摘要
【目的】获得牦牛(Bos grunniens)皱胃全长转录组数据库,深入挖掘牦牛皱胃功能基因。【方法】采用PacBio Sequel高通量测序系统,使用单分子实时(single molecular real time,SMRT)测序技术对成年牦牛皱胃全长转录组进行测序,对原始数据进行质控和去冗余分析,再比对参考基因组获取过滤后的非重复序列(Unigenes),使用多种生物信息软件对牦牛皱胃全长转录本数据进行功能注释、转录因子注释、编码区预测、简单重复序列(simple sequence repeats,SSR)分析及可变剪接分析。【结果】通过测序共获得14467420条子序列,平均子序列长度为3344.23 bp,质控得到循环一致性序列(CCS)有296840条,全长非嵌合(FLNC)序列有277402条,过滤和去冗余后对比参考基因组最终获得8556条Unigenes。通过与NR、Swiss-Prot、KEGG、KOG、eggNOG、GO和Pfam数据库比对,对Unigenes进行注释,其中NR数据库注释了8544条Unigenes;Swiss-Prot数据库注释了8475条Unigenes;KEGG数据库注释了1721条Unigenes;KOG数据库注释了6572条Unigenes;eggNOG数据库注释了8491条Unigenes;GO数据库注释了7725条Unigenes;Pfam数据库注释了8162条Unigenes。此外,经鉴定或预测,还获得了943个转录因子、8544个编码区片段、3596个SSR位点和1825个可变剪接事件。【结论】本研究获得了较为可靠的牦牛皱胃全长转录组数据,可为进一步研究牦牛皱胃生物学特性、相关代谢途径、信号通路及其分子机制提供数据支持。
【Objective】In order to obtain the full-length transcriptome database of abomasum in yak(Bos grunniens),the functional genes of abomasum of yak were deeply excavated.【Method】The full-length transcriptome of abomasum of adult yak was sequenced by single molecular real time(SMRT)sequencing technology using high-throughput sequencing PacBio Sequel high-throughput sequencing system.The original data were quality controlled and de redundant analysis,and then compared with the reference genome to obtain filtered non repetitive sequences(Unigenes).A variety of bioinformatics software were used to compare the full-length transcriptome data of abomasum in yak for functional annotation,transcription factor annotation,coding region prediction,simple sequence repeats(SSR)analysis and alternative splices analysis.【Result】A total of 14467420 subsequences were obtained by sequencing,with an average length of 3344.23 bp.296840 CCS sequences and 277402 FLNC sequences were obtained by quality control.After filtering and de redundancy,the reference genome was compared,and 8556 Unigenes were finally obtained.By comparing with NR,Swiss-Prot,KEGG,KOG,eggNOG,GO and Pfam databases,Unigenes were annotated,of which 8544 Unigenes were annotated in NR database.Swiss-Prot database annotated 8475 Unigenes.The KEGG database annotated 1721 unigenes.The KOG database annotated 6572 Unigenes.The eggNOG database annotated 8491 Unigenes.GO database annotated 7725 Unigenes;The Pfam database annotated 8162 Unigenes.In addition,943 transcription factors,8544 CDS fragments,3596 SSR sites and 1825 alternative splicing events were identified or predicted.【Conclusion】In this study,reliable full-length transcriptome data of yak abomasum were obtained,it could provide data support for the further study of the biological characteristics,related metabolic pathways,signal pathways and molecular mechanisms of abomasum in yak.
作者
谢书琼
马士龙
唐娇
刘益丽
江明锋
XIE Shuqiong;MA Shilong;TANG Jiao;LIU Yili;JIANG Mingfeng(Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization,Ministry of Education and Sichuan Province,Southwest Minzu University,Chengdu 610041,China;Institute of Tibetan Plateau Research,Southwest Minzu University,Chengdu 610041, China;College of Animal and Veterinary Sciences,Southwest Minzu University, Chengdu 610041,China)
出处
《中国畜牧兽医》
CAS
北大核心
2022年第5期1610-1620,共11页
China Animal Husbandry & Veterinary Medicine
基金
西南民族大学研究生创新型科研项目(CX2021SZ23)
西南民族大学中央高校基本科研业务费专项资金资助(3300221780)
四川省科技计划项目/四川省重点研发项目(2021YFYZ0001)
四川省重点研发项目(2021YFN0001)。
关键词
牦牛
皱胃
全长转录组
第3代测序
功能注释
yak
abomasum
full-length transcriptome
the third generation sequencing
functional notes
