转录组测序-Transcriptomecomparison.pdfVIP

Plant Mol Biol DOI 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 Abstract Ramie is an old fiber crop, cultivated for thou- Keywords Ramie · Transcriptome · Ka/Ks · sands of years in China. The cultivar ramie evolved from Domestication · Selective pattern 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 Introduction characterize the selective pattern in ramie domestication, orthologous genes between the transcriptomes of domes- Plant domestication is the genetic modification of a wild ticated ramie variety Zhongzhu 1 (ZZ1) and wild QYZM species to create a new form of a plant altered to meet were assessed using bidirectional best-hit method and ratio human needs (Doebley et al. 2006). Severe phenotypic of non-synonymous (Ka) to synonymous (Ks) nucleo- divergence is generated in response to the domestication tide substitutions was estimated. Sequence comparison selection. The genetic basis of domestication-associated of 56,932 and 59,246 unigenes from the wild QYZM and traits has been characterized in many crops, including rice, domesticated ZZ1, respectively, helped identify 10,745 maize, tomato, and wheat (Frary et al. 2000; Fan et al. orthologous unigene pairs with a total orthologous length 2006; Li et al. 2006; Tan