中华蜜蜂泛素基因及其全长转录本的发掘及分析
Exploration and investigation of Apis cerana cerana ubiquitin genes and their full-length transcripts
刘小玉 1张佳欣 1高旭泽 1冯佩林 1蔡宗兵 1那志豪 1陈大福 2郭睿 2徐国钧2
作者信息
- 1. 福建农林大学蜂学与生物医药学院,福州 350002
- 2. 福建农林大学蜂学与生物医药学院,福州 350002;天然生物毒素国家地方联合工程实验室,福州 350002;福建省蜂疗研究所,福建 350002
- 折叠
摘要
旨在利用三代Nanopore测序技术发掘中华蜜蜂(Apis cerana cerana)泛素(ubiquitin)基因及其全长转录本.基于前期获得的中华蜜蜂工蜂 4～6 日龄幼虫肠道的全长转录组数据,使用BLAST工具将全长转录本的序列比对到 KEGG 和 Nr 数据库以鉴定泛素基因及其全长转录本.采用 Astalavista 软件分析泛素基因的可变剪接(alternative splicing,AS)事件,并通过RT-PCR加以验证.通过TAPIS pipeline软件分析泛素基因的可变多聚腺苷酸化(alternative polyadenylation,APA)位点.共鉴定到 48个中华蜜蜂泛素基因和 435条泛素基因相关全长转录本.共发掘到 48个泛素基因的 74次AS事件,包括 31次内含子保留事件,19次可变 3'端剪接事件,16次可变5'端剪接事件及 8次外显子互斥事件.RT-PCR结果证实了 3种AS事件类型的真实性.共预测到 38个泛素基因含有 1个及以上的APA位点,并且在APA位点的上游鉴定到多个motif,一致性序列为:KCWYTDYTMWSYGMW SCARAWCCAGAATGAYCCWYWGGHWVMWGWDRTRGC.研究结果丰富了中华蜜蜂泛素基因及其全长转录本信息,为持续深入开展相关功能研究提供参考和依据.
Abstract
This study aimed to explore ubiquitin genes and their full-length transcripts in Apis cerana cerana using three-generation Nanopore sequencing technology.Based on the previously obtained full-length transcrip-tome data of the intestinal tract of 4-6-day-old worker larvae of Apis cerana cerana,the sequences of full-length transcripts were aligned to KEGG and Nr databases using BLAST tools to identify ubiquitin genes and their full-length transcripts.Astalavista software was used to analyze alternative splicing(AS)events of ubiquitin genes and verified by RT-PCR.Additionally,the TAPIS pipeline software was employed to analyze alternative polyad-enylation(APA)sites of ubiquitin genes.A total of 48 ubiquitin genes of Apis cerana cerana and 435 ubiquitin gene related full-length transcripts were identified.A total of 74 AS events of 48 ubiquitin genes were identified,including 31 intron retention events,19 variable 3′-end splicing events,16 variable 5′-end splicing events and 8 exon mutual exclusion events.RT-PCR results confirmed that the three randomly selected AS event types were real and reliable.Furthermore,38 ubiquitin genes were forecasted to contain one or more of the APA site,and in the upstream of the APA site identification to multiple motifs,consistency sequence was:KCWYTDYTMWSYG MWSCARAWCCAG AATGAYCCWYWGGHWVMWGWDRTRGC.The results of this study enrich the data-base of ubiquitin genes and their full-length transcripts information of Apis cerana cerana,and provide resource and foundation for further research on related functions.
关键词
东方蜜蜂/中华蜜蜂/全长转录本/泛素/可变剪接/可变多聚腺苷酸化Key words
Apis cerana/Apis cerana cerana/full-length transcript/ubiquitin/alternative splicing/alterna-tive polyadenylation引用本文复制引用
基金项目
国家自然科学基金项目(32172792)
国家自然科学基金项目(31702190)
国家现代农业产业技术体系专项资金项目(CARS-44-KXJ7)
福建省自然科学基金面上项目(2022J01131334)
福建农林大学硕士生导师团队项目(郭睿)()
福建农林大学科技创新专项基金项目(郭睿)()
宁夏回族自治区重点研发项目(2022BBF02037)
福建农林大学动物科学学院(蜂学学院)科研扶持项目()
出版年
2024
国家科技期刊平台
NSTL
万方数据