猪circRNAs的系统鉴定及特征分析

doi:10.11843/j.issn.0366-6964.2020.12.007

畜牧兽医学报 ›› 2020, Vol. 51 ›› Issue (12): 2972-2979.doi: 10.11843/j.issn.0366-6964.2020.12.007

猪circRNAs的系统鉴定及特征分析

李巧伟^1,2,3,4, 杨亚岚^2,3,4, 易国强^2,3,4, 陈慕雅^2,3,4, 王斌虎^2,3,4, 范新浩^2,3,4, 唐中林^1,2,3,4*

1. 中国农业科学院北京畜牧兽医研究所, 北京 100193;
2. 中国农业科学院农业基因组研究所, 深圳 518124;
3. 农业部农业基因数据分析重点实验室, 深圳 518124;
4. 岭南现代农业科学与技术广东省实验室, 深圳 518124

收稿日期:2020-07-07 出版日期:2020-12-25 发布日期:2020-12-23
通讯作者: 唐中林,主要从事猪基因组设计育种研究,E-mail:tangzhonglin@caas.cn
作者简介:李巧伟(1993-),女,河南范县人,硕士,主要从事circRNA相关的研究,E-mail:liqiaowei@caas.cn
基金资助:
广东省重点领域研发计划（现代种业）项目（2018B020203002；2018B020203003）；国家自然科学基金（31830090）；转基因生物新品种培育重大专项（2016ZX08009-003-006）

Systematic Identification and Characteristics Analysis of Sus scrofa Circular RNAs

LI Qiaowei^1,2,3,4, YANG Yalan^2,3,4, YI Guoqiang^2,3,4, CHEN Muya^2,3,4, WANG Binhu^2,3,4, FAN Xinhao^2,3,4, TANG Zhonglin^1,2,3,4*

1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
2. Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
3. Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Shenzhen 518124, China;
4. Lingnan Guangdong Laboratory of Modern Agriculture, Shenzhen 518124, China

Received:2020-07-07 Online:2020-12-25 Published:2020-12-23

摘要/Abstract

摘要： 旨在系统鉴定猪基因组中的环状RNAs（circular RNAs，circRNAs），并对其分子特征进行分析。本研究采集长白、通城和五指山猪16个发育阶段（妊娠33、40、50、55、60、65、70、75、80、85、90、95、100和105 d的胚胎以及出生后0和10 d）9种不同组织（背最长肌、心、脾、肺、肝、肾、胃、小肠和腿肌）样品，提取RNA再进行等量混合，构建链特异性转录组文库后，利用Illumina Genome Analyzer II平台进行测序，共获得1.18亿条总reads。采用CIRI2软件鉴定circRNAs，再利用生物信息学工具对鉴定的circRNAs进行分子特征分析。结果，共鉴定了8 486条circRNAs，其主要分布在1、6和13号染色体，91%的circRNAs为外显子型，平均长度为350 nt，平均GC含量为47.11%，每条染色体上的circRNAs数目与mRNAs数目显著正相关（R=0.84，P=1.285×10^-5）。最后，筛选出3条与骨骼肌生长发育相关的circRNAs（sus-MYH2_0025、sus-CDK13_0002和sus-FANCL_0003）。分析结果表明，sus-MYH2_0025具有高度的组织特异性，sus-CDK13_0002在猪、人和小鼠中高度保守，sus-FANCL_0003在猪和大鼠中高度保守。本研究利用转录组数据在猪基因组中对circRNAs进行系统鉴定和分子特征分析，为circRNA的功能和机制研究提供了丰富的信息，并为猪分子育种提供新的潜在候选基因。

关键词: 猪, 环状RNA, 鉴定, 分子特征, 骨骼肌

Abstract: The objective of this study was to identify Sus scrofa circular RNAs (circRNAs) systematically and analyze their molecular characteristics. The samples from 16 developmental stages of Landrace, Tongcheng and Wuzhishan pigs (Embryonic 33, 40, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 and 105 days as well as postnatal days 0 and 10) and 9 different tissues (longissimus dorsi, heart, spleen, lung, liver, kidney, stomach, small intestine, and leg muscle) were collected. RNA was extracted from samples and then mixed with equal quantities. A strand-specific RNA-seq library was constructed and sequenced on the Illumina Genome Analyzer II sequencing platform. A total of 118 million reads were obtained. The circRNAs were identified using CIRI2 software and their molecular characteristics were analyzed using bioinformatics tools. A total of 8 486 circRNAs were identified. These circRNAs mainly located on chromosome 1, 6 and 13, and 91% of them were located on the exonic regions in genome. The average length of these circRNAs was 350 nt and GC content was 47.11%. The number of circRNAs was significantly positively correlated with the number of mRNAs (R=0.84, P=1.285×10^-5) on each chromosome. Finally, three circRNAs (sus-MYH2_0025, sus-CDK13_0002, and sus-FANCL_0003) that were associated with skeletal muscle growth and development were identified. The results suggested that sus-MYH2_0025 had higher tissue-specificity, sus-CDK13_0002 was highly conserved among swine, human and mouse, and sus-FANCL_0003 was highly conserved between swine and rat. The transcriptome data was used to systematically identify circRNAs in pig genome and their molecular characteristics were analyzed, which provided rich information for the study of circRNA functions and mechanisms, and provided new potential candidate genes for molecular breeding of pigs.

Key words: Sus scrofa, circRNA, identification, molecular characteristics, skeletal muscle

中图分类号:

S828.2

李巧伟, 杨亚岚, 易国强, 陈慕雅, 王斌虎, 范新浩, 唐中林. 猪circRNAs的系统鉴定及特征分析[J]. 畜牧兽医学报, 2020, 51(12): 2972-2979.

LI Qiaowei, YANG Yalan, YI Guoqiang, CHEN Muya, WANG Binhu, FAN Xinhao, TANG Zhonglin. Systematic Identification and Characteristics Analysis of Sus scrofa Circular RNAs[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(12): 2972-2979.

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猪circRNAs的系统鉴定及特征分析

Systematic Identification and Characteristics Analysis of Sus scrofa Circular RNAs

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