Chromosome-level assembly of the Hypophthalmichthys molitrix (Cypriniformes: Cyprinidae) genome provides insights into its ecological adaptation.
Chromosome-level assembly of the Hypophthalmichthys molitrix (Cypriniformes: Cyprinidae) genome provides insights into its ecological adaptation.
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鲢鱼（鲤形目：鲤科）基因组的染色体水平组装为其生态适应提供了见解。
DOI：
10.1016/j.ygeno.2021.06.024
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发表时间：
2021-06
期刊：
影响因子：
4.4
通讯作者：
Zhou Luojing
中科院分区：
文献类型：
--
作者：
Zhou Yi;Qin Weiling;Zhong Huan;Zhang Hong;Zhou Luojing
鲢鱼（Hypophthalmichthys molitrix，银鱼）是一种食植物性鱼类，具有重要的经济和生态价值。作为一种著名的入侵物种，许多与该物种的生态适应相关的因素在很大程度上是未知的。在这里，我们提出了基于PacBio Sequel II平台和Hi-C支架技术的物种染色体水平组装。基于高质量的基因组序列和之前的基因组测序计划，H基因组中存在许多可能受到正选择的基因。molitrix和H.莫来石贵族身份被确认。其中一些基因可能部分解释了H. molitrix的生存损害由于有毒藻类。种群历史估计表明，该物种的有效种群大小（EPS）可能随着青藏高原的隆升而沿着增加，在第四纪冰期开始时开始下降，并在新仙女木期进一步下降。此外，H.贵族基于全基因组测序数据证实了molitrixin North America，并且渗入区域的比例估计为约5.8%。在高质量装配的基础上，分析了H。molitrix适应其特有的和入侵的位置进行了剖析。
Hypophthalmichthys molitrix(silver carp) is phytoplanktivorous and is an economically and ecologically important fish species. As a well-known invasive species, a number of factors associated with the ecological adaptations of this species are largely unknown. Here, we present a chromosomal-level assembly of the species based on the PacBio Sequel II platform and Hi-C scaffolding technology. Based on the high-quality genome sequences and previous genome sequencing projects, a number of genes that were probably subject to positive selection reside in the genome ofH. molitrix, and the last common ancestors ofH. molitrixandH. nobiliswere identified. Some of these genes may partially explain the mechanisms ofH. molitrixfor surviving damage due to toxic algae. Demographic history estimation suggests that the effective population size (EPS) of the species may have constantly increased along with the uplift of the Qinghai-Tibet Plateau, started to decline when quaternary glaciation started, and further declined during the Younger Dryas Period. Moreover, the introgression fromH. nobilistoH. molitrixin North America was corroborated based on the whole-genome sequencing data, and the proportion of introgressed regions was estimated to be approximately 5.8%. Based on the high-quality assembly, the possible mechanisms by whichH. molitrixadapts to its endemic and invaded locations were profiled.