基于PacBio平台的黄颡鱼全长转录组测序及分析

doi:10.14088/j.cnki.issn0439-8114.2023.04.035

摘要/Abstract

摘要： 为进一步丰富黄颡鱼（Pelteobagrus fulvidraco）信息数据库, 采用PacBio测序平台对黄颡鱼的肝脏、肾、背部肌肉、脑、脾、心脏、皮肤、血液、鳃、性腺等组织进行全长转录组混样测序。共获得685 574个全长非嵌合（Full-length non-chimeric read, FLNC）序列,通过与黄颡鱼基因组比对分析,共获得72 509个非冗余isoforms,平均长度为2 918 bp。共鉴定到3 169个LncRNA、45 872个可变剪接事件、4 881个基因存在可变多聚腺苷酸化位点和304个融合基因。将12 492个新基因与NR、GO、KEGG、KOG和Swwassprot 5个公共数据库进行比对,成功注释了7 233个isoforms。GO分析发现,新基因主要集中于细胞过程（Cellular process）、细胞组分（Cell）和结合功能（Binding）。KEGG pathway分析显示,新基因主要在信号转导（Signal transduction）和免疫系统（Immune system）信号通路中得到富集,此外,涉及黄颡鱼生殖与繁殖相关的内分泌系统代谢途径包括催产素信号通路、雌二醇信号通路、孕酮介导的卵母细胞成熟、促性腺激素释放激素信号通路和卵巢类固醇合成。

关键词: 黄颡鱼（Pelteobagrus fulvidraco）, PacBio, 全长转录组, 可变剪接, 信号通路

Abstract: In order to further enrich the genomic information database of yellow catfish （Pelteobagrus fulvidraco）, the full-length transcriptome of liver, kidney, muscle, brain, spleen, heart, skin, blood, gill, and gonad tissues of yellow catfish was sequenced using the PacBio sequel platform. A total of 685 574 full-length non-chimeric read （FLNC） sequences were obtained, and 72 509 non-redundant isoforms with an average length of 2 918 bp were acquired by aligning with the genome of yellow catfish. 3 169 LncRNA, 45 872 alternative splicing events, 4 881 genes with variable polyadenylation sites, and 304 fusion genes were identified. After analyzing the 12 492 identified new genes in five public databases including NR, GO, KEGG, KOG, and Swissprot, 7 233 isoforms were successfully annotated. The new genes were mainly enriched in the Cellular process, Cell, and Binding categories according to GO analysis. KEGG pathway analysis indicated that the new genes were mainly enriched in the Signal transduction and Immune system signaling pathways. In addition, the metabolic pathways of the endocrine system related to reproduction and breeding of yellow catfish included the Oxytocin, Estrogen, Progesterone-mediated oocyte maturation, Gonadotropin releasing hormone, and Ovarian steroidogenesis signaling pathways.

Key words: yellow catfish（Pelteobagrus fulvidraco）, PacBio, full-length transcriptome, alternative splicing, signaling pathway

中图分类号:

S917

王家琪, 熊阳, 韩庆庆, 皇培培, 梅洁. 基于PacBio平台的黄颡鱼全长转录组测序及分析[J]. 湖北农业科学, 2023, 62(4): 194-201.

WANG Jia-qi, XIONG Yang, HAN Qing-qing, HUANG Pei-pei, MEI Jie. Full-length transcriptome sequencing and analysis of yellow catfish based on PacBio platform[J]. HUBEI AGRICULTURAL SCIENCES, 2023, 62(4): 194-201.

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