基于转录组测序的花斑裸鲤SSR、SNP和InDel位点特征分析

SSR,SNP and InDel locus characteristics analysis in Gymnocypris eckloni based on transcriptome sequencing

为利用分子标记规模化开发与辅助花斑裸鲤(Gymnocypris eckloni)良种选育,以花斑裸鲤(2+龄)的鳃、肾脏和肝脏组织为材料,经总RNA提取和cDNA文库构建后采用Illumina Novaseq 2000平台进行转录组测序,并采用MISA和GATK3软件分析转录组的SSR、SNP和插入缺失标记(InDel)位点特征。结果表明:在486221条Unigenes序列中共发现了128727个SSR,出现频率为26.47%,平均每3.76 kb出现1个SSR;花斑裸鲤SSR包括6个重复类型,以单碱基和二碱基重复基元类型为主,分别占总SSR位点数的46.53%和42.45%,重复基元类型共77种,其中,A/T和AC/GT两种基元的出现频率最高,是花斑裸鲤SSR的优势重复基元;所有重复次数中出现次数最多的为5~15次,占所有SSR位点的87.52%;通过GATK3软件搜索得到399080个SNP位点,转换类型多于颠换类型,分别占总SNP的56.29%和43.71%,转换类型中A/G发生频率略高于C/T,而颠换类型中A/T发生频率最高,C/G发生频率最低;InDel分析显示,从花斑裸鲤转录组Unigenes中共筛选出254065个InDel位点,平均每1903 bp出现1个InDel位点,且SNP位点和InDel位点均以含1个位点的Unigenes数最多。研究表明,花斑裸鲤转录组中SSR、SNP和InDel位点非常丰富,这些位点对花斑裸鲤种质资源鉴定、种群遗传学研究及保护管理具有重要价值。

In order to utilize molecular markers for large-scale development and marker-assisted selection in breed-ing of Gymnocypris eckloni,the transcriptome was sequenced by Illumina Novaseq 2000 platform,and the SSR,SNP and InDel loci were analyzed using MISA and GATK3 software in gill,kidney,and liver of G.eckloni,after total RNA extraction and cDNA library construction.The results showed that a total of 128727 SSR were found in 486221 Unigenes,with a frequency of 26.47%and an average of one SSR per 3.76 kb;There were six repeat types in G.eckloni SSR,among which mononucleotide and dinucleotide were dominant,accounting for 46.53%and 42.45%of the total number of SSR loci,respectively.The total number of repeat motif types was 77,among which the frequency of the two motifs,A/T and AC/GT,were the most frequent,and they were the dominant repeat mo-tifs in the SSRs of G.eckloni;Among all the repeats,the number of repeats between 5 and 15 was the largest,ac-counting for 87.52%of all SSR loci.In addition,399080 SNP loci were obtained by GATK3 software,and the transitions types were more than the transversion types,accounting for 56.29%and 43.71%of the total SNPs,re-spectively.The distribution frequency of A/G was slightly higher than C/T in the transition type,while the fre-quency of A/T was the highest and that of C/G was the lowest in the transversion type.The analysis showed that a total of 254065 InDel loci were identified from the transcriptome of G.eckloni,with an average of one InDel locus per 1903 bp.The largest number of unigenes was found in both SNP and InDel loci,and the unigenes containing one locus of SNP and InDel were the largest.The SSR,SNP and InDel loci were shown to be abundant in the tran-scriptome of G.eckloni,and the findings will be of great value for the identification of germplasm resources,popula-tion genetics and conservation management of the G.eckloni in the future.