摘要
为探明半夏属内物种的地理亲缘关系以及发掘有价值基因资源,促进新品种选育,利用Illumina HiSeq测序平台对半夏、石蜘蛛和滴水珠进行转录组测序,对获得的原始数据进行过滤处理,去除低质量、接头污染以及未知碱基N含量过高的reads,之后进行de novo组装,最终获得Unigene,用软件MISA对测序数据中的SSR进行分析。结果表明:半夏、石蜘蛛、滴水珠转录组中分别有SSR位点19 270个、17 725个和16 585个,发生频率分别为17.06%、17.59%和18.67%,平均分布距离分别为3.39kb、3.50kb和3.60kb。3个物种的SSR都以单核苷酸、二核苷酸、三核苷酸为主要重复类型,主要重复次数以4～10次为主,SSR序列长度主要在12～20bp。从滴水珠到石蜘蛛再到半夏,3个物种的SSR发生频率和出现频率逐渐降低。SSR位点特征表明,从滴水珠祖先局部地区群体演化出的后代石蜘蛛、半夏继承了较少类型祖先SSR序列,与3物种的进化历史和亲缘关系一致。
The transcriptome of Pinellia ternata,Pinellia integrifolia and Pinellia cordata was sequenced by using Illumina HiSeq sequencing platform firstly,secondly the acquired original data were conducted by filtration treatment to eliminate the data of low quality,junction contamination and reads with higher N content of unknown bases,thirdly the Unigene is acquired by de novo assembly and finally the SSR in sequencing data were analyzed by MISA software to verify the geographic genetic relationship of species in Pinellia tenore and explore valuable gene resources for breeding of new varieties.Result:19 270,17 725 and 16 585 SSR loci are identified in transcriptome of P.ternata,P.integrifolia and P.cordata respectively.The SSR occurrence frequency and mean distribution distance of P.ternata,P.integrifolia and P.cordata are 17.06%,17.59%and 18.67%,and 3.39 kb,3.50 kb and 3.60 kb separately.Mononucleotide,dinucleotide and trinucleotide repetition of SSR are major types for all three species.The times of repetition are 4-10 mainly and SSR sequence length is 12-20 bp.The SSR occurrence frequency and unigene frequency of three species gradually decrease from P.cordata to P.integrifolia and to P.ternata.The SSR locus characteristics shows that P.integrifolia and P.ternata originated from community evolution of P.cordata ancestor in different local areas inherit less ancestor SSR sequence types and the evolutionary history of three species is consistent with the genetic relationship.
作者
刘丹
罗睿
陈海丽
夏丽莎
高华霞
LIU Dan;LUO Rui;CHEN Haili;XIA Lisha;GAO Huaxia(College of Life Science,Guizhou University,Guiyang,Guizhou 550025,China)
出处
《贵州农业科学》
CAS
2018年第11期5-8,共4页
Guizhou Agricultural Sciences
基金
国家自然科学基金资助项目"半夏珠芽发育的激素调节和关键基因克隆研究"(31560081)
关键词
半夏属
转录组
SSR
地理分布
进化
Pinellia tenore
transcriptome
SSR
geographical distribution
evolution
