11]㊂另外,本研究还在P f a m数据库中发现,该家族90%以上的成员中,这2个特征结构域是共存的(2148条蛋白序列中有1961条序列包含这2个特征结构域)㊂本研究还发现,D U F3475特征结构域均位于D U F668保守结构域的前面,在进化过程中这2个结构域的排列顺序高度保守,推测两者之间在功能上可能存在着一定的联系㊂本研究中,系统进化分析将大麦D U F668蛋白分为3个亚族㊂其他物种研究中,将其分为2个亚族[10-11]㊂不同亚族间的基因结构及基序排列都有一定差异㊂依据多物种系统进化树可知,第Ⅰ亚族与第Ⅲ亚族均含有单双子叶植物,推测D U F668家族基因起源于共同祖先,是一个高度保守的基因家族㊂研究发现,四倍体棉花品种比二倍体的棉花品种的D U F668家族成员多两倍,推测D U F668家族成员在物种中数量与几倍体相关㊂本研究材料大麦为二倍体植物,共鉴定出9个D U F668基因,与前人研究8种禾本科代表作物(103个)得出单子叶禾本科植物中D U F668家族成员数量相近[11]的结论一致㊂本研究在共线性分析中发现,大麦与拟南芥及棉花基因组间虽然存在着共线区块,但未发现共线性基因对(结果未给出);但在大麦与水稻间存在的共线性基因对中,发现1个大麦的H v D U F668基因对应2个O s D U F668基因,同时也有1个水稻O s D U F668基因对应2个大麦H v D U F668基因;在大麦和玉米间存在的共线性基因对中,存在1个大麦的H v D U F668对应3个玉米Z m D U F668基因的现象,这可能是由串联和片段复制驱动的基因扩增事件所导致的㊂在水稻中,许多具有高度相似序列的基因在染色体上以同源基因对的形式聚集[11],但在本研究大麦种内共线性分析中,鉴定出的9个基因之间并没有共线性关系㊂本研究对表达模式分析后发现,H v D U F668-01㊁H v D U F668-02和H v D U F668-09在8个组织中都表达,并且这3个基因均是高量表达,且同属于一个亚组㊂这在棉花中也出现了类似情况[11]㊂大麦H v D U F668-04㊁H v D U F668-05和H v D U F668-08在黄矮病病毒侵染下呈现高量表达,这3个大麦成员与水稻包含A v r9/C f-9的成员[10]同属一个亚族,推测这3个基因有助于提高大麦对病原菌的防御能力,也可能含有A v r9/C r-9,介导大麦的生物防御反应㊂有关此家族在大麦生长发育和抗胁迫反应中的具体功能及机制尚需更多研究㊂参考文献:[1]B A T E MA N A,C O G G I L LP,F I N N R D.D U F s:F a m i l i e s i n s e a r c ho f f u n c t i o n[J].A c t a C r y s t a l l o g r a p h i c a.S e c t i o n F, S t r u c t u r a l B i o l 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一种基于Chimera软件的分子动力学模拟方法

一种基于Chimera软件的分子动力学模拟方法

2021.13科学技术创新一种基于Chimera 软件的分子动力学模拟方法马学婧*李俊甫宋立立张兆英王悦孙琳琳(沧州师范学院生命科学学院,河北沧州061001)Chimera 由美国加州大学旧金山分校的生物计算可视化和信息学中心开发,并得到了美国国立卫生研究院的部分支持[1]。

作为一个可高度延伸的程序,它可应用于密度图、超分子组装、序列比对、对接结果、轨迹和构象集合,也可以生成高质量图像和动画[2-4]。

Chimera 的官方网站(/chimera/)上可以查阅快速入门、用户手册、命令行索引和一些教程与视频,还可以观赏用该软件制作的图片和动画。

在下载页面,它还提供了Windows ,Mac 和Linux 三个版本供学术、政府和非营利机构和个人使用者免费下载使用。

Chimera 功能强大,界面友好,可帮助没有编程基础的教师和科研人员利用其提供的多种模块化工具进行简单的分子动力学模拟,并且可用于多种操作系统,无需购买昂贵的服务器也可以满足基本的分析需求。

因此,本文将对基于Chimera 软件的分子动力学模拟方法进行阐述。

1蛋白质结构准备1.1蛋白质结构可视化首先打开一个已经下载的蛋白质结构文件(后缀为.PDB )或选择Fetch by ID ,输入蛋白质结构的ID 调入蛋白质结构文件。

在Presets 中根据需要选择展示模式。

在Select 中,Chain 选项可以选择蛋白质复合物不同的链;Chemistry 选项可以根据化学性质,如元素、功能基团和原子轨道对蛋白质进行选择;Residue 选项可以对20种标准氨基酸进行选择,也可以按照性质对某一类氨基酸进行选择;Structure 选项可以对蛋白质的骨架、离子、配体、核酸和特定的二级结构等进行选择。

选择完毕后,可应用Actions 中的工具对选定的对象进行编辑,如:Atoms/Bonds 选项可以隐藏或显示原子或键,设置显示模式为棍型、球棍型等;Ribbon 选项可以隐藏或显示蛋白质的某一部分,还可以改变带状模式的类型;Surface 选项可以隐藏或显示蛋白质的表面,并设置显示模式和透明度;Color 选项可以对选中的对象进行上色;Label 选项可以对原子、氨基酸残基进行标注,且可自主选择标注的格式。

ID4基因的研究进展

ID4基因的研究进展

ID4基因的研究进展冯燕;李薇;党艳辉;卢学春【摘要】@@ 癌基因的活化(如ras基因、bcr-abl基因)或/和抑癌基因的失活(如P53基因、Rb基因)与肿瘤的发生密切相关.ID4基因是1994年Riechmann等首次从小鼠中分离鉴定的,发现该基因在胚胎发育的9.5d -13.5d是上调的,且在成人的脑、睾丸和肾脏器官高表达[1].在1995年,人的ID4基因被成功定位在染色体6p21.3-p22,同时发现通过增强ID4蛋白的表达可以抑制肌酸激酶E-box增强子的活化作用.ID4在不同肿瘤和同一肿瘤的不同阶段可能具有不同的作用,本文对ID4基因的研究现状做一小结.【期刊名称】《中国实验诊断学》【年(卷),期】2011(015)007【总页数】3页(P1227-1229)【作者】冯燕;李薇;党艳辉;卢学春【作者单位】吉化集团公司总医院,化疗科,吉林,吉林,132022;吉林大学第一医院肿瘤中心,吉林,长春,130021;吉化集团公司总医院,化疗科,吉林,吉林,132022;吉林大学第一医院肿瘤中心,吉林,长春,130021;解放军总医院,老年血液科,北京,100853;解放军总医院,老年血液科,北京,100853【正文语种】中文癌基因的活化(如 ras基因、bcr-abl基因)或/和抑癌基因的失活(如P53基因、Rb基因)与肿瘤的发生密切相关。

ID4基因是1994年Riechmann等首次从小鼠中分离鉴定的,发现该基因在胚胎发育的9.5d-13.5d是上调的,且在成人的脑、睾丸和肾脏器官高表达[1]。

在1995年,人的ID4基因被成功定位在染色体6p21.3-p22,同时发现通过增强ID4蛋白的表达可以抑制肌酸激酶E-box增强子的活化作用。

ID4在不同肿瘤和同一肿瘤的不同阶段可能具有不同的作用,本文对ID4基因的研究现状做一小结。

1 ID4基因的分子结构特点ID4基因是碱性螺旋环螺旋转录因子(bHLH)的抑制因子,其编码的ID4蛋白的HLH 区域能调节各种bHLH的同源或异源二聚体,但由于缺少碱性DNA结合的区域因此不能序列特异性结合到DNA共同的E-box盒上调节转录功能,但却可以与bHLH结合形成异二聚体,阻止了DNA与bHLH的结合从而形成转录失活,稳定这些碱性转录蛋白调节子二聚体,调节细胞的分化、增殖和凋亡。

骨髓细胞核型分析及方法研究

骨髓细胞核型分析及方法研究

骨髓细胞核型分析及方法研究中山大学生命科学学院08生物技术及应用基地班王敬羽08330042[摘要] 染色体核型或组型分析(Chromosome karyotype analysis) 是染色体研究中的一个基本方法。

对染色体核型分析,不仅有助于了解生物的遗传组成、遗传变异规律和发育机制,而且对预测鉴定种间杂交和多倍体育种的结果、了解性别遗传机理以及基因组数、物种起源、进化和种族关系的鉴定都具有重要的参考价值。

本实验采用虎纹蛙为实验材料,用Giemsa染色法制备骨髓细胞染色体标本,用显微拍摄技术采集染色体的电子图片信息,后期用可牛软件优化处理照片,获得完整、清晰的染色体核型。

结果为:染色体组型为K(2n)=26=13m。

[关键词] 虎纹蛙骨髓细胞核型分析图像处理一、引言染色体是细胞内遗传物质的载体。

骨髓细胞具有丰富的细胞质和高度的分裂能力,可直接观察到细胞周期中的各个时相。

但通常情况下,中期染色体在镜下的数量较少,如经秋水仙素处理后,分裂的骨髓细胞大多被阻断在有丝分裂中期,再经离心、低渗、固定、滴片等步骤,便可得到理想的染色体标本,用以观察中期染色体形态和染色体组型分析等实验。

染色体核型或组型分析(Chromosome karyotype analysis) 是染色体研究中的一个基本方法。

对染色体核型分析,不仅有助于了解生物的遗传组成、遗传变异规律和发育机制,而且对预测鉴定种间杂交和多倍体育种的结果、了解性别遗传机理以及基因组数、物种起源、进化和种族关系的鉴定都具有重要的参考价值。

本次实验的目的是分析青蛙染色体有丝分裂中期的染色体数目、大小、着丝粒位置和随体等形态特征,学习染色体组型分析的方法。

得到雌性虎纹蛙染色体组型为K(2n)=26=13m,有5对大染色体和8对小染色体。

各种生物染色体的形态,结构和数目都是相对稳定的。

每一生物细胞内有丝分裂中期的表型,包括染色体数目、大小、形态等,这种特定的染色体组成叫染色体组型。

细胞练习题及答案

细胞练习题及答案

二、是非判断1.蛋白核定位信号(nuclear localization signal)富含碱性氨基酸。

2.有亮氨酸拉链模式的Jun和Fos蛋白质是以二聚体或四聚体的形式结合DNA的。

3.端粒酶以端粒DNA为模板复制出更多的端粒重复单元,以保证染色体末端的稳定性。

4.核纤层蛋白B受体(1amln B receptor,LBR)是内核膜上特有蛋白之一。

5.现在认为gp210的作用主要是将核孔复合体锚区定在孔膜6.由RNA聚合酶I转录的rRNA分子是在胞质中与核糖体蛋白结合成RNP颗粒的,rRNA的转运需要能量。

7.核内有丝分裂指核内DNA多次复制而细胞不分裂,产生的子染色体并行排列,且体细胞内的同源染色体配对,紧密结合在一起成为体积很大的多线染色体。

8.已有的研究表明,组蛋白去乙酰化伴随着对染色质转录的抑制,与活性X染色体相比,雌性哺乳动物失活的X染色体及其组蛋白没有乙酰化修饰。

9.gp210是结构性跨膜蛋白,位于核膜的孔膜区,具有介导核孔复合体与核被膜的连接、将核孔复合体锚定在“孔膜区”的功能。

从而为核孔复合体装配提供一个起始位点。

10.p62是核膜上的功能性核孔复合体蛋白,在脊椎动物中具有两个功能结构域,其c端区可能在核孔复合体功能活动中直接参与核质交换。

11.第一个被确定的NLS来自猴肾病毒(SV40)的T抗原,由7个氨基酸残基构成。

12.常染色质在间期核内折叠压缩程度低,处于伸展状态(典型包装率750倍),包含单一序列DNA 和中度重复序列DNA(如组蛋白基因和tRNA基因)。

13.异染色质化可能是关闭基因活性的一种途径。

14.T带是C带的反带,显示染色体的末端区。

15.染色质的区间性是通过基因座位控制区( locus control region,LCR)和隔离子(insulator)等顺式作用元件维持的。

三、填空1.细胞核外核膜表面常常附着有颗粒,与相连通。

2.核孔复合体是特殊的跨膜运输蛋白复合体,在经过核孔复合体的主动运输中,核孔复合体具有严格的选择性。

与细菌有关的生物数据库

与细菌有关的生物数据库
与细菌有关的生物数据库
/nar/database/a/
• 毒力基因鉴定 • 噬菌体及前噬菌体 • 分泌系统 • 细菌基因组注释 • 细菌基因组比对 • 细菌宿主相互作用
• rRNA
毒力基因鉴定
Isfinder
• A database of bacterial Insertion Sequences http://www-is.biotoul.fr
GenoBase
• E. coli genome database at Nara Institute http://ecoli.aist-nara.ac.jp/
GenProtEC
• Escherichia coli K-12 genome, gene products, and homologs
• Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive.
• It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage “quality” and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views.Furthermore, tests indicate that PHAST is as accurate or slightly more accurate than all available phage finding tools, with sensitivity of 85.4% and positive predictive value of 94.2%.

分子生物学名词解释(Molecularbiologicalterms)

分子生物学名词解释(Molecularbiologicalterms)

分子生物学名词解释(Molecular biological terms)The beanmail polar tropical fish is set to exitDouban-douban-douban-douban-douban-douban-douban-douban-dou ban-douban-douban-douban stationDouban searchThe home page of my douban my group of the city browse discoveryExplanation of molecular biology terms.Confused の detectiveThe 2010-05-21 20:43:54 from: confused の detective (if you want to let me live please give me happy pain)Title: molecular biology noun explanation (personal arrangement, only a lot of ~ exams are risky, review should be cautious ~ true love life, far away from the point of birth)Meristematic name solutionProbe: molecular hybridization and the tagged nucleotide chain with specific sequences of nucleotide nucleotide nucleotides can be used to detect specific genes in nucleic acid samples.Molecular hybridization: a technique for qualitative or quantitative analysis of DNA or RNA using the basic properties of DNA degeneration and renature.Gene chip: the support of a specific piece of DNA that is closely aligned in a unit area.Gene library: a clone group that contains the entire DNA sequence of an object in a lifetime.CDNA library: it is contain a tissue cells under certain conditions all mRNA expression by the reverse transcription and synthesis of cDNA sequence of clone population, it is stored in the form of cDNA fragments with the tissue cell gene expression information.Genomic DNA library: a clone population stored in the form of fragments of DNA (including all coding and non-coding regions) of the genome of a living organism.Transgenic technology: gene transfer technology is used to integrate the target genes into the fertilized egg cells or embryonic stem cells, then the cells are imported into the animal's uterus to develop into individual technology.Transgenic: the gene that is being imported in transgenic technologyTransgenic animals: the receptor animals that are genetically engineered to be genetically engineeredNuclear transfer technique: an individual cell nucleus of an animal is introduced into the activated egg cell of another individual to develop into an individual, namely, clone.Gene elimination: a technique for removing certain genes in animals based on homologous recombination.Functional cloning: cloning the pathogenic gene by understanding the function of a pathogenic gene.Location cloning: gradually narrowing the range from the chromosomal localization of a pathogenic gene and finally cloning the gene.Gene diagnosis: direct detection of gene structure and its expression level is normal, so as to diagnose the disease.Gene therapy: an exogenous gene that functions as a defective cell can be used to correct or compensate for its genetic defects to achieve therapeutic purposes.Viral oncogene: a type of gene that is present in tumor viruses (mostly retroviruses) that can cause malignant transformation of the target cell.Proto-oncogene: is the oncogene in normal cells, and its expression products regulate the normal growth and differentiation of cells. When activated, can cause cell growth differentiation abnormality, form tumour. Also called cell carcinoma genes.Oncogene: a normal gene in a living organism or in a cell, which controls the growth and differentiation of cells. Cell carcinogenesis can only be caused when its structure changes or expresses an abnormality.Tumor suppressor gene: inhibits the proliferation and proliferation of cells and thus inhibits the genes of tumor formation.Transformation action: by automatically obtaining or artificially supplying exogenous DNA, the cells obtain a new genetic phenotype, which is called transformation.Conjugation: when a cell or bacterium interacts with the bacteria, the plasmid DNA can be transferred from one cell (bacteria) to another (bacteria). This DNA transfer is called the conjugation.Transduction function: when the release of the virus from infected cells, infected again another cell, occurred in donor cells and DNA transfer and recombination between receptor cells is called transduction.Plasmid: small ring double stranded DNA molecule outside the bacterial chromosomeHomologous recombination: a recombination between the homologous sequences, which is also called fundamental recombinationSite specific recombination: the integration of integrase catalysis between the specific sites of two DNA sequences.Transposition: the translocation or rearrangement of genes mediated by insertion sequence and transposon is referred toas transpositionTransposon: a discrete sequence of repeated sequences that can be transferred from one chromosome site to another.Clone: a collection of identical copies or copies from the same ancestor.Cloning: the process of obtaining the same copy, i.e. asexual reproduction.DNA cloning: the method of application enzymology to reorganize the target gene and carrier DNA in vitro, transform or transfect host cells, and gain a large number of genes. It is also called gene cloning and recombinant DNAGenetic engineering: the methods and related work for gene cloning are described as genetic engineering.Compatibility terminal: some of the restriction enzyme recognition sequences are not exactly the same, but after cutting DNA, they produce the same sticky end, which is called the compatibility terminal.Restriction endonuclease: a specific sequence of DNA that identifies a DNA, and an enzyme that cuts double strand DNA around the identification site or its surroundings.CDNA: transcriptional synthesis of single stranded DNA that complements mRNA. Double stranded cDNA can be synthesized with single stranded cDNA as template and polymerized.Genomic DNA: a complete set of genetic information (chromosomes and mitochondria) of a cell or organism.Gene carrier: some of the DNA molecules used to reproduce or express a meaningful protein for the purpose of carrying a target gene.Gene: a genetic base unit located on a chromosome that carries a DNA fragment of a specific genetic information that can encode a single biological product, including RNA and polypeptide chains.Genome: a complete set of genetic information from a living organism, which is the entire genetic information or whole gene that a cell or virus carries.Gene expression: the process of transcription and translation of genesTime specificity: the expression of a specific gene takes place in a certain chronological order according to the function, which is called the time specificity of gene expressionSpace specificity: in the whole process of individual growth, a certain gene product appears in the order of individual tissue space, which is called the spatial specificity of gene expressionHousekeeping genes: some genes continue to be expressed in almost all cells of an individual, often referred to ashousekeeping genesConstitutive gene expression: usually a gene expression similar to the expression of a butler gene, also known as basic expression.Coordinate expression: under certain mechanism control,A set of genes related to function, no matter how they are expressed, should be coordinated and expressed in a coordinated manner.Trans action: the protein factor expressed by one gene interacts with the specific cis-acting component of another gene to regulate its expression. This conditioning is known as the trans action.Cis: protein factor can recognize, regulate the sequence of its own genes, regulate the expression of its own genes, and call it cis.Self - control: regulation of protein is generally used in automrna, inhibiting the synthesis of itself, and self-controlMonocistron: a coding gene transcribed to generate an mRNA molecule that translates into a polypeptide chain.Protein biosynthesis is the process of synthesizing proteins in the sequence of nucleotides in mRNA molecules.S - D sequence: in prokaryotes initiation codon upstream 8 to13 AUG nucleotide site there are 4-9 consensus sequence, high in purine bases, is with small ribosome binding sites of mRNA, known as the S - D sequence.Ribosomal circulation: the peptide chain is extended continuously in the nucleoprotein body, also known as prolongation. This includes carry, peptide and peptide.Polyribosome: the polymer that mRNA forms with multiple nucleosomes is called polyribosomeMolecular partner: the molecular partner is a nonnatural conformation that identifies a type of protein in the cell that can recognize the right folding of the functional domain and the whole protein.Cistron: a genetic unit that codes for a polypeptide.Signal sequence: all sorting signals exist in the targeted delivery of protein structure, mainly was the specific N terminal amino acid sequence, may guide protein metastasize to the appropriate target cells, the sequences are called signal sequence.Open reading framework: the sequence of nucleotide sequences from the mRNA initiation codon AUG to the termination codon.The degeneracy of the genetic code: an amino acid can have two or more codons coded for it, a feature known as the degeneracy of the genetic code.Enhancers: a sequence of DNA that binds specific gene regulation proteins to promote the expression of specific genes near or far away. The distance of the enhancement subscriptional start point varies greatly, but it always ACTS on the most recent promoter.Transcription is the process by which an organism USES DNA as a template to synthesize RNAStructural genes: segments of RNA that are transcribed from DNA molecules called structural genesAsymmetric transcription: in the genome, the genes are transcribed only by the genes of different developmental timing, conditions and physiological needs of the cell. In the DNA molecule double strand, a strand is used as a template for transcription, and the other strand is not transcribed. The template chain is not always on the same chain.Manipulation: transcription is not continuous. Each transcriptional block can be considered as a transcriptional unit, called the operator. The manipulators include several structural genes and their upstream regulatory sequences.Cis-acting elements: the sequence of DNA that is involved in transcriptional regulation at the beginning of the transcription starting point, consisting of promoters, enhancers, and silences.Anti-type action factor: the ability to recognize and combine the homeopathic components, and reverse the transcriptionaleukaryotic proteins that are transcribed by other genes.Transcription factor: in the trans action factor,The direct or indirect combination of RNA polymerase is called transcription factor.Exon: a sequence of nucleic acid sequences of mature rnas in eukaryotic organisms that appear in the fault gene and its primary transcription products.Intron: linear expression of the partition gene in eukaryotes and the sequence of nucleic acids removed during the splicing process.Nuclease: RNA that has enzymatic activity is called a nucleaseReproduction: refers to the generation of genetic material, the process of synthesizing subchain DNA by the mother chain DNA.Semi - reserved replication: when DNA biosynthesis, the mother chain DNA is unwound into two single strands, each acting as a template by the base pairing rule, and the subchain complemented by the template. The DNA of the daughter cell, a single strand is fully accepted from the parent, and the other single strand is completely resynthesized. The DNA of the two subcells is identical to the parental DNA base sequence. This replication method is called semi-retained replication.Bidirectional replication: when the prokaryote replicates, the DNA dissolves the chain from the starting point to the twodirections, forming the opposite of the two directions of the replication fork, called bidirectional replication.Initiator: a compound structure formed at the beginning of DNA replication, containing helicases, DnaC proteins, primers, and DNA replication initiation regions.Replicator: the unit that completes the replication independently, from the replication point to the replication endpoint.Okazaki fragment: a discontinuous fragment formed in the following chain replication during DNA replication.The double strand of DNA is divided into two segments, each acting as a template, and the subchain lengthens the formed y-font structure along the template to be called a replication fork.Half-discontinuous replication: the lead chain replicates continuously and the attendant chain discontinuous replication is called semi-discontinuous replication.Reverse transcription: the process of synthesizing DNA with RNA as a template for reverse transcriptase.Telomere: the structure of the end of the linear DNA molecule of the eukaryotic biosomatic chromosome, which makes the ends of chromosomes become granule.Transcriptional initiation complex: a compound formed by thebinding of the prokaryotic RNA polymerase, the transcriptional pppGpN - product and template DNA.Boundary sequence: the eukaryotic introns start with GU at 5 'end and AG is 3' end. 5 '- GU... Ag-oh3 is called a boundary sequence, also known as a splice interface.Splicing: removing introns from RNA molecules so that exons can be connected together.Promoter: a sequence of DNA in the upstream of the transcription starting point of RNA polymerase. If the RNA polymerase is combined with it, it can initiate transcription.Central rule: the law of transmission of genetic information from DNA to RNA to protein.Transcriptase: transcriptional complex, which is composed of the nuclease of RNA polymerase and the product of its template DNA, transcribed.Silencing: the negative regulating element in the eukaryotic element, which ACTS as a repressor when it binds the specific protein factor.Gene: the structure of eukaryotic gene, by a number of coding and non-coding area interval with each other, but embedded in a row, after connected to again unless the coding regions, can translate the continuous complete protein amino acid composition. These genes are called broken genes.[figure]DavidDavid (I'm looking for the book direction)It is also the common touch of biochemistryYour response? Who? Who? Who? Who? Who? , ah ha... Good thing ~ plus go> medical student's home groupLatest topic:Molecular biology noun explanation (individual, only a lot more to test a risk... (confused の detective)N reasons you attended medical school (breba)I was depressed. (hh)How microbes learn?Everybody work first or take the exam first. (MaoMaoQ)My man is studying medicine (summer)The division room chooses the direction, especially lost... (ssu xiaawn)Are there any graduate students in Concorde? Seek counsel (summercool)> to report bad information2005-2010 , all rights reserved about , contact us · disclaimer · help center · douban service (API) · mobile phone douban · brand club。

转基因食品成分检测技术研究进展

转基因食品成分检测技术研究进展

转基因食品成分检测技术研究进展候吉超,吴 斌,姜 蕾,宋晶晶,任小娜,王 东*(喀什大学 生命与地理科学学院,新疆帕米尔高原生物资源与生态重点实验室,新疆喀什 844000)摘 要:随着转基因技术的发展及应用,转基因作物品种和食品种类不断增加,给人们带来经济利益的同时,也存在安全方面的争论。

研发新的转基因检测技术已经迫在眉睫。

本文对转基因蛋白和核酸检测技术的研究进展进行综述,并对不同检测方法的优缺点进行阐述,以期为转基因产品快速、高通量检测技术的研发提供更多思路。

关键词:转基因食品;检测技术;研究进展Research Progresses in Detection Technologies for TransgenicFood IngredientsHOU Jichao, WU Bin, JANG Lei, SONG Jingjing, REN Xiaona, WANG Dong*(College of Life and Geographic Sciences, Kashi University, Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi 844000, China) Abstract: With the development and application of transgenic technology, the varieties of transgenic crops and foods are increasing. While genetically modified foods bring economic benefits to people, there are also safety disputes. It is extremely urgent to develop new transgenic detection technology. In this paper, the research progress of transgenic protein and nucleic acid detection technology is reviewed, and the advantages and disadvantages of different detection methods are described, in order to provide more ideas for the research and development of rapid and high-throughput detection technology of transgenic products.Keywords: transgenic food; detection technology; research progress随着世界人口的高速增长,“全球粮食危机”已经成为全世界关注的焦点,而转基因技术的诞生为解决“全球粮食危机”带来了希望[1-2]。

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ORIGINAL ARTICLEChromosomal localization of 45S and 5S rDNA in 14species and the implications for genome evolution of genus EpimediumMao-Yin Sheng •Ling-Jiao WangReceived:17April 2010/Accepted:13August 2010/Published online:17September 2010ÓSpringer-Verlag 2010Abstract Studying the genome structure of Epimedium has been hindered by the large genomes and uniform kar-yotypes.Consequently our understanding of the genome organization and evolutionary changes of Epimedium is extremely limited.In the present study,the 45S and 5S rDNA loci of 14Epimedium species were physically mapped by double-probe FISH for the first time.Results showed the following:(1)Chromosomes I and II of all 14species examined,except for E.shuichengense ,hosted one pair of 45S rDNA sites,respectively.Most of the 45S rDNA sites gave clear signals and were positioned in the distal regions of the short arms.(2)All species studied of section Diphyllon were found to have one pair of 5S rDNA sites localized in the interstitial regions of the long arm of chromosome IV,and the two species of section Epimedi-um ,E.alpinum and E.pubigerum ,had two pairs of 5S rDNA sites localized in the interstitial regions of the long arm of chromosomes IV and V,respectively.(3)In section Diphyllon ,all species of small flower taxa,except E.shuichengense ,had three pairs of 45S rDNA sites,clearly more than species of big flower taxa,except E.davidii ,with two pairs of 45S rDNA sites.Based on the45S and 5S rDNA distribution patterns and other chro-mosomal morphological characteristics,six pairs of chro-mosomes can be unambiguously identified in all 14Epimedium species.The stable differentiation in 45S and 5S rDNA FISH patterns between the two sections suggests that chromosomal rearrangements and transpositional events played a role in the splitting of the two sections,and section Diphyllon may be more primitive than section Epimedium .In the same way,big flower taxa may be more primitive than small flower taxa in section Diphyllon .Keywords 45S and 5S rDNA ÁFISH ÁEpimedium ÁPhylogenesisIntroductionBarrenwort (Epimedium ,Berberidaceae)is a traditional Chinese medicine known as Yinyanghuo,Xianlinpi,and Yangheye in China (Zhang et al.2002;Xie and Sun 2006).The plant is effective in strengthening the kidneys and ameliorating rheumatism,and is widely used in the treat-ment of osteoporosis,hypertension,coronary heart disease (Guo and Xiao 1999),senility,cancer,etc.(Xie and Sun 2006;Zhang et al.2002).Many flavonol glycosides have been isolated from a number of Epimedium plants,although the relation between these flavonol glycosides and the pharmacological activities of the drug is still obscure (Guo and Xiao 1999).In Japan,Europe,and North America,barrenwort species are also very popular as graceful garden plants.Epimedium is a genus of the Old World.Members are dispersed from Japan to Algeria and mainly occur in eastern Asia and the Mediterranean countries (Stearn 2002).Approximately 80%of the species are found inM.-Y.Sheng (&)Postgraduate Administration Office,Guizhou Normal University,Guiyang,Guizhou 550001,China e-mail:shmoy@M.-Y.ShengSchool of Life Science,Nanjing University,Nanjing,Jiangsu 210093,China L.-J.WangSchool of Vocation and Technology,Guizhou Normal University,Guiyang,Guizhou 550001,ChinaPlant Syst Evol (2010)290:65–73DOI 10.1007/s00606-010-0349-3central-southeastern China(Ying2002).Linnaeus recorded this genus and its type species E.alpinum in1753.After that,Morren and Decaisne(1834),Franchet(1886), Komarov(1908),and Stearn(1938,2002)made mono-graphic and systematic studies of Epimedium(Stearn 2002).Thus far,more than60species of Epimedium are recognized.Stearn(2002)established the most compre-hensive classification system of this genus.In his mono-graph,he arranged the genus into two subgenera, Epimedium L.and Rhizophyllum(Fischer&Meyer)Stearn, mainly based on whether theflowering stem has leaves or not,and he divided the subgenus,Epimedium,into four sections mainly according to their geographical distribution and infrageneric relationship.Among the four sections, members of section Diphyllon(Kom.)Stearn were all endemic to China and subdivided into four series:Cam-panulatae Stearn,Davidianae Stearn,Dolichocerae Stearn, and Brachycerae Stearn based on corolla characteristics such as petal type,the form and relative size of the inner sepals and petals,andflower dimension.Up to now,many studies have been dedicated to deducing the system and evolution of this genus,including studies of pollen morphology(Zhang and Wang1983;Liang and Yan1991),isozymes(Koga et al.1991),molecular biology (Nakai et al.1996;Sun2004;Sun et al.2005),biogeography (Ying2002;Zhang et al.2007),and chemical classification (Guo and Xiao1999;Koga et al.1991;Guo et al.2008). Results showed that the infrageneric classification was gen-erally consistent with its phytogeographic distribution,and the phylogenetic relationship among sections was basically clear in Epimedium.However,the system and evolution of Chinese Epimedium species still is not revealed well for many Epimedium species with multifarious petals are nested together in China and the petal evolution is unintelligible (Guo et al.2008).Recently,much additional research has been performed to study the system and phylogeny of Epi-medium(Kim et al.2004;Zhang et al.2007;Sheng et al. 2008).As an intractable genus in taxonomy,however,several problems remain regarding the classification and phyloge-netic relationship of Epimedium species,especially for the Chinese Epimedium species.Many works on karyotype and chromosome C-banding of the genus Epimedium have also been undertaken to deduce the phylogenesis of Epimedium(Tanaka and Takahashi1981;Takahashi1989;Sheng and Chen 2007a,b,2008;Zhang et al.2008).The results of all of this work showed that karyotypes of all species studied were symmetrical(1A,2A,or3A of Stebbins)and similar to each other.Thus,it is very difficult to identify the chro-mosomes and study the genome organization and evolution of this genus based on the common karyotype analyses.Ribosomal DNAs(45S and5S rDNA)are valuable genetic units in plant genome research.The45S rDNA,encoding18S–5.8S–25S ribosomal RNA,is present in many hundreds of repeated units generally arranged in tandem arrays corresponding to the nucleolus organizer region(NOR)(Lapitan1992;Sastri et al.1992).Although the5S rDNA,encoding5S ribosomal RNA,has a similar organization to45S rDNA,its site along the chromosome is not revealed by any morphological characteristics.Ribo-somal DNAs have been physically mapped in many plants byfluorescence in situ hybridization(FISH),and the dis-tribution and numbers of rDNA in the genome differ among different plants(Abbo et al.1994;Hanson et al. 1996;Adachi et al.1997;Taketa et al.1999;Martina et al. 2010).They are excellent cytological markers for karyo-type analysis especially in species with many small and equal chromosomes.The use of FISH for mapping and detecting ribosomal DNAs directly on the chromosomes provides a useful approach for chromosome identification and studies of genome organization and evolution.Thus far,however,the physical location of the rDNA genes of barrenwort has not been reported yet.Thus,there is a clear need tofind out more about the localization of rDNA loci in Epimedium to generalize the patterns of rDNA loci distribution in this genus and the differentiation among species.In the present study,the45S and5S rDNA loci localization patterns in14species of Epimedium are investigated using DNA probes for the45S rDNA and5S rDNA to address the following questions:(1)Do the number and location of rDNA loci differ among species of Epimedium?(2)Does the difference in rDNA loci number correlate with a difference in the genome of Epimedium?(3)Can the variations in FISH patterns be explained with a phylogenetic framework of Epimedium?Materials and methodsPlant materialsFourteen species of Epimedium were examined,including 12species of section Diphyllon endemic to China and2 species of section Epimedium collected from the Munich Arboretum,Germany(Table1).They were cultivated in pots at a greenhouse of the Institute of Plant Genetics and Breeding,Guizhou Normal University,Guiyang,Guizhou, China.Voucher samples were stored at the Institute.Preparation of chromosome spreadsChromosome slides were prepared according to Sheng and Chen(2007a).Briefly,the root tips werefirst treated with 0.3%8-hydroxyquinoline for15–20°C for3h,fixed in Carnoy Isolution overnight,treated in4%(v/v)cellulose-pectinase at37°C for4h,then washed and soaked in66M.Sheng,L.WangT a b l e 1T h e E p i m e d i u m m a t e r i a l s t u d i e d a n d t h e 45S a n d 5S r D N A l o c iT a x aP o p u l a t i o n sV o u c h e r s N o .o f c h r o m o s o m e s N o .o f r D N A l o c i45S 5SS e c t i o n D i p h y l l o n (K o m .)S t e a r n (n a t i v e t o C h i n a )B i g flo w e r t a x aE .a c u m i n a t u mF r a n c h .K a i y a n g ,G u i z h o u ,C h i n a2004050101K Y 2n =124(I S S A T ,I I S )2(I V L )E .l e p t o r r h i z u m S t e a r n W u c h u a n ,G u i z h o u ,C h i n a 2009020101W C 2n =124(I S S A T,I I S )2(I V L )E .w u s h a n e n s e T .S .Y i n gK a i l i ,G u i z h o u ,C h i n a2007030201K L 2n =124(I S S A T ,I I S )2(I V L )E .l i s h i h c h e n i i S t e a r nY i s h a n ,T o n g r e n ,G u i z h o u ,C h i n a2008030201Y S 2n =124(I S S A T ,I I S )2(I V L )E .p a u c i flo r u m K .C .Y e nM a o x i a n ,S i c h u a n ,C h i n a2008060210M X 2n =124(I S S A T ,I I S )2(I V L )E .d a v i d i iF r a n c h .K u n m i n g ,Y u n n a n ,C h i n a2007070301K M 2n =126(I SS A T,I I S ,I V S )2(I V L )E .b a o j i n g e n s e Q .L .C h e n &B .M .Y a n g B a o x i n g ,S i c h u a n ,C h i n a2008060210B X 2n =124(I SS A T,I I S )2(I V L )S m a l l flo w e r t a x aE .p u b e s c e n s M a x i m .G u i y a n g A r b o r e t u m ,G u i z h o u ,C h i n a2007052001G Y2n =126(I S S A T ,I I S ,I V S )2(I V L )E .e c a l c a r a t u m G .Y .Z h o n gQ i n g c h e n g s h a n ,S i c h u a n ,C h i n a2008030201Q C2n =126(I S S A T ,I I S ,I V S )2(I V L )E .s a g i t t a t u m (S i e b .&Z u c c .)M a x i m .K a i y a n g ,G u i z h o u ,C h i n a2007110405K Y2n =126(I SS A T,I I S ,I V S )2(I V L )E .d o l i c h o s t e m o n S t e a r n Q i n g c h e n g s h a n ,G u i z h o u ,C h i n a2008110502Q C2n =126(I SS A T,I I S ,I V S )2(I V L )E .s h u i c h e n g e n s e S .Z .H e L i u p a n s h u i ,G u i z h o u ,C h i n a2009032001L P S2n =124(I SS A T,I V S )2(I V L )S e c t i o n E p i m e d i u m (n a t i v e t o E u r o p e a n d C a u c a s u s )E .a l p i n u m L .M u n i c h ,G e r m a n y2008121401M U2n =126(I S S A T ,I I S ,I V S )4(I V L ,V L )E .p u b i g e r u m M o r r .&D e c n e .M u n i c h ,G e r m a n y2008121405M U2n =128(I SS A T,I I S ,I V S ,V S )4(I V L ,V L )I S S h o r t a r m o f c h r o m o s o m e I ,I I S s h o r t a r m o f c h r o m o s o m e I I ,I V S s h o r t a r m o f c h r o m o s o m e I V ,V S s h o r t a r m o f c h r o m o s o m e V ,I V L l o n g a r m o f c h r o m o s o m e I V ,V L l o n g a r m o f c h r o m o s o m e V ,S A T s a t e l l i t e c h r o m o s o m eChromosomal localization of 45S and 5S rDNA in 14species and their implications67distilled water for90min,followed by smear preparation. The prepared slides were stored at-20°C or immediately used for FISH.Probe preparation and FISHThe probes of45S and5S rDNA cloned in the vector were kindly provided by Prof.Adelaide,Heidelberg University, and were labelled by the random priming method using Klenow fragment(Promega).Biotin-16-dUTP(Roche)was used for labeling5S rDNA and digoxigenin(DIG)-11-dUTP(Roche)for45S rDNA.FISH was carried out according to the manufacturer’s instructions.The chromosomal slides were treated with 100l L RNase(100l g mL-1in29SSC)at37°C for1h and then soaked twice for5min in29SSC.The chro-mosomes were then digested with proteinase K (1l g mL-1,Promega)at37°C for10min.The slides were dehydrated in a series of70,95,and100%ethanol and then air-dried.A20l L hybridization solution containing10% dextran sulfate,50%formamide,10ng l L-1of sheared salmon sperm DNA,2ng l L-1of denatured probes,and 29SSC was added to each slide.The slides were placed in a moisture chamber,denatured at85°C for13min,then immediately placed in a hybridization oven and kept at 37°C overnight for probe hybridization.The slides were then washed with20%formamide in0.19SSC at42°C for 10min,followed by two washes with29SSC at37°C for 5min,and29SSC at room temperature for5min.In situ hybridization was repeated on three tofive chromosome spreads for each species.DetectionBefore detection,the slides were soaked in detection buffer (5%BSA,100mM Tris-HCl pH7.5,150mM NaCl,0.1% Triton X-100)at37°C for30min.The45S rDNA signals were detected using anti-DIG-rhodamine(2ng mL-1; Roche),and5S rDNA signals were detected using avidin-FITC(2l g mL-1;Sigma,USA).The slides were coun-terstained with100l L DAPI(2l g mL-1)and observed under afluorescence microscope(BX51,Olympus)at 100910magnification.The FISH images were captured by a cooled CCD color chromatic camera.The arm lengths of chromosomes in the CCD-captured images of ten cells from each of two or three chromosome spreads of each species were measured.The arm ratio was calculated,and the average values were used to construct an ideogram of the karyotype for each species.The chro-mosomes were assigned consecutively according to their lengths,with the longest being assigned as I and the shortest as VI.For chromosomes of equal length,the chromosome with the longest short arm was assignedfirst.In addition to the length and arm ratios of the chromo-somes,secondary constrictions and FISH patterns are also informative characters for karyotyping.The location of rDNA loci on each chromosome is shown on the ideo-grams.The mapped positions are not precise quantitative representations,although the relative distances of each rDNA site from the centromere and telomere were con-sidered when constructing the ideograms.ResultsThe FISH results showed that the metaphase chromosomes were blue,while the signals were green(5S rDNA)and red (45S rDNA)after counterstaining(Figs.1,2).Clear,repro-ducible,unambiguous FISH signals from three tofive FISH replicates of each species were registered.Weak signals in centromeric regions were not analyzed.Examples of the45S and5S rDNA FISH patterns obtained for each species are shown in Figs.1and2,and an ideogram of the karyotypes is presented in Fig.3.The karyotype features of the14Epi-medium species are similar to those reported by Tanaka and Takahashi(1981),Takahashi(1989),and Sheng and Chen (2007a,b,2008).Chromosomes I–VI were found in all cases to be metacentric or submetacentric and to have similar lengths,except that chromosomes VI of E.sagittatum and E.letorrhizum were subtelocentric.However,the chromo-somal distribution patterns of the45S and5S rDNA sites differed considerably among the14species.In E.acuminatum(Figs.1a,3a), E.leptorrhizum (Figs.1b,3b),E.wushanense(Figs.1c,3c),E.lishihchenii (Figs.1d,3d),E.pauciflorum(Figs.1e,3e),and E.bao-jingense(Figs.1f,3f),two pairs of intense45rDNA site signals were detected,one localized on the secondary constrictions of their SAT chromosomes(the short arm of chromosome I),another localized at the end of the short arm of chromosome II.One pair of5S rDNA sites was detected in the interstitial region close to the centromere in the long arm of chromosome VI.In E.davidii(Figs.2a,3g),E.pubescens(Figs.2b,3h), E.ecalcaratum(Figs.2c,3i),E.sagittatum(Figs.2d,3j), and E.dolichostemon(Figs.2e,3k),three pairs of45S rDNA and one pair of5S rDNA sites were detected.One pair of45S rDNA loci was localized in the secondary constrictions of their SAT chromosomes(the short arm of chromosome I),and the other two were localized at the end of the short arms of chromosomes II and VI,respectively. The5S rDNA sites were localized in the interstitial region of the long arm of chromosome VI.A notable feature was that the short and long arms of chromosome VI hosted one pair of45S and5S rDNA sites,respectively.In E.shuichengense(Figs.2f,3l),two pairs of45S rDNA and one pair of5S rDNA sites were detected.One68M.Sheng,L.Wangpair of 45S rDNA was found in the secondary constrictions of the SAT chromosomes (the short arm of chromosome I)and another in the distal region on the long arm of chro-mosome VI.One pair of 5S rDNA sites was found in the interstitial regions of the long arm of chromosome VI.In E.alpinum (Figs.2g,3m),three pairs of 45S rDNA and two pairs of 5S rDNA sites were detected.One pair of 45S rDNA loci was found in the secondary constric-tions of the SAT chromosomes (the short arm of chro-mosome I),and the other two were found on the ends of the short arms of chromosomes II and VI,respectively.In contrast to the above species studied,two pairs of 5S rDNA sites were detected and localized in the interstitial regions of the long arms of chromosomes VI and V,respectively.In E.pubigerum (Figs.2h,3n),four pairs of 45S rDNA and three pairs of 5S rDNA sites were detected.Three pairs of 45S rDNA sites were localized in the distal regions of the short arms of chromosomes II,VI,and V,respectively.The others were localized in the secondary constrictions of the SAT chromosomes (the short arm of chromosome I).Similar to E.alpinum ,two pairs of 5S rDNA sites were found in the interstitial regions of the long arms of chro-mosomes VI and V,respectively.Fig.1FISH localization of 45S rDNA (red )and 5S rDNA (green )loci on somatic chromosomes in a E.acuminatum ,b E.letorrhizum ,c E.wushanense ,d E.lishihchenii ,e E.pauciflorum ,andf E.baojingense .Arrowheadsindicate the 5S rDNA signals.Scale bar 5l mChromosomal localization of 45S and 5S rDNA in 14species and their implications 69Fig.2FISH localization of 45S rDNA (red )and 5S rDNA (green )loci on somaticchromosomes in a E.davidii ,b E.pubescens ,c E.ecalcaratum ,d E.sagittatum ,e E.dolichostemon ,f E.shuichengense ,g E.alpinum ,andh E.pubigerum .Arrowheads indicate the 5S rDNA signals.Scale bar 5l m70M.Sheng,L.WangIn the Epimedium species examined,except for E.shuichengense ,chromosomes I and II all hosted one pair of 45S rDNA sites,respectively.Most of the 45S rDNA sites gave clear signals and were positioned in the distal regions of the short arms.No clear,unambiguous 45S signals were observed at the centromere in any case,although weak signals were detected in centromeric regions of one or two pairs of chromosomes in some species.All species studied were found with one pair of 5S rDNA sites localized in the interstitial regions of the long arm of chromosome VI,except two species,E.alpinum and E.pubigerum ,with two pairs of 5S rDNA sites localized in interstitial regions of the long arms of chromosomes VI and V,respectively.Based on the 45S and 5S rDNA distribution patterns and other chromo-somal morphological characteristics,six pairs of chro-mosomes can be unambiguously identified in all 14Epimedium species.In E.davidii , E.pubescens ,E.ecalcaratum ,E.sagittatum ,E.dolichostemon ,E.alp-inum ,and E.pubigerum ,chromosome VI hosted one pair of 45S and 5S rDNA sites on its short and long arms,respectively.DiscussionSince Kuroki did the studies of chromosome comparisons of Epimedium species in 1967(Kuroki 1967),the karyo-types of more than 40species of this genus have been observed (Kuroki 1970;Tanaka and Takahashi 1981;Takahashi 1989;Sheng and Chen 2007a ,b ,2008;Zhang et al.2008).All of these results indicate that all species studied are diploid (2n =12)with only two types of chromosomes,metacentric and submetacentric.Karyotypes of all species studied were symmetrical—1A,2A,or 3A of Stebbins—and similar to each other.Karyotype analyses of Epimedium species have revealed that the chromosomal morphology is highly conserved within the genus,and that most of the chromosomes have similar lengths and arm ratios,making precise karyotyping difficult (Sheng and Chen 2007a ).The chromosomes of Epimedium can not be identified precisely by the karyotype analyses.The correct ordering of chromosomes II–V has been ambiguous to date (Sheng and Chen 2007a ).The use of double-or multiple-probe FISH,in combination with other chromosomal characters,has facilitated the identification ofhomologousFig.3Ideograms of a E.acuminatum ,b E.letorrhizum ,c E.wushan-ense ,d E.lishihchenii ,e E.pauciflorum ,f E.baojingense ,g E.davidii ,h E.pubescens ,i E.ecalcaratum ,j E.sagittatum ,k E.dolichostemon ,l E.shuichengense ,m E.alpinum ,and n E.pubigerum karyotypes.The white dots represent signals of 45S rDNA and the white asterisks represent 45S rDNA signalsChromosomal localization of 45S and 5S rDNA in 14species and their implications 71chromosomes and the inference of genome evolution among plant species(Brown et al.1999;Heslop-Harrison 2000;Marcon et al.2005;Taketa et al.2005;Vaio et al. 2005;Cai et al.2006;Martina et al.2010).In the present study,among14species studied,chromosomes I,II,VI, and V can be detected with hybridization signals.In combination with other chromosomal characters,the alignment of all six homologous chromosomes of the barrenwort genome can be made precisely.This study reports,for thefirst time,the physical locations of45S and5S rDNA loci in species of genus Epimedium as determined by double FISH.The features of45S and5S rDNA loci distribution in the14Epimedium species can be discerned.The numbers of45S and5S rDNA loci ranged from two to four pairs,and from one to two pairs,respec-tively(Table1;Fig.3),similar to other plants in Berberid-aceae(Liu et al.2006),which suggests that the number of changes of45S and5S rDNA loci has been small within family Berberidaceae.According to the classification by Stearn,12species among the14species studied were from section Diphyllon,native to China,including7bigflower taxa and5smallflower taxa.The other two species,E.alp-inum and E.pubigerum,were from section Epimedium, collected from Germany(Table1).The results of the present study show the distribution pattern of5S rDNA loci of E.alpinum and E.pubigerum with two pairs of signals(4L and5L),obviously different from the other12species.The number of45S rDNA loci of E.alpnium and E.pubigerum—three and four pairs of signals,respectively—is also more than in the other12species.All of this supports the division of the sections Diphyllon and Epimedium within the genus Epimedium by Stearn(2002).The changes in rDNA loci may be attributed to the chromosomal rearrangement,exchange of unequal values, and amplification of latent rDNA copies by transposons, and during the course of the evolutionary process,the number of rDNA loci will have increased from the ancestral genome(Cai et al.2006).We therefore concluded that section Diphyllon should be a more ancestral taxon than section Epimedium in genus Epimedium.Results of previous karyotype analyses showed that the genome sizes of species E.alpinum and E.pubigerum were smaller than those of species of section Diphyllon(Sheng and Chen 2007a,b,2008).So there is a tendency for the genome to have decreased from the ancestral taxa in genus Epimedium over evolutionary time.For a long time,China has been considered as the origin centre of Epimedium,but this has not been confirmed owing to insufficient evidence.In the present study,results support China as the origin centre of Epimedium.In China,species of Epimedium can be divided into two groups based on theflower dimension:the smallflower and the bigflower groups(Guo and Xiao1999;Sheng and Chen2008).According to the present study,the5S rDNA loci were very conservative within section Diphyllon,and the12species studied all have one pair(4L)of sites. However,all species of smallflower taxa,except E.shui-chengense,have three pairs of45S rDNA sites,obviously more than the species of bigflower taxa,except E.davidii, with two pairs of45S rDNA loci,supporting the division based on theflower dimension and suggesting that the big flower taxa are more primitive than the smallflower taxa in Chinese Epimedium species.45S rDNA loci participate the structure of nucleolus organizer region(NOR),generally mapped on the sec-ondary constriction in morphology.Lima-de-Faria ana-lyzed the NOR of700species and found that the NOR site of87%species was on the short arm of the chromosome (Lima-de-Faria1973).In most species studied,the site of 45S rDNA was on the NOR or the short arm end of the chromosomes(Adachi et al.1997;Han et al.2002;Li and Arumuganathan2001;Liu et al.2006;Singh et al.2009). In the present study,the45S rDNA sites were located as expected on the NOR and the ends of the chromosomes. In the present study,the detection rate(about100%)of 45S and5S rDNA hybridization signals at interphase was higher than that at metaphase,suggesting that the target sequence with a lower degree of condensation was hybridized more easily at interphase.Results of the present study also showed that the signals of45S rDNA were stronger than those of5S rDNA,suggesting that the copies of45S rDNA should be more numerous than5S rDNA in the Epimedium genome.Until now,the physical location of45S or5S rDNA loci in family Berberidaceae had only be studied by Liu et al. (2006).In Liu et al.(2006),the45S rDNA of Berberis thunbergii DC(Berberidaceae)was single and physically located on the secondary constriction of the short arm of chromosome IX.Based on the data of chromosome num-bers,and the number and site of45S rDNA,the evolution of the genome in family Berberidaceae is likely to have experienced aneuploidy,chromosome break,rearrange-ment,cross,and so pared with45S rDNA,the change in the site and number of5S rDNA is smaller(Xu et al.2007).Mantovani et al.(2005)reported that there were only one or two pair sites of5S rDNA in most species studied,but did not state the pattern of distribution in chromosomes.However,the site,number,and distribution pattern of5S rDNA are observably conservative (Mantovani et al.2005;Liu et al.2003).In the present study,the5S rDNA was physically located on the long arm of the chromosome in the14Epimedium species for the first time,providing important data for genome evolution research in the genus 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