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 LI Linlin,et al..De novo assembly of leaf transcriptome of Lespedeza bicolor (Fabaceae: Papilionoideae) and characterization of expressed sequence tag-derived simple sequence repeats markers[J].Chinese Journal of Applied & Environmental Biology,2018,24(06):1338-1349.[doi:10.19675/j.cnki.1006-687x.2018.01034]





De novo assembly of leaf transcriptome of Lespedeza bicolor (Fabaceae: Papilionoideae) and characterization of expressed sequence tag-derived simple sequence repeats markers
李林霖 高信芬 李诗琦 陈金元 郭丽娜 何海 徐波
1重庆师范大学生命科学学院 重庆 401331 2中国科学院成都生物研究所,中国科学院山地生态恢复与生物资源利用重点实验室 成都 610041 3兰州大学生命科学学院 兰州 730000 4六盘水师范大学生命科学与技术学院 六盘水 553004
LI Linlin et al.
1 College of Life Science, Chongqing Normal University, Chongqing 401331, China 2 CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China 3 College of Life Science, Lanzhou University, Lanzhou 730000, China 4 College of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui 553004, China
Lespedeza bicolor transcriptome functional annotation EST-SSR marker
胡枝子(Lespedeza bicolor)系豆科胡枝子属植物,性耐旱,是防风固沙及水土保持的优良植物. 报道胡枝子的转录组序列,对其进行注释,并开发一系列EST-SSR标记用于进化研究. 主要研究结果如下:(1)采用二代测序技术对胡枝子叶片进行转录组测序,得到120 913 unigenes,其平均长度为608 bp,N50的长度是978 bp.(2)分别在KEGG和KOG等数据库中对unigenes进行注释,总共注释72 613(60.05%)unigenes的功能.(3)筛选识别13 551个潜在的EST-SSR标记;根据重复单位的核苷酸数目以及重复次数的多少,从中选择173个EST-SSR标记进行引物设计.(4)对胡枝子和其他9种近缘种植物进行PCR扩增实验,最后得到56对引物可全部成功扩增出条带并表现出一定的多态性. 本研究获得了较高质量的胡枝子转录组数据库,可进一步用于比较和功能基因组研究以及胡枝子及其近缘类群的基因表达研究;开发的EST-SSR标记将提供一个强大的工具,可用于研究遗传多样性和种群结构、构建DNA指纹图谱数据库、生成遗传图谱、预测分子标记辅助育种和保存遗传信息. (图4 表3 参54 附表1)
Lespedeza bicolor Turcz., which belongs to the family Fabaceae, is a drought-tolerant plant that is helpful for wind prevention, sand fixation, water and soil conservation, and improving ecosystem. However, the plant currently lacks genomic or transcriptomic resources, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed. To our knowledge, this is the first study to reveal the transcriptome sequence of this species and annotate the transcriptome and developed a set of EST-SSR markers for evolutionary studies. Approximately 64.76 million clean reads from the leaves of L. bicolor were generated using transcriptome sequencing by using Illumina sequencing technology, and 120 913 unigenes with mean length of 608 bp and N50 of 978 bp were obtained. The function of a total of 72 613 (60.05%) unigenes was annotated, and 25 658 and 28 950 unigenes could be aligned to the KEGG and KOG database, respectively. Search against the Gene Ontology (GO) led to the assignment of 47 561 unigenes to 55 different functional pathway categories, including three major pathways, i.e., biological process, cellular component, and molecular function. In addition, a total of 13 551 potential EST-SSR sites were identified. The EST-SSR sites identified might provide additional resources for developing molecular markers for further evolutionary studies on this species and congeners. The 173 selected EST-SSRs were used to amplify 56 markers with the expected size in L. bicolor and nine other Lespedeza species. The transcriptome dataset reported in this study might serve as an important public information platform for comparative and functional genomic as well as gene expression studies in L. bicolor and other closely related species. These EST-SSR markers provide a powerful tool for assessing the genetic diversity and population structure, constructing a DNA fingerprint database, generating genetic maps, predicting molecular marker-assisted breeding, and preserving genetic information.


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更新日期/Last Update: 2018-12-25