京海黄鸡卵巢转录组研究:基因结构分析与新基因发掘注释

doi:10.16431/j.cnki.1671-7236.2016.04.002

›› 2016, Vol. 43 ›› Issue (4): 854-861.doi: 10.16431/j.cnki.1671-7236.2016.04.002

京海黄鸡卵巢转录组研究:基因结构分析与新基因发掘注释

韩昆鹏^1,2, 段炼^1,2, 李婷婷^1,2, 王金玉^1,2, 张涛^1,2, 李国辉^1,2, 张跟喜^1,2, 薛倩^1,2

1. 扬州大学动物科学与技术学院, 扬州 225009;
2. 江苏省动物遗传繁育与分子设计重点实验室, 扬州 225009

收稿日期:2015-10-13 出版日期:2016-04-20 发布日期:2016-04-27
通讯作者: 王金玉 E-mail:jywang@yzu.edu.cn
作者简介:韩昆鹏(1990-),男,山东青岛人,硕士生,研究方向:动物遗传育种与繁殖,E-mail:275287095@qq.com
基金资助:
国家肉鸡产业技术体系(nycytx-42-G1-05);江苏高校优势学科建设工程;江苏省动物遗传繁育与分子设计重点实验室

Study on RNA-Seq of Jinghai Yellow Chicken Ovary:Analysis of Gene Structure and Mining New Genes

HAN Kun-peng^1,2, DUAN Lian^1,2, LI Ting-ting^1,2, WANG Jing-yu^1,2, ZHANG Tao^1,2, LI Guo-hui^1,2, ZHANG Gen-xi^1,2, XUE Qian^1,2

1. College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
2. Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China

Received:2015-10-13 Online:2016-04-20 Published:2016-04-27

摘要/Abstract

摘要： 本试验通过对京海黄鸡卵巢组织进行转录组分析,旨在为完善京海黄鸡部分基因结构和发掘新基因提供参考。选取高、低产京海黄鸡各4只,利用转录组测序(RNA-Seq)技术对其卵巢转录组进行测序,然后对得到的测序数据进行生物信息学分析。测序数据经过质量控制后,8个样品共得到484 992 074条有效数据(Clean Reads),总计61.09 Gb。筛选出1 445 264个京海黄鸡品种内SNP位点,其中位于基因区的SNP位点916 108个,位于基因间区的SNP位点552 168个。8个样品中平均新预测的可变剪接12 883个,并对7 481个基因结构进行了优化。与所选的参考基因组序列对比分析,共发掘4 431个新基因,通过与各数据库进行序列对比,1 809个新基因得到功能注释。本研究通过转录组测序技术检测了京海黄鸡卵巢组织的基因结构,为进一步完善京海黄鸡的基因结构信息及发掘潜在的新基因提供分子水平的依据。

关键词: 转录组测序; 京海黄鸡; 基因结构; SNP; 新基因

Abstract: In the present study, in order to improve part of the gene structure and mine new genes, transcriptome of ovary of 4 low and 4 high egg production Jinghai Yellow chickens were analyzed using RNA-Seq technology.The sequencing data was analyzed by bioinformatics methods.After quality control, 484 992 074 clean reads with a total of 61.09 Gb were obtained from the ovary library.1 445 264 SNPs were scanned in which 916 108 SNPs were located in gene region and 552 168 were located in intergenic region.The average new alternative splicing of 8 samples were 12 883. 7 481 genes were optimized gene structure.4 431 novel genes were mined by comparing to the chicken reference genome.1 809 novel genes were obtained by sequence alignment in different database after function annotations.The current study detected the structure of genes in ovary of Jinghai Yellow chicken using RNA-Seq technology, which improved the gene structure information of Jinghai Yellow chicken and provided basis for mining new genes at the molecular level.

Key words: RNA-Seq; Jinghai Yellow chicken; gene structure; SNP; new genes

中图分类号:

韩昆鹏, 段炼, 李婷婷, 王金玉, 张涛, 李国辉, 张跟喜, 薛倩. 京海黄鸡卵巢转录组研究:基因结构分析与新基因发掘注释[J]. , 2016, 43(4): 854-861.

HAN Kun-peng, DUAN Lian, LI Ting-ting, WANG Jing-yu, ZHANG Tao, LI Guo-hui, ZHANG Gen-xi, XUE Qian. Study on RNA-Seq of Jinghai Yellow Chicken Ovary:Analysis of Gene Structure and Mining New Genes[J]. , 2016, 43(4): 854-861.

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京海黄鸡卵巢转录组研究:基因结构分析与新基因发掘注释

Study on RNA-Seq of Jinghai Yellow Chicken Ovary:Analysis of Gene Structure and Mining New Genes

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