Year
Month
(Peer-Reviewed) Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing
Mao-Sen Ye 叶茂森 ¹ ², Jin-Yan Zhang 张金燕 ¹ ², Dan-Dan Yu 余丹丹 ¹ ³, Min Xu 徐敏 ¹ ³, Ling Xu 许凌 ¹ ³, Long-Bao Lv 吕龙宝 ³, Qi-Yun Zhu 朱启运 ⁴, Yu Fan 范宇 ¹ ³, Yong-Gang Yao 姚永刚 ¹ ² ³
¹ 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
中国 云南 昆明 中国科学院昆明动物研究所 中国科学院和云南省动物模型与人类疾病机理重点实验室 KIZ-CUHK生物资源与疾病分子机理联合实验室
² Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
中国 云南 昆明 中国科学院大学昆明生命科学学院
³ 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
中国 云南 昆明 中国科学院昆明动物研究所 国家非人灵长类实验动物资源库 模式动物表型与遗传研究国家重大科技基础设施(灵长类设施)
⁴ State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
中国 甘肃 兰州 中国农业科学院兰州兽医研究所 家畜疫病病原生物学国家重点实验室
Zoological Research, 2021-09-26
Abstract

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 chromosome-level tree shrew genome. We obtained a total of 3 514 newly annotated coding genes and 50 576 lncRNA genes. We also characterized the tissue-specific 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.
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing_1
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing_2
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing_3
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing_4
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