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濒危四川雉鸡（）的基因组草图及其进化意义。

The Draft Genome of the Endangered Sichuan Partridge () with Evolutionary Implications.

机构信息

Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.

College of Life Sciences, Leshan Normal University, Leshan 614004, China.

出版信息

Genes (Basel). 2019 Sep 5;10(9):677. doi: 10.3390/genes10090677.

DOI:10.3390/genes10090677
PMID:31491910
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6770966/
Abstract

The Sichuan partridge (, Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. About 1.94 million heterozygous single-nucleotide polymorphisms (SNPs) were detected, 17,519 protein-coding genes were predicted, and 9.29% of the genome was identified as repetitive elements. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. Comparisons between the Sichuan partridge genome and chicken genome revealed a conserved genome structure, and phylogenetic analysis demonstrated that possessed a basal phylogenetic position within Phasianidae. Gene Ontology (GO) enrichment analysis of positively selected genes (PSGs) in Sichuan partridge showed over-represented GO functions related to environmental adaptation, such as energy metabolism and behavior. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. Our data and findings provide valuable genomic resources not only for studying the evolutionary adaptation, but also for facilitating the long-term conservation and genetic diversity for this endangered species.

摘要

四川雉鹑（雉科，鸡形目）分布于中国西南部，被列为濒危等级。为了研究四川雉鹑的进化和基因组特征，我们从头组装了四川雉鹑参考基因组。最终的草稿组装约为 10.9 亿碱基对，支架 N50 为 457 万碱基对。大约检测到 194 万个杂合单核苷酸多态性（SNP），预测了 17519 个蛋白质编码基因，9.29%的基因组被鉴定为重复元件。四川雉鹑共发现 56 个嗅觉受体（OR）基因，并检测到保守基序。四川雉鹑基因组与鸡基因组的比较显示出保守的基因组结构，系统发育分析表明，在雉科中， 具有基础的系统发育地位。四川雉鹑中阳性选择基因（PSG）的基因本体论（GO）富集分析显示，与环境适应相关的 GO 功能过度表达，如能量代谢和行为。成对顺序马尔可夫抽样分析揭示了四川雉鹑最近的种群动态轨迹。我们的数据和发现不仅为研究进化适应提供了有价值的基因组资源，也为保护这一濒危物种的长期保护和遗传多样性提供了帮助。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/d5ae774c33a2/genes-10-00677-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/10a66a1a839d/genes-10-00677-g001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/ee6af3facfd3/genes-10-00677-g003a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/a904e30d7f66/genes-10-00677-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/49108a584784/genes-10-00677-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/5156b5caeee6/genes-10-00677-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/043ea607666d/genes-10-00677-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/d5ae774c33a2/genes-10-00677-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/10a66a1a839d/genes-10-00677-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/315d2a661754/genes-10-00677-g002a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/ee6af3facfd3/genes-10-00677-g003a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/a904e30d7f66/genes-10-00677-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/49108a584784/genes-10-00677-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/5156b5caeee6/genes-10-00677-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/043ea607666d/genes-10-00677-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0acd/6770966/d5ae774c33a2/genes-10-00677-g008.jpg

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