山地虎耳草和棒腺虎耳草转录组SSR和SNP分析  

Analysis of SSR and SNP in Transcriptome of Saxifraga sinomontana and Saxifraga consanguinea

作　　者：李彦 焦秀洁 更吉卓玛 贾留坤 王智华 陈世龙[1] 高庆波[1,4] LI Yan;JIAO Xiujie;GENGJI Zhuoma;JIA Liukun;WANG Zhihua;CHEN Shilong;GAO Qingbo(Key Laboratory of Adaptation and Evolution of Plateau Biota,Northwest Institute of Plateau Biology,Chinese Academy of Sciences,Xining 810001,China;University of Chinese Academy of Sciences,Beijing 100039,China;Editorial Department of Library and Journal,Northwest Institute of Plateau Biology,Chinese Academy of Sciences,Xining 810001,China;Key Laboratory of Crop Molecular Breeding of Qinghai Province,Northwest Institute of Plateau Biology,Chinese Academy of Sciences,Xining 810001,China)

机构地区：[1]中国科学院西北高原生物研究所,高山植物适应与进化重点实验室,西宁810001 [2]中国科学院大学,北京100039 [3]中国科学院西北高原生物研究所,信息与学报编辑部,西宁810001 [4]中国科学院西北高原生物研究所,青海省作物分子育种重点实验室,西宁810001

出　　处：《西北植物学报》2018年第7期1244-1253,共10页Acta Botanica Boreali-Occidentalia Sinica

基　　金：中国科学院“西部之光”人才培养引进计划;中国科学院青年创新促进会项目(2016378)

摘　　要：利用Illumina HiSeqTM2000对山地虎耳草和棒腺虎耳草进行转录组测序,分析和比较其SSR和SNP特征。结果表明:山地虎耳草63 763条Unigene序列中含有4 622个SSR,发生频率为7.25%,有110种重复基元,平均每10.00kb出现一个SSR位点;棒腺虎耳草60 972条Unigene序列中含有4 542个SSR,发生频率为7.45%,有85种重复基元,平均每10.40kb出现一个SSR位点,略低于山地虎耳草。山地虎耳草和棒腺虎耳草转录组序列的SSR优势基元均为三核苷酸重复。2个物种的转录组SSR以5~10次的较低重复次数为主,长度主要集中于12~30bp,具有较高的多态性。山地虎耳草和棒腺虎耳草中分别获得118 424个和112 006个SNP位点,编码区的SNP位点分别占30.40%和28.59%,且在编码SNP中同义突变所占比例(30.27%、28.48%)远高于非同义突变(0.13%、0.11%)。比较发现,2个物种的各项检索结果基本一致,推测与选取的组织部位、组织的发育阶段以及物种的亲缘关系有关。Transcriptome analyses of Saxifraga sinomontana and Saxifraga consanguinea were carried out by Illumina HiSeq TM 2000,then the characteristics of SSR and SNP were generalized according to the sequences.The result indicated that:4 622 SSR sites were identified among 63 763 Unigenes with the frequency of 7.25%in S.sinomontana,there were 110 repeat motifs and the density of SSRs was 1/10.00 kb;for S.consanguinea,4 542 SSRs were distributed in 60 972 Unigenes which accounted for 7.45%,there were 85 kinds of repeat motifs and SSRs occurred every 10.40 kb in length,which was slightly lower than that of S.sinomontana.For the two species,the tri-nucleotide was dominant repeat motif.The repeat numbers of SSRs were mainly from 5 to 10 and their motif length mainly ranged from 12-30 bp,which suggested that these SSRs displayed high levels of polymorphism.Besides,there were 118 424 and 112 006 SNPs in S.sinomontana and S.consanguinea.The proportion of SNPs in the coding region were 30.40%and 28.59%respectively,and the proportion of the synonymous mutations in the coding region(30.27%,28.48%)was significantly higher than that of the nonsynonymous mutations(0.13%,0.11%).It was found that the relevant indicators of the two species showed no significant difference,which was probably related to the tissue and its development stage,as well as the phylogenetic relationships of the species.

关 键 词：山地虎耳草 棒腺虎耳草 转录组 简单重复序列(SSR) 单核苷酸多态性(SNP) 

分 类 号：Q346.5[生物学—遗传学] Q789