基于转录组测序的椰心叶甲啮小蜂SSR、SNP和InDel位点分析  

SSR,SNP and InDel Analysis Based on Tetrastichus brontispae Transcriptome

作　　者：刘华伟 李朝绪[1,3,4] 李芬 吕朝军[1,3,4] 吴少英[2] 覃伟权 LIU Huawei;LI Chaoxu;LI Fen;LYU Chaojun;WU Shaoying;QIN Weiquan(Coconut Research Institute,Chinese Academy of Tropical Agricultural Sciences,Wenchang,Hainan 571399,China;Hainan University,Haikou,Hainan 570228,China;Hainan Innovation Center of Academician Team(Integrated Management of Arecanut Yellow Leaf Disease),Wenchang,Hainan 571339,China;Hainan Key Laboratory of Tropical Oil Crops Biology,Wenchang,Hainan 571399,China.)

机构地区：[1]中国热带农业科学院椰子研究所,海南文昌571399 [2]海南大学,海南海口570228 [3]海南省院士团队创新中心(槟榔黄化病综合治理),海南文昌571339 [4]海南省热带油料作物生物学重点实验室,海南文昌571399

出　　处：《热带作物学报》2021年第10期2828-2833,共6页Chinese Journal of Tropical Crops

基　　金：海南省重大科技计划项目(No.ZDKJ201817);热带木本油料产业技术创新团队-热带木本油料主要病虫害防控技术研究(No.1630152017010);农业农村部海南省入侵生物监测项目(No.1630042020020)。

摘　　要：椰心叶甲啮小蜂(Tetrastichus brontispae)是外来有害生物椰心叶甲(Brontispa longissima)的蛹期寄生蜂,分析其转录组序列中的SSR、SNP和InDel位点信息,可以为开发新的分子标记,深入研究其遗传多样性、种群遗传结构和历史动态等提供数据支撑。本研究基于转录组数据,利用MISA软件和Varscan软件对Unigene进行SSR、SNP和InDel位点进行搜索。在11802条Unigene中共获得29754个SSR位点,平均每1.72 kb含有1个SSR位点,发生率为39.96%。SSR片段为10~382 bp,长度具有显著差异,平均长度为23.91 bp。SSR片段中,单碱基重复最多(60.82%),其次是二碱基重复(27.69%),再次为三碱基重复(10.79%)。其中优势重复基元类型为A/T(59.32%),其次为AT/AT(15.28%)。在6895个Unigene中发掘出51334个SNP位点,转换位点37445个(72.94%),颠换位点13975个(27.22%),平均每条Unigene上含有7.45个SNP位点。还在6040个Unigene中筛选出15644个InDel位点,平均每条Unigene上有2.59个InDel位点。椰心叶甲啮小蜂转录组中SSR、SNP和InDel位点数量多,出现频率高,类型丰富,具有较高的多态性潜能。Tetrastichus brontispae is the pupal parasitic wasp of Brontispa longissima,an exotically invasive pest.The analysis of SSR,SNP and InDel sites in the transcriptome sequences of T.brontispae can provide data support for the development of new molecular markers and the in-depth study of its genetic diversity,population genetic structure and historical dynamics.Based on transcriptional data,MISA software and Varscan software were used to search the SSR,SNP and InDel sites of Unigenes.A total of 29754 SSR sites were obtained in 11802 Unigenes,with an average of 1 SSR per 1.72 kb,with an incidence of 39.96%.The length of the SSR fragments was 10-382 bp,with an average length of 23.91 bp.In the SSR segment,mononucleotide was dominant(60.82%),followed by dinucleotide(27.69%)and trinucleotide(10.79%).In all repeating motifs,the dominant repeating motif was A/T(59.32%),followed by AT/AT(15.28%).Among 6895 Unigenes,51334 SNP sites were discovered,and each Unigene contained 7.45 SNP on average.There were 37445 transition sites(72.94%)and 13975 transversion points(27.22%).15644 InDel sites were also identified out of 6040 Unigene,with an average of 2.59 InDel per Unigene.SSR,SNP and InDel sites are abundant in the transcriptome of T.brontispae,with a large number,high occurrence frequency,rich type and polymorphism potential.

关 键 词：椰心叶甲啮小蜂 转录组 SSR SNP INDEL 

分 类 号：S476[农业科学—农业昆虫与害虫防治]