猪circRNAs的系统鉴定及特征分析

doi:10.11843/j.issn.0366-6964.2020.12.007

Abstract

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

CLC Number:

S828.2

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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Systematic Identification and Characteristics Analysis of Sus scrofa Circular RNAs

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