山羊5个组织的全长转录组构建与分析  

The Construction and Analysis of Full-Length Transcriptome of Five Tissues in Goat

作　　者：魏文景 孙学良 占思远[1] 陈瑜 张国俊 苗斌 张红平[1] 郭家中[1] WEI Wenjing;SUN Xueliang;ZHAN Siyuan;CHEN Yu;ZHANG Guojun;MIAO Bin;ZHANG Hongping;GUO Jiazhong(College of Animal Science and Technology,Sichuan Agricultural University,Chengdu 611130,China;Bazhong Naiijiang Yellow Goat Scientific Research Institute,Nanjiang 635600,Sichuan,China)

机构地区：[1]四川农业大学动物科技学院,成都611130 [2]巴中市南江黄羊科学研究所,四川南江635600

出　　处：《四川农业大学学报》2022年第3期421-426,共6页Journal of Sichuan Agricultural University

基　　金：四川省科技计划项目(2021YFYZ0003,优质肉羊育种材料和方法创新及新品种选育);香港促进会南江黄羊科研扶贫项目。

摘　　要：【目的】构建山羊(Capra hircus)全长转录组,旨在改进参考基因组的功能注释。【方法】利用PacBio长读段测序技术对南江黄羊肝、脾、肾周脂肪、背最长肌和睾丸5个组织的混合样本进行高通量测序;对原始数据进行校正、聚类去冗余,最后用KEGG数据库对预测转录本序列进行功能注释。【结果】质控后获得28 432条高质量一致性全长序列,其中99.49%的序列被成功比对到山羊基因组;得到源自9 879个基因的19 115个转录本。进一步分析得到表达基因总数的41.39%发生了可变剪接;其中起始外显子可变剪接占比最高(36.47%),外显子互斥占比最低(1.78%)。另外,144条序列未被比对到参考基因组上,这些序列的平均GC含量高达56.50%;利用KEGG数据库对其进行功能注释,揭示28个转录本与免疫系统相关。【结论】获得的测序数据全面涵盖混合样本中表达的转录本,证明了山羊基因组转录的复杂性。研究结果总体上提高了每个基因平均表达的转录本数量,证明可变剪接的广泛存在;未成功比对的转录本序列GC含量较高且许多转录本来自免疫基因的表达。【Objective】This study aimed to construct the full-length transcriptome in goats(Capra hircus),which could to improve the functional annotation of the goat reference genome. 【Method】The PacBio long-read sequencing technology was used to obtain the full-length transcriptome in a mixed sample of the liver,spleen,perirenal fat,longissimus dorsi,and testis tissues from a Nanjiang Yellow goat. After quality control that mainly included the iterative clustering and the error correction,the potential transcript sequences were then annotated by using the KEGG database. 【Result】A total of 28 432polished consensus reads were obtained and then aligned against the reference genome. The mapping ratio achieved at 99.49%,and 19 115 transcripts were derived from the total 9 879 expressed genes. We identified that 41.39% of the total expressed genes underwent alternative splicing,among which the proportion of alternative first exon was the highest(36.47%),while the mutually exclusive exon was the lowest(1.78%). A total of 144 transcripts were not successfully mapped to the reference genome and had an average high GC content of 56.50%,among which 28 transcripts were annotated to immune-related pathways based on the functional annotation using the KEGG database. 【Conclusion】The sequencing data obtained in this study comprehensively covered the transcripts expressed in the mixed samples and demonstrated widespread alternative splicing in goats. The transcripts that failed to be mapped to the reference genome generally had high GC content,many of which were derived from immune-related genes.

关 键 词：南江黄羊 全长转录组 功能注释 可变剪接 

分 类 号：S827[农业科学—畜牧学]