中华大仰蝽转录组学研究及SSR新标记开发

【目的】中华大仰蝽Notonecta chinensis为中国和日本冲绳分布的重要水生天敌昆虫,可用于蚊虫的生物防治。本研究旨在建立中华大仰蝽转录组数据库,挖掘其基因信息。【方法】采用高通量测序平台Illumina NextSeq500对中华大仰蝽进行转录组测序、de novo组装及生物信息学分析;利用MISA软件基于转录组unigenes数据进行SSR新分子标记筛选。毛细管电泳检测SSR多态性。【结果】总计获得34782282条clean reads(NCBI SRA数据库登录号:SRR13259254),组装成37801条unigenes,N50为913 bp。将unigenes与已知数据库比对进行基因功能注释,分别有36474,32470,27781,35079和5638条序列注释到nr,Swiss-Prot,GO,eggNOG和KEGG数据库。通过GO数据库注释,unigenes的功能可分为生物学过程、细胞组分和分子功能三大类,其中参与细胞、细胞部分及结合功能的unigenes比例较大。eggNOG数据库注释结果显示,37801条unigenes归到25个基因家族,注释到未知功能的最多。KEGG代谢通路富集分析显示,5638条unigenes注释到245个代谢通路,注释到核糖体的数目最多。此外,用MISA软件在转录组测序数据中的37801条unigenes中搜索到3124个SSR位点(占总unigenes的8.26%),发生频率为7.07%。通过PCR筛选出16个SSR位点。7个中华大仰蝽地理种群3个位点NcCF/NcCR,NcKF/NcKR和NcLF/NcLR的多态信息含量(PIC)分别为0.870,0.902和0.857,具高度多态性。【结论】本研究成功获得了中华大仰蝽转录组数据,为其基因功能分析提供了分子理论基础;SSR新标记的开发为中华大仰蝽遗传多样性分析、隐存种鉴定及基因图谱构建提供了更丰富的候选分子标记。     

中华大仰蝽转录组学研究及SSR新标记开发

[目的]中华大仰蝽Notonecta chinensis为中国和日本冲绳分布的重要水生天敌昆虫,可用于蚊虫的生物防治.本研究旨在建立中华大仰蝽转录组数据库,挖掘其基因信息.[方法]采用高通量测序平台Illumina NextSeq500对中华大仰蝽进行转录组测序、de novo组装及生物信息学分析;利用MISA软件基于...     

OrchidBase: a collection of sequences of the transcriptome derived from orchids

Orchids are one of the most ecological and evolutionarily significant plants, and the Orchidaceae is one of the most abundant families of the angiosperms. Genetic databases will be useful not only for gene discovery but also for future genomic annotation. For this purpose, OrchidBase was established from 37,979,342 sequence reads collected from 11 in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting in 84,617 non-redundant transcribed sequences with an average length of 459 bp. The analysis pipeline of the database is an automated system written in Perl and C#, and consists of the following components: automatic pre-processing of EST reads, assembly of raw sequences, annotation of the assembled sequences and storage of the analyzed information in SQL databases. A web application was implemented with HTML and a Microsoft .NET Framework C# program for browsing and querying the database, creating dynamic web pages on the client side, analyzing gene ontology (GO) and mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers with a high-quality genetic resource for data mining and facilitate efficient experimental studies on orchid biology and biotechnology. The OrchidBase database is freely available at http://lab.fhes.tn.edu.tw/est.     

基于短序列测序数据的四倍体拟南芥转录组研究

为了促进对四倍体拟南芥(A.suecica)的研究,阐明多倍体植物在染色体加倍过程中遗传物质的变化,从而在分子层面上解释多倍体植物的环境适应和进化机制,描述了一套基于第二代测序技术的转录组短序列组装和生物信息学分析方法.通过对23 000 000条来至于Illumina测序平台的序列数据进行SOAPdenovo组装,以...