A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation.

IF 11.8 2区 生物学 Q1 MULTIDISCIPLINARY SCIENCES
Yujin Pu, Yang Zhou, Jun Liu, Haibin Zhang
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引用次数: 0

Abstract

Background: Chiridota heheva is a cosmopolitan holothurian well adapted to diverse deep-sea ecosystems, especially chemosynthetic environments. Besides high hydrostatic pressure and limited light, high concentrations of metal ions also represent harsh conditions in hydrothermal environments. Few holothurian species can live in such extreme conditions. Therefore, it is valuable to elucidate the adaptive genetic mechanisms of C. heheva in hydrothermal environments.

Findings: Herein, we report a high-quality reference genome assembly of C. heheva from the Kairei vent, which is the first chromosome-level genome of Apodida. The chromosome-level genome size was 1.43 Gb, with a scaffold N50 of 53.24 Mb and BUSCO completeness score of 94.5%. Contig sequences were clustered, ordered, and assembled into 19 natural chromosomes. Comparative genome analysis found that the expanded gene families and positively selected genes of C. heheva were involved in the DNA damage repair process. The expanded gene families and the unique genes contributed to maintaining iron homeostasis in an iron-enriched environment. The positively selected gene RFC2 with 10 positively selected sites played an essential role in DNA repair under extreme environments.

Conclusions: This first chromosome-level genome assembly of C. heheva reveals the hydrothermal adaptation of holothurians. As the first chromosome-level genome of order Apodida, this genome will provide the resource for investigating the evolution of class Holothuroidea.

海参 Chiridota heheva 的高质量染色体基因组组装及其热液适应性。
背景:Chiridota heheva是一种世界性的百足类动物,能很好地适应各种深海生态系统,尤其是化合环境。除了高静水压和有限的光照外,高浓度的金属离子也代表了热液环境中的苛刻条件。能在如此极端条件下生活的百足虫物种少之又少。因此,阐明C. heheva在热液环境中的适应性遗传机制具有重要价值:在此,我们报告了来自凯雷喷口的C. heheva的高质量参考基因组组装,这是Apodida的第一个染色体组水平的基因组。染色体级基因组大小为1.43 Gb,支架N50为53.24 Mb,BUSCO完整性得分为94.5%。对等位基因序列进行了聚类、排序并组装成 19 条天然染色体。比较基因组分析发现,C. heheva的扩展基因家族和正选基因参与了DNA损伤修复过程。扩展基因家族和独特基因有助于在富铁环境中维持铁平衡。具有10个正选位点的正选基因RFC2在极端环境下的DNA修复中发挥了重要作用:C.heheva的首个染色体级基因组组装揭示了热液适应性。作为Apodida目第一个染色体水平的基因组,该基因组将为研究Holothuroidea类的进化提供资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
GigaScience
GigaScience MULTIDISCIPLINARY SCIENCES-
CiteScore
15.50
自引率
1.10%
发文量
119
审稿时长
1 weeks
期刊介绍: GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.
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