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引用本文:李喜莲,顾志敏,慎佩晶,徐洋,张宇飞,高强,程海华,陈雪峰.基于RNA-seq技术的罗氏沼虾(Macrobrachium rosenbergii)不同组织转录组比较分析.海洋与湖沼,2021,52(1):231-241.
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基于RNA-seq技术的罗氏沼虾(Macrobrachium rosenbergii)不同组织转录组比较分析
李喜莲, 顾志敏, 慎佩晶, 徐洋, 张宇飞, 高强, 程海华, 陈雪峰
农业农村部淡水渔业健康养殖重点实验室 浙江省淡水水产遗传育种重点实验室 浙江省淡水水产研究所 湖州 313001
摘要:
罗氏沼虾(Macrobrachium rosenbergii)是我国重要的淡水虾养殖品种,为探讨罗氏沼虾不同组织基因表达差异,本研究使用Illumina Hiseq平台分析了罗氏沼虾的7个组织(眼柄、肝脏、卵巢、鳃、心脏、肌肉、精巢)转录组,质控后获得高质量的clean reads 36325476、56796932、36328098、51370140、45010606、43240160、42404294条,共计46.2 Gb的clean reads数据。测序结果经denovo组装共获得95220个Unigenes,每个Unigenes的平均长度为1064.9bp。经过生物信息学方法与五个数据库(NR,GO,COG,KEGG,SWSS-PRO)比对,共注释到20368个Unigenes。其中GO功能注释将Unigenes分为生物过程、细胞组分和分子功能3个大类50个分支;在与COG数据库比对中,共有15798条比对到了同源序列,且一共被分为25类;KEGG代谢通路包括6大类33个小类,可将Unigenes映射到330条代谢通路中。分子标记筛选后获得37751个潜在SSR位点,共发现3228575个SNP位点。本研究通过对罗氏沼虾7个不同组织进行转录组测序,数据组装及功能注释,为进一步深入挖掘和开发利用罗氏沼虾功能基因提供参考。
关键词:  罗氏沼虾  转录组  RNA-seq技术  不同组织  功能基因  比较分析
DOI:10.11693/hyhz20200600181
分类号:
基金项目:国家重点研发计划蓝色粮仓科技创新专项,2018YFD0901303号;浙江省农业(水产)新品种选育重大科技专项,2016C02055-2号;现代农业产业技术体系专项资金资助,CARS-48号。
COMPARATIVE TRANSCRIPTOME ANALYSIS OF DIFFERENT TISSUES IN GIANT FRESHWATER PRAWNS (MACROBRACHIUM ROSENBERGII) BASED ON RNA-SEQ
LI Xi-Lian, GU Zhi-Min, SHEN Pei-Jing, XU Yang, ZHANG Yu-Fei, GAO Qiang, CHENG Hai-Hua, CHEN Xue-Feng
Key Laboratory of Healthy Freshwater Aquaculture of Ministry of Agriculture and Rural Development, Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China
Abstract:
The giant freshwater prawns (Macrobrachium rosenbergii) is an important freshwater shrimp breeding species in China. By using Illumina Miseq platform, transcriptome from seven tissus/organs (eyestalk, liver, ovary, gill, heart, muscle, and testis) were analyzed, from which high quality clean reads (36325476, 56796932, 36328098, 51370140, 45010606, 43240160, and 42404294) were obtained, respectively, in total of 46.2Gb data after quality control. A total of 95220 Unigenes were obtained by the Denovo assembly. The average length of each Unigenes was 1064.9 bp. After the bioinformatics method was compared with five databases (NR, GO, COG, KEGG, SWSS-PROT), 20368 Unigenes were annotated. Among them, GO functional annotation divided Unigenes into three categories:biological process, cell component and molecular function, and 50 branches. In comparison with COG database, 15798 items were compared to homologous sequences, and were divided into 25 categories. The KEGG metabolic pathway includes 6 categories and 33 subcategories, which can map Unigenes to 330 metabolic pathways. After molecular marker screening, 37751 potential SSR sites were obtained. In addition, 3228575 SNP markers were found. Transcriptome sequencing, data assembly, and functional annotation were performed on 7 different tissues of M. rosenbergii, providing references for further exploration and development of functional genes of M. rosenbergii.
Key words:  Macrobrachium rosenbergii  transcriptome  RNA-seq  different tissues  functional genes  comparative analysis
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