Laboratory of Adaptation and Evolution of Aquatic Animals, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
Int J Mol Sci. 2019 Mar 27;20(7):1529. doi: 10.3390/ijms20071529.
The Yenyuan stream salamander () has been previously evaluated with regards to phylogeny, population genetics, and hematology, but genomic information is sparse due to the giant genome size of salamanders which contain highly repetitive sequences, thus resulting in the lack of a complete reference genome. This study evaluates the encoding genetic sequences and provides the first transcriptome assembly of Yenyuan stream salamander based on mixed samples from the liver, spermary, muscle and spleen tissues. Using this transcriptome assembly and available encoding sequences from other vertebrates, the gene families, phylogenetic status, and species divergence time were compared or estimated. A total of 13,750 encoding sequences were successfully obtained from the transcriptome assembly of Yenyuan stream salamander, estimated to contain 40.1% of the unigenes represented in tetrapod databases. A total of 88.79% of these genes could be annotated to a biological function by current databases. Through gene family clustering, we found multiple possible isoforms of the gene-whose function is related to regeneration-based on sequence similarity. Meanwhile, we constructed a robust phylogenetic tree based on 56 single-copy orthologues, which indicates that based on phylogenetic position, the Yenyuan stream salamander presents the closest relationship with the Chinese giant salamander () of the investigated vertebrates. Based on the fossil-calibrated phylogeny, we estimated that the lineage divergence between the ancestral Yenyuan stream salamander and the Chinese giant salamander may have occurred during the Cretaceous period (~78.4 million years ago). In conclusion, this study not only provides a candidate gene that is valuable for exploring the remarkable capacity of regeneration in the future, but also gives an interesting insight into the understanding of Yenyuan stream salamander by this first transcriptome assembly.
原尾溪蟾（）在系统发育、种群遗传学和血液学方面已经进行了评估，但由于蝾螈基因组较大，包含高度重复的序列，因此基因组信息较为匮乏，导致缺乏完整的参考基因组。本研究评估了编码遗传序列，并基于来自肝脏、精巢、肌肉和脾脏组织的混合样本，提供了原尾溪蟾的首个转录组组装。利用这个转录组组装和来自其他脊椎动物的可用编码序列，比较或估计了基因家族、系统发育地位和物种分化时间。从原尾溪蟾的转录组组装中成功获得了 13750 个编码序列，估计包含四足动物数据库中 40.1%的基因。这些基因中共有 88.79%可以通过当前数据库注释到一个生物学功能。通过基因家族聚类，我们发现了基因的多个可能的同工型，该基因的功能与再生有关，基于序列相似性。同时，我们构建了一个基于 56 个单拷贝直系同源物的稳健系统发育树，该树表明，基于系统发育位置，原尾溪蟾与调查的脊椎动物中的中国大鲵（）关系最为密切。根据化石校准的系统发育树，我们估计原尾溪蟾和中国大鲵的祖先谱系分化可能发生在白垩纪时期（约 7840 万年前）。总之，本研究不仅提供了一个有价值的候选基因，可用于未来探索再生的非凡能力，而且通过首个转录组组装，也为我们了解原尾溪蟾提供了有趣的见解。
