依据云南栘[木衣]种子萌发至成苗期间转录组的SSR、SNP及InDel特征  

SSR,SNP,and InDel Characteristics of the Transcriptome During Seed Germination to Seedling Formation in Docynia delavayi

作　　者：张浩 田金红 王大玮[1] 李菊彩 Zhang Hao;Tian Jinhong;Wang Dawei;Li Jucai(Southwest Forestry University,Kunming 650224,P.R.China;Xishan Forestry Farm,Kunming)

机构地区：[1]西南林业大学,昆明650224 [2]昆明市西山林场

出　　处：《东北林业大学学报》2025年第2期52-57,74,共7页Journal of Northeast Forestry University

基　　金：国家自然科学基金项目(32060350);云南省基础研究重点项目(202401AS070042);云南省万人计划青年拔尖人才专项(YNWR-QNBJ-2020-230)。

摘　　要：依据云南栘[木衣](Docynia delavayi(Franch.)Schneid.)种子萌发至成苗期间的转录组数据,分别使用MISA、GATK3软件对SSR、SNP、InDel位点进行挖掘并进行特征分析。结果表明:从转录组数据的63782个非冗余基因序列(unigene)中,共挖掘出76981个SSR位点,其发生频率为30.18%。在各种不同的重复基元种类里,重复出现频次最高的为单碱基重复基元,频次最低的是六碱基重复基元。就所有基元而言,A/T基元的出现频率最高,占总SSR位点数量的38.09%;其次是AG/GT,占总SSR位点数量的27.63%。各类重复基元的重复次数介于5~15次,SSR序列长度为10~66 bp。15个样品中,SNP位点数量介于202602~278026个,平均每个样品包含253064个SNP,且每个样品的转换类型与颠换类型数量比都在6∶4左右。InDel位点数量介于35609~48977个,平均每个样品中含有44642个InDel位点。云南栘[木衣]种子萌发至成苗期间,转录组中的SSR、SNP、InDel位点丰富,且具有较高的多态性。Based on the transcriptome data from the seed germination to seedling formation stages of Docynia delavayi,SSR,SNP,and InDel loci were identified using MISA and GATK3 software,followed by feature analysis.The results showed that from the 63782 non-redundant gene sequences(unigenes)in the transcriptome data,a total of 76981 SSR loci were mined,resulting in an occurrence frequency of 30.18%.Among the different types of repeat motifs,the most frequently occurring were mononucleotide repeats,while the least frequent were hexanucleotide repeats.In terms of all motifs,A/T motifs had the highest occurrence frequency,accounting for 38.09%of the total SSR loci,followed by AG/GT motifs,which represented 27.63%of the total SSR loci.The number of repeats for various motifs ranged from 5 to 15 times,with SSR sequence lengths between 10 to 66 bp.The number of SNP loci across 15 samples ranged from 202602 to 278026,with an average of 253064 SNPs per sample.The ratio of transition to transversion types was approximately 6∶4 for each sample.The number of InDel loci varied from 35609 to 48977,with an average of 44642 InDel loci per sample.The SSR,SNP,and InDel loci in the transcriptome during the seed germination to seedling formation period of D.delavayi were found to be abundant and highly polymorphic.

关 键 词：云南栘[木衣] 种子萌发至成苗期间 转录组 SSR SNP INDEL 

分 类 号：Q943.2[生物学—植物学]