Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing
Mao-Sen Ye, 中国科学院昆明动物研究所中国科学院/云南省动物模型与人类疾病重点实验室，中科院昆明动物研究所-香港中文大学生物资源与疾病分子机理联合实验室，云南 昆明 650204，中国, Jinyan Zhang, Dandan Yu, Min Xu, Ling Xu, Longbao Lv, Qiyun Zhu, Yu Fan, Yong‐Gang Yao, 中国科学院大学昆明生命科学学院，云南 昆明650204，中国, 中国科学院昆明动物研究所模式动物表型与遗传研究国家重大科技基础设施，国家非人灵长类实验动物资源库，云南 昆明650107，中国, 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，兰州 甘肃 730046，中国
Abstract
The Chinese tree shrew (<i>Tupaia</i> <i>belangeri</i> <i>chinensis</i>) 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 (<i>IL6</i>) and STT3 oligosaccharyltransferase complex catalytic subunit B (<i>STT3B</i>), 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 (<i>PURA</i>) gene and the <i>STT3B</i> 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.