转录组测序-Transcriptome comparison

1 3Plant Mol BiolDOI 10.1007/s11103-014-0214-9

Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud)

Touming Liu · Shouwei Tang · Siyuan Zhu · Qingming Tang · Xia Zheng

Received: 2 May 2014 / Accepted: 10 June 2014 © Springer Science+Business Media Dordrecht 2014

Keywords Ramie · Transcriptome · Ka/Ks · Domestication · Selective patternIntroductionPlant domestication is the genetic modification of a wild species to create a new form of a plant altered to meet human needs (Doebley et al. 2006). Severe phenotypic divergence is generated in response to the domestication selection. The genetic basis of domestication-associated traits has been characterized in many crops, including rice, maize, tomato, and wheat (Frary et al. 2000; Fan et al. 2006; Li et al. 2006; Tan et al. 2008; Gegas et al. 2010; Lu et al. 2013). These studies reached the common conclu-sion that the rapid phenotypic divergence associated with domestication is often attributable to very few genetic loci (Gross and Olsen 2010). With the development of the next generation sequencing technology, it is becoming increas-ingly feasible to investigate the effects of domestication at the whole-genome level. On the basis of genome-wide re-sequencing, only a few loci (no more than 10 %) were found to have strong selective sweeps by positive selection in the rice, maize, and cucumber genomes (Hufford et al. 2012; Huang et al. 2012; Qi et al. 2013).Ramie (Boehmeria nivea L. Gaud), commonly known as China grass, is a perennial herbaceous plant that belongs to the family Urticaceae and produces both the strong-est and finest vegetative fiber from its stem bark (Ahuja 1988). Ramie fibers possess many excellent characteristics, such as smooth texture, long strands, and excellent tensile strength, making ramie a widely cultivated crop in China, India, and other Southeast Asian and Pacific Rim countries. As one of the oldest fiber crops, ramie has been cultivated for thousands of years in China (Li 1970; Sen and Reddy Abstract Ramie is an old fiber crop, cultivated for thou-sands of years in China. The cultivar ramie evolved from the wild species Qingyezhuma (QYZM, Boehmeria nivea var. tenacissima). However, the mechanism of domestica-tion of this old fiber crop is poorly understood. In order to characterize the selective pattern in ramie domestication, orthologous genes between the transcriptomes of domes-ticated ramie variety Zhongzhu 1 (ZZ1) and wild QYZM were assessed using bidirectional best-hit method and ratio of non-synonymous (Ka) to synonymous (Ks) nucleo-tide substitutions was estimated. Sequence comparison of 56,932 and 59,246 unigenes from the wild QYZM and domesticated ZZ1, respectively, helped identify 10,745 orthologous unigene pairs with a total orthologous length of 10.18 Mb. Among these unigenes, 85 and 13 genes were found to undergo significant purifying and positive selection, respectively. Most of the selected genes were homologs of those involved in abiotic stress tolerance or disease resistance in other plants, suggesting that abiotic and biotic stresses were important selective pressures in ramie domestication. Two genes probably related to the fiber yield of ramie were subjected to positive selection, which may be caused by human manipulation. Thus, our results show the pervasive effects of artificial and natural selections on the accelerated domestication of ramie from its wild relative.

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T. Liu (*) · S. Tang · S. Zhu · Q. Tang · X. Zheng Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, Chinae-mail: liutouming@gmail.com Plant Mol Biol1 32011). Archaeologists have found that the ramie fiber has been used as textile for over 4,700 years, and it was the most important fiber crop in China until cotton entered the country 700 years ago (Liao et al. 2014). Nowadays, ramie still is the second most important fiber crop in China, with its growth acreage and quantity of fiber production being second only to those of cotton (Liu et al. 2014).The genus Boehmeria Jacq. contains about 120 species, of which 32 species, including B. nivea L. Gaud, have been found in China (Wu et al. 2003). B. nivea L. Gaud includes the domesticated species B. nivea var. nivea, which is known as ramie, and three wild species B. nivea var. nipononivea, B. nivea var. tenacissima, and B. nivea var. viridula (Wang 1981a, b). Among these four species, B. nivea var. viridula is considered to be the most primi-tive taxon, from which B. nivea var. tenacissima evolved; thereafter, B. nivea var. tenacissima evolved either into B. nivea var. nivea or as B. nivea var. nipononivea (Jiang and Jie 2005). However, according to the taxonomic result of Wu et al. (2003), B. nivea L. Gaud gave rise to the domes-ticated species B. nivea var. nivea and the wild B. nivea var. tenacissima. The morphological differences between these two include that B. nivea var. nivea shows long and wide stems with dense, long, spreading epidermal hairs, free stipules, and broadly ovate to suborbicular leaf blades, whereas the wild B. nivea var. tenacissima has connate stipules, and the epidermal hairs on the stems and leaves are short and appressed to assurgent (Wu et al. 2003). Although there are two different taxonomic results for B. nivea L. Gaud, both concluded that the domesticated spe-cies B. nivea var. nivea was derived from the direct evo-lution of wild B. nivea var. tenacissima. Interestingly, the domesticated B. nivea var. nivea and wild B. nivea var. tenacissima are not reproductively isolated from one another (Liu et al. 2014).Previous studies had proposed that ramie had been domesticated in the middle and lower regions of the Yang-tze Valley (Vavilov 1992; Liao et al. 2014). However, because of the shortage of ramie genomic information, the footprint of domestication is poorly understood for this old fiber crop. Using the Illumina sequencing platform, the transcriptome of Zhongzhu 1 (ZZ1), a variety of the domes-ticated ramie species, B. nivea var. nivea, was de novo assembled by our previous studies (Liu et al. 2013a, b, c; Zhu et al. 2014). However, the transcriptome of wild B. nivea var. tenacissima, from which the domesticated ramie evolved directly, is still uncharacterized. In this study, the transcriptome of wild B. nivea var. tenacissima [Chinese name is Qingyezhuma (QYZM)] will be deeply sequenced, and the expressed sequence will be aligned between the domesticated ZZ1 variety and wild B. nivea var. tenacis-sima to find the natural variation. Our analysis will provide ample evidence for evolution in response to environmental cues in ramie relatives and suggests interesting differences between artificial and natural selections.