Chromosome-level genome assembly of the Chinese three-keeled pond turtle (Mauremys reevesii) provides insights into freshwater adaptation
Chromosome-level genome assembly of the Chinese three-keeled pond turtle (Mauremys reevesii) provides insights into freshwater adaptation
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DOI：
10.1111/1755-0998.13563
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发表时间：
2021-12-09
影响因子：
7.7
通讯作者：
Nie, Liuwang
中科院分区：
文献类型：
--
作者：
Liu, Jianjun;Liu, Siqi;Nie, Liuwang
毛龟是一种濒临灭绝的淡水龟，在中国文化中象征着长寿。尽管它很重要，但对该物种的遗传研究仍然有限，迄今为止没有基因组序列的报道。在这里，我们报告了使用纳米孔和Hi-C测序技术组合获得的高质量，染色体水平的m.r evesii基因组序列。2.37 Gb的M. reevesii基因组是由226.80 Gb的纳米孔测序数据组装而成的。M. reevesii基因组N50为34.73 Mb，是已发表的龟类基因组中最高的。总共有18,238个基因被功能注释。这些contigs被聚集并排序到27条假染色体上，覆盖了Hi-C数据组装的基因组的96.55%。为探讨淡水龟和地龟基因组的进化规律，对淡水龟和地龟进行了基因组的同源性分析。一般来说，每条染色体都对应一条染色体，但根据组装的基因组，两种物种之间存在一些染色体间重排。这些染色体间重排通过长读纳米孔数据映射到组装进一步证实。重建的种群历史表明，淡水龟、海龟和陆龟的有效种群规模存在差异。我们还发现M. reevesii中与先天免疫系统相关的基因的扩增可能提供对淡水病原体的防御。高质量的基因组序列为进一步研究海龟的遗传学和基因组进化提供了宝贵的遗传资源。
Mauremys reevesii is an endangered freshwater turtle that symbolizes longevity in Chinese culture. Despite its importance, genetic studies of this species remain limited, with no genomic sequence reported to date. Here, we report a high-quality, chromosome-level genomic sequence of M. reevesii obtained using a combination of Nanopore and Hi-C sequencing technologies. The 2.37 Gb M. reevesii genome was assembled from a total of similar to 226.80 Gb of Nanopore sequencing data. The M. reevesii genome contig N50 is 34.73 Mb, the highest value in published turtle genomes. In total, 18,238 genes were functionally annotated. The contigs were clustered and ordered onto 27 pseudochromosomes covering similar to 96.55% of the genome assembled with Hi-C data. To explore genome evolution, synteny analysis was performed between M. reevesii (freshwater turtle) and Gopherus evgoodei (terrestrial turtle) genomes. In general, each chromosome of M. reevesii corresponded to one chromosome of Gopherus evgoodei, but some interchromosomal rearrangements occurred between the two species based on the assembled genomes. These interchromosomal rearrangements were further confirmed by mapping of the long-read nanopore data to the assembly. The reconstructed demographic history showed varied effective population size among freshwater, marine and terrestrial turtles. We also discovered expansion of genes related to the innate immune system in M. reevesii that may provide defence against freshwater pathogens. The high-quality genomic sequence provides a valuable genetic resource for further studies of genetics and genome evolution in turtles.