基于PacBio Iso-Seq红棕象甲全长转录组测序分析
Using PacBio Iso-Seq to determine the transcriptome of Rhynchophorus ferrugineus
杨红军 胡佳萌 王治博 徐丹萍 卓志航
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DOI：10.7679/j.issn.2095-1353.2021.066
作者单位：西华师范大学，南充 637002；海南大学林学院，海口 570228；农业部华南作物有害生物综合治理重点实验室，广州 510642
中文关键词：红棕象甲；转录组；基因组注释；高通量测序
英文关键词：Rhynchophorus ferrugineus; transcriptome; genome annotation; high-throughput sequencing
中文摘要：
【目的】 建立红棕象甲Rhynchophorus ferrugineus全长转录组数据库，深入挖掘红棕象甲基因数据信息。【方法】 采用高通量测序平台，利用二代测序（Illumina RNA-seq）校正三代测序（PacBio Iso-Seq）的方法对红棕象甲进行全长转录组测序，并对转录组数据进行生物信息学分析。【结果】 红棕象甲全长转录组平均长度为2 302 bp，N90长度为1 321 bp，N50长度为2 785 bp；经CD-Hit程序去冗余，获得转录本63 801条，主要长度范围为0.5-6 k。基因功能注释表明，在NR、Swiss-Prot、KEGG、KOG、GO、NT和Pfam数据库中，分别有50 280、40 109、47 197、33 511、27 707、27 253 和 27 707条转录本被注释；其中，12 508条转录本均在7个数据库中有注释，54 999条转录本至少在一个数据库有注释。此外，经鉴定或预测，获得2 184个可变剪接（AS）、66 230个SSR、2 084个转录因子（TFs）和9 618条长链非编码RNA（LncRNA）。CDS长度的主要分布范围为0-2 500 nt。【结论】 本研究获得了红棕象甲全长转录组数据库，为红棕象甲后续分子生物学基础研究奠定基础。
英文摘要：
[Objectives] To obtain genetic data on, and establish a transcriptome database for, Rhynchophorus ferrugineus. [Methods] The transcriptome of R. ferrugineus was sequenced using a high-throughput sequencing platform with second-generation sequencing (Illumina RNA-seq) to correct third-generation sequencing (PacBio Iso-Seq) data, and analyzed with bioinformatic software. [Results] The mean number of R. ferrugineus transcripts was 2 302 bp and the N90 and N50 lengths were 1 321 bp and 2 785 bp, respectively. An additional 63 801 transcripts were obtained using the CD-Hit program with the majority ranging in length between 0.5 and 6 k. Of the transcripts found, 50 280 were annotated in the NR database, 27 253 in the NT database, 47 197 in the KEGG database, 40 109 in the Swiss-Prot database, 27 707 in the Pfam database, 27 707 in the GO database and 33 511 in the KOG database. 54 999 were annotated in at least one database and 12 058 were annotated in all databases. Furthermore, 2 184 AS, 66 230 SSR, 20 84 TFs and 9 618 LncRNA were predicted, or identified, respectively, and the main CDS length range was 0-2 500 nt. [Concusion] The transcriptome database of R. ferrugineus was successfully obtained. The results provide a foundation for further study of the molecular biology of this species.