不同休眠时期珠芽魔芋球茎转录组SSR和SNP位点信息分析
Analysis of SSR and SNP Loci in Corm Transcriptome of Amorphophallus bulbifer at Different Dormancy Stages
王天喜 1王蕊嘉 1张利娜 1谢雨琪 1吴学尉 1张达 1郑莉1
作者信息
摘要
为了解珠芽魔芋球茎转录组中SSR以及SNP的具体情况,对珠芽魔芋不同休眠时期(休眠期,萌动期,萌芽期)的球茎进行转录组测序,利用MISA和Varscan程序对测序得到的unigene进行分析,筛选并识别出SSR和SNP位点.结果显示,从珠芽魔芋292 086条unigene中发现52 324个SSR位点和807 836个SNP位点,SSR位点的出现频率为17.91％;单核苷酸(33.97％)、二核苷酸(47.83％)和三核苷酸(16.77％)重复占比较高,6～11次的重复占65.71％;重复基元共130种,其中二核苷酸重复基元AG/CT是优势重复基元类型,占总SSR的30.64％;基元长度在10～20 bp的SSR占80.33％;SNP变换类型中转换(523 617个)远高于颠换(284 219个).本研究从珠芽魔芋球茎转录组测序结果中挖掘到大量的SSR和SNP位点,为珠芽魔芋的球茎休眠及解除、分子辅助育种等提供一定的科学数据.
Abstract
To understand the SSR and SNP information in corm transcriptome of Amorphophallus bulbifer,RNA-Seq was carried out with corm of A.bulbifer at three different dormancy stages(dormancy stage,germina-tion stage and budding stage).MISA and Varscan were used to identify and analyze the features of SSR and SNP in unigenes from RNA-Seq.The results showed that 292 086 unigenes contained 52 324 SSRs and 807 836 SNPs.The frequency of SSR was 17.91％respectively.The proportions of single nucleotide(33.97％),dinucleotide(47.83％),and trinucleotide(16.77％)repeats were notably high,with repeats occurring 6 to 11 times comprising 65.71％of the total.There were 130 types of repeat units;among these,the dinucleotide repeat unit AG/CT was the dominant type,representing 30.64％of the total SSRs.SSRs with a unit length of 10～20 bp accounted for 80.33％of all SSRs.In terms of SNP mutation types,transitions(523 617)far exceeded transversions(284 219).The SSR and SNP sites obtained from the corm of A.bulbifer based on the analysis of transcriptional sequencing were abun-dant in number,which can provide scientific datas for breaking dormancy analysis and molecular assisted breeding of the A.bulbifer.
关键词
珠芽魔芋/休眠时期/转录组/SSR/SNPKey words
Amorphophallus bulbifer/Dormancy period/Transcriptome/SSR/SNP引用本文复制引用
基金项目
云南省科技厅科技计划项目(202004AC10001-A06)
云南省科技厅科技计划项目(202102AE090001)
云南大学研究生科研创新基金项目(2020320)
出版年
2024
NETL
NSTL
万方数据