基于刚毛柽柳转录组测序的EST-SSR标记识别与开发

Identification and development of EST-SSR markers in Tamarix hispida based on transcriptome sequencing

表达序列标签-简单序列重复(EST-SSR)能为植物适应环境提供分子基础。通过对5个不同样地刚毛柽柳(Tamarix hispida)进行转录组测序、组装及比较,共识别出该物种1187个多态性EST-SSR位点。其中,三核苷酸重复数目最多(54.42%),其次是二核苷酸重复(37.66%)。分别有500、176和211个EST-SSRs位于829个转录本的编码区(CDSs)、3′非翻译区(UTRs)和5′UTRs中;AGC/GCT、AT/AT和AG/CT重复类型的EST-SSRs分别在各基因区域内出现频率最高;含多态性SSRs的基因序列主要被注释到“调节转录”、“转录因子活性”、“细胞核”等GO条目,以及“代谢途径”和“植物激素信号转导”等KEGG代谢通路;通过PCR扩增、测序及毛细管电泳验证,从15个随机挑选的SSR位点中开发出13个多态性SSR标记。本研究为开展刚毛柽柳的种群遗传学和SSR变异相关的适应进化机理研究奠定了基础。

Expressed sequence tag-simple sequence repeats(EST-SSR)may provide a molecular basis for plant adaptation.In this study,we sequenced five individual transcriptomes of Tamarix hispida from different locations,and identified 1187 polymorphic EST-SSRs.Of the identified SSRs,tri-nucleotide repeats were the most common(54.42%),followed by dinucleotide repeats(37.66%).A total of 500,176,and 211 EST-SSRs were located in coding region,3′untranslated regions(UTRs),and 5′UTRs in 829 transcripts,respectively.AGC/GCT,AT/AT,and AG/CT were the most abundant repeats in each gene region.Gene ontology functional annotation showed that the identified SSR-containing sequences were enriched in"regulation of transcription","transcription factor activity",and"nucleus"terms.KEGG pathway analysis showed that"metabolic pathways"was the most common and abundant term,followed by"plant hormone signal transduction".Using polymerase chain reaction amplification,sequencing,and capillary electrophoresis validation,13 out of the 15 randomly selected polymorphic SSR markers were developed.The results of this study lay the foundation for the investigation of population genetics and adaptation evolution mechanisms underlying SSR variations in T.hispida.