海兰褐壳蛋鸡小黄卵泡颗粒细胞全长转录组测序分析

doi:10.16431/j.cnki.1671-7236.2023.05.003

摘要/Abstract

摘要： 【目的】获取鸡小黄卵泡颗粒细胞(granulosa cells of small yellow follicle,SYFG)全长转录组数据,为深入挖掘鸡卵泡发育内在分子调控信息提供参考。【方法】采用PacBio高通量测序平台,对海兰褐壳蛋鸡SYFG进行测序、过滤、聚类和矫正原始数据,获取全长转录本序列。通过生物信息学软件对全长转录本数据进行功能注释、转录因子注释、编码区序列(coding sequence,CDS)预测、长链非编码RNA(long non-coding RNA,lncRNA)预测筛选、简单重复序列(simple sequence repeats,SSR)检测及可变剪接(alternative splicing,AS)和选择性多聚腺苷酸化(alternative polyadenylation,APA)分析。【结果】通过测序共获得52 311条海兰褐壳蛋鸡SYFG全长转录本,长度主要分布于1~3 500 bp。通过与GO、KEGG、COG、NR、Swiss-Prot和Pfam数据库比对,对转录本序列进行注释,其中GO数据库注释了26 525条转录本,KEGG数据库注释了25 233条转录本,COG数据库注释了31 303条转录本,NR数据库注释了34 284条转录本,Swiss-Prot数据库注释了30 701条转录本,Pfam数据库注释了24 622条转录本。此外,经鉴定或预测,还获得了559个转录因子、40 944个CDS、14 699个lncRNAs、7种类型的SSR、28 423个AS和2 747个APA事件。【结论】本研究获得了鸡SYFG全长转录组测序数据,提升了转录本的数量和长度,完善了转录本的功能注释,分析了AS和APA事件的类型,揭示了转录本的复杂性,为进一步从转录组水平解析鸡卵泡发育的分子调节机制提供数据支持。

关键词: 海兰褐壳蛋鸡; 小黄卵泡颗粒细胞(SYFG); 三代测序; 卵泡发育

Abstract: 【Objective】 This study was amied to obtain the full-length transcriptome database of granulosa cells of small yellow follicle (SYFG),and provide references for further exploring the internal molecular regulation of chicken follicular development.【Method】 The SYFG of Hy-Line variety Brown was sequenced using PacBio high-throughput sequencing platform,and the full-length transcriptome sequence was finally obtained by filtering, clustering and correction.Bioinformatics analysis software was used to compare the full-length transcriptome data for function annotation,transcription factor annotation,coding sequence (CDS) prediction,long non-coding RNA (lncRNA) prediction and screening,simple sequence repeats (SSR) detecting and alternative splicing (AS),and alternative polyadenylation (APA) analysis.【Result】 A total of 52 311 full-length transcripts of SYFG of Hy-Line variety Brown were obtained,and the length was mainly distributed in 1-3 500 bp.By comparing with GO,KEGG,COG,NR,Swiss-Prot,and Pfam databases,the full-length transcriptomes were annotated,of which 26 525 full-length transcriptomes were annotated in GO database.The KEGG database annotated 25 233 full-length transcriptomes.The COG database annotated 31 303 full-length transcriptomes.The NR database annotated 34 284 full-length transcriptomes.The Swiss-Prot database annotated 30 701 full-length transcriptomes.The Pfam database annotated 24 622 full-length transcriptomes.In addition,559 transcription factor,40 944 CDS,14 699 lncRNAs,7 types of SSR,28 423 AS,and 2 747 APA events were identified or predicted.【Conclusion】 This study obtained the full-length transcriptome sequencing data of SYFG of chicken,which improved the number and length of transcripts,perfected the functional annotation of transcripts,analyzed the type of AS and APA,and revealed the complexity of transcriptome,which could provide data support to further analyze the molecular regulatory mechanism of chicken follicular development from the transcriptome level.

Key words: Hy-Line variety Brown; granulosa cells of small yellow follicle(SYFG); the third generation sequencing; follicle development

中图分类号:

S831.2

片慧芳, 杜旭彬, 李妍, 张雨辰, 刘斐, 虞德兵. 海兰褐壳蛋鸡小黄卵泡颗粒细胞全长转录组测序分析[J]. 中国畜牧兽医, 2023, 50(5): 1754-1763.

PIAN Huifang, DU Xubin, LI Yan, ZHANG Yuchen, LIU Fei, YU Debing. Sequencing Analysis of the Full-length Transcriptome of Granulosa Cells of Small Yellow Follicle in Hy-Line Variety Brown[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(5): 1754-1763.

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