摘要
基因内部的简单重复序列(Genic-SSR)可在植物适应环境变化中发挥重要作用。通过对阿拉善5个样点多枝柽柳(Tamarix ramosissima)的转录组进行测序、组装和比较,经CandiSSR软件分析,共鉴定出代表157个基序类型的1 185个多态性Genic-SSR位点,位于1123个转录本中。其中,三核苷酸重复序列(596,50.30%)最多,其次是二核苷酸重复序列(486,41.01%)。定位分析表明,分别有411、239和163个Genic-SSRs位于相应基因的CDSs、5′UTRs和3′UTRs;78.47%的三核苷酸重复SSRs位于基因的CDSs,94.07%的二核苷酸重复SSRs位于基因的UTRs;在CDS中,AGC/GCT、AGG/CCT、AAG/CTT、CCG/CGG和ATC/GAT重复相对丰富,占所有Genic-SSRs的64.48%;AG/CT和AT/AT是UTRs中最丰富的重复类型,占UTR中所有Genic-SSRs的55.22%。功能注释表明,含有多态Genic-SSRs的基因可注释到多个与植物逆境应答相关的GO条目和KEGG通路中。在随机选取的15个多态性SSR位点中, 14个被成功扩增,共检测到64个等位基因。遗传多态性估算表明,它们的期望杂合度(He)、观测杂合度(Ho)和多态性信息含量(PIC)平均值分别为0.553、0.421和0.493,均属于中、高多态SSR标记,表明利用RNA-seq技术开发SSR标记可行。
Simple sequence repeats located in gene transcribed regions(Genic-SSR) can play important roles in plant adaptation to environmental changes.In this study,the transcriptomes of Tamarix ramosissima from five different locations in Alax were sequenced,assembled,and compared.By using CandiSSR software,a total of 1 185 polymorphic Genic-SSRs representing 157 motif types were identified in 1 123 transcripts.Among them,the trinucleotide repeats(596,50.30%) were the most abundant,followed by dinucleotide repeats(486,41.01%).Location analysis showed that 411,239,and 163 Genic-SSRs were located in CDSs,5’UTRs,and 3’UTRs of the relevant transcripts,respectively;78.47% of the trinucleotide SSRs were located in CDSs,and 94.07% of the dinucleotide SSRs were located in UTRs.Among SSRs distributed in CDSs,AGC/GCT,AGG/CCT,AAG/CTT,CCG/CGG,and ATC/GAT were relatively abundant,accounting for 64.48% of all the Genic-SSRs;AG/CT and AT/AT were the most abundant repeat types in UTRs,which together account for 55.22% of all the Genic-SSRs in UTRs.Functional annotation showed that polymorphic Genic-SSRs containing genes enriched in a wide range of GO terms and KEGG pathways that highly related to stress response in T.ramosissima.Of the 15 randomly selected Genic-SSRs,14 were successfully amplified by using polymerase chain reaction technology and 64 alleles were found in these SSR loci.Genetic polymorphism estimation showed that the mean of expected and observed heterozygosity(He,Ho),polymorphism information content(PIC) of these SSRs were 0.553,0.421,and 0.493,respectively,demonstrating the feasibility of developing SSR markers by RNA-seq.
作者
张雅楠
黄蕾
李佳彬
张雷
党振华
Yanan Zhang;Lei Huang;Jiabin Li;Lei Zhang;Zhenhua Dang(Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateaullnner Mongolia Key Laboratory of Grassland Ecology,School of Ecology and Environment,Inner Mongolia University,Hohhot 010021,China;Inner Mongolia Academy of Forestry Sciences,Hohhot 010010,China;Daqing Mountains Forest Ecosystem Research Station,Hohhot 010010,China)
出处
《植物学报》
CAS
CSCD
北大核心
2021年第4期433-442,共10页
Chinese Bulletin of Botany
基金
国家林业和草原局林业科技发展项目(No.KJZXSA2019047)
内蒙古自然科学基金(No.2020MS03005)。
