Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

Mao-Sen Ye; Jin-Yan Zhang; Dan-Dan Yu; Min Xu; Ling Xu; Long-Bao Lv; Qi-Yun Zhu; Yu Fan; Yong-Gang Yao

首页> 中文期刊> 《动物学研究》 >Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

开具论文收录证明 >>

期刊封面封底目录下载 >>

文献代查 >>

页面导航

摘要
著录项
相似文献
相关主题

摘要

The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding RNA(lncRNA)is crucial for developing animal models using this species.In the current study,we collected a total of 234 high-quality RNA sequencing(RNA-seq)datasets and two long-read isoform sequencing(ISO-seq)datasets and improved the annotation of our previously assembled high-quality chromosomelevel tree shrew genome.We obtained a total of 3514 newly annotated coding genes and 50576 lncRNA genes.We also characterized the tissuespecific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome.We identified 144 tree shrew-specific gene families,including interleukin 6(IL6)and STT3 oligosaccharyltransferase complex catalytic subunit B(STT3B),which underwent significant changes in size.Comparison of the overall expression patterns in tissues and pathways across four species(human,rhesus monkey,tree shrew,and mouse)indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level.Notably,the newly annotated purine rich element binding protein A(PURA)gene and the STT3B gene family showed dysregulation upon viral infection.The updated version of the tree shrew genome annotation(KIZ version 3:TS_3.0)is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.

著录项

来源
《动物学研究》 |2021年第6期|692-709|共18页
作者
Mao-Sen Ye; Jin-Yan Zhang; Dan-Dan Yu; Min Xu; Ling Xu; Long-Bao Lv; Qi-Yun Zhu; Yu Fan; Yong-Gang Yao;
展开▼
作者单位

Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences&Yunnan Province;

KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases;

Kunming Institute of Zoology;

Chinese Academy of Sciences;

Kunming;

Yunnan 650204;

China;

Kunming College of Life Science;

University of Chinese Academy of Sciences;

Kunming;

Yunnan 650204;

China;

National Resource Center for Non-Human Primates;

National Research Facility for Phenotypic&Genetic Analysis of Model Animals;

Primate Facility);

Kunming Institute of Zoology;

Chinese Academy of Sciences;

Kunming;

Yunnan 650107;

China 4 State Key Laboratory of Veterinary Etiological Biology;

Lanzhou Veterinary Research Institute;

Chinese Academy of Agricultural Sciences;

Lanzhou;

Gansu 730046;

China;

展开▼
原文格式 PDF
正文语种 chi
中图分类肿瘤学;
关键词
Tree shrew; Genome annotation; Transcriptome; Gene family; Virus infection;

相似文献

中文文献
外文文献

1. Chromosomal level assembly and population sequencing of the Chinese tree shrew genome [J] . Yu Fan ,Ping Zheng ,Dong-Dong Wu . 动物学研究 . 2019,第006期
2. Sequencing and analysis for the full-length genome RNA of foot-and-mouth disease virus China/99 [J] . ZHANG ,Xiansheng ,LIU . 中国科学 . 2004,第001期
3. Genome sequencing and comparative transcriptomics of a filamentous fungus Aspergillusfumigatus Z5 [C] . 缪有志 . 第十六次全国环境微生物学学术研讨会 . 2013
4. Large-scale identification of ESTs from Nicotiana tabacum by normalized cDNA library sequencing [A] . Sandra Pérez Alvarez . 2005

Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

摘要

著录项

相似文献

相关主题

期刊订阅