不同生长速度的雌性罗氏沼虾肌肉组织转录组测序分析

Transcriptome sequencing analysis of muscle tissues of female Macrobrachium rosenbergii with different growth rates

  • 摘要: 【目的】鉴定筛选出与罗氏沼虾生长性状相关的候选基因及信号通路,为揭示其生长发育的分子调控机制提供参考依据。【方法】以同一全同胞家系雌性罗氏沼虾中不同生长速度的个体为试验材料,采用Illumina HiSeqTM 2500进行转录组测序,经过滤、质控后利用Trinity进行拼接组装获得Unigenes,并在数据库(Nr、Nt、KO、Swiss-Prot、Pfam、GO、KOG和KEGG)中进行功能注释,通过DESeq2进行快速生长组与慢速生长组间的差异表达基因(DEGs)分析,运用GOseq和KOBAS进行GO富集分析和KEGG通路分析,采用MISA进行SSR位点挖掘。【结果】罗氏沼虾肌肉组织转录组测序共计获得321706038条Raw reads,经过滤筛选得到310075274条Clean reads,拼接组装后得到38969条Unigenes; 18160条(46.60%) Unigenes成功注释在Nr、Nt、KO、Swiss-Prot、Pfam、GO、KOG和KEGG 8个数据库中。经DEGs分析,快速生长组与慢速生长组间共鉴定到DEGs 937个,其中上调表达基因235个,下调表达基因702个。937个DEGs分别富集到230个GO条目和21条KEGG信号通路中,包含氨基糖和核苷酸糖代谢(Amino sugar and nucleotide sugar metabolism)、糖酵解/糖质新生(Glycolysis/Gluconeogenesis)、氧化磷酸化(Oxidative phosphorylation)等信号通路。此外,在38969条Unigenes中共鉴定到22476个SSRs。【结论】不同生长速度的雌性罗氏沼虾肌肉转录组测序分析共筛选出937个DEGs,主要富集在氨基糖和核苷酸糖代谢、糖酵解/糖质新生、氧化磷酸化等信号通路上,在罗氏沼虾的生长发育过程中发挥重要作用。

     

    Abstract: 【Objective】To provide references to reveal the molecular regulation mechanism for growth and development in Macrobrachium rosenbergii, the candidate genes and signaling pathways related to its growth traits were identified and screened.【Method】 Female individuals with different growth rates from the same full-sibling family were selected to perform transcriptome sequencing by Illumina HiSeqTM 2500 platform. After filtering and quality control,Trinity was used for assembly to obtain Unigenes.Furthermore,functional annotation in databases(Nr,Nt,KO, Swiss-Prot,Pfam, GO, KOG, KEGG)were conducted. Differentially expressed genes(DEGs)between the fast-growing group and slow-growing group were identified by DESeq2. GOseq and KOBAS software were adopted to conduct GO enrichment analysis and KEGG pathway analysis. Additionally, MISA was used for detecting the SSR loci.【Result】 A total of 321706038 Raw reads were obtained in the muscle tissue transcriptome sequencing of M. rosenbergii. After filtering,310075274 Clean reads were obtained,and then assembled into 38969 Unigenes. A total of 18160(46.60%)Unigenes were successfully annotated in above databases(Nr,Nt,KO,Swiss-Prot,Pfam,GO,KOG,KEGG). After DEGs analysis,937 DEGs were identified between the two groups,including 235 up-regulated genes and 702 down-regulated genes. A total of 937 DEGs were enriched in 230 GO terms and 21 KEGG signaling pathways respectively, including amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis and oxidative phosphorylation signaling pathways. Meanwhile, 22476 SSRs were identified from 38969 Unigenes.【Conclusion】A total of 937 DEGs are screened out based on muscle transcriptome sequencing analysis of female M. rosenbergii with different growth rates,which are mainly enriched in several signaling pathways including amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis and oxidative phosphorylation signa-ling pathway, playing an important role in the growth and development of M. rosenbergii.

     

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