CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
J Adv Res. 2024 Aug;62:91-103. doi: 10.1016/j.jare.2023.09.015. Epub 2023 Sep 20.
Whole-genome duplication (WGD) is one of the most sudden and dramatic events rarely reported in invertebrates, but its occurrence can lead to physiological, morphological, and behavioral diversification. WGD has also never been reported in barnacles, which is one of the most unique groups of crustaceans with extremely speciallized morphology (calcareous shells) and habits (intertidal sessile lifestyle).
To investigate whether WGD has occurred in barnacles and examine its potential role in driving the adaptive evolution and diversification of barnacles.
Based on a newly sequenced and assembled chromosome-level barnacle genome, a novel WGD event has been identified in barnacles through a comprehensive analysis of interchromosomal synteny, the Hox gene cluster, and synonymous substitution distribution.
We provide ample evidences for WGD in the barnacle genomes. Comparative genomic analysis indicates that this WGD event predates the divergence of Thoracicalcarea, occurring more than 247 million years ago. The retained ohnologs from the WGD are primarily enriched in various pathways related to environmental information processing, shedding light on the adaptive evolution and diversification of intertidal sessile lifestyle. In addition, transcriptomic analyses show that most of these ohnologs were differentially expressed following the ebb of tide. And the cytochrome P450 ohnologs with differential expression patterns are subject to subfunctionalization and/or neofunctionalization for intertidal adaptation. Besides WGD, parallel evolution underlying intertidal adaptation has also occurred in barnacles.
This study revealed an ancient WGD event in the barnacle genomes, which is potentially associated with the origin and diversification of thoracican barnacles, and may have contributed to the adaptive evolution of their intertidal sessile lifestyle.
全基因组复制（WGD）是在无脊椎动物中很少报道的最突然和最剧烈的事件之一，但它的发生会导致生理、形态和行为的多样化。WGD 在藤壶中也从未有过报道，藤壶是甲壳类动物中最独特的群体之一，具有极其特化的形态（钙质壳）和习性（潮间带固着生活方式）。
研究藤壶是否发生了 WGD，并探讨其在驱动藤壶的适应性进化和多样化中的潜在作用。
基于新测序和组装的藤壶染色体水平基因组，通过对染色体间同线性、Hox 基因簇和同义替换分布的综合分析，在藤壶中鉴定出一个新的 WGD 事件。
我们为藤壶基因组中的 WGD 提供了充分的证据。比较基因组分析表明，这一 WGD 事件发生在 Thoracicalcarea 分化之前，距今超过 2.47 亿年。WGD 保留的同源基因主要富集在与环境信息处理相关的各种途径中，揭示了潮间带固着生活方式的适应性进化和多样化。此外，转录组分析表明，这些同源基因中的大多数在退潮后表现出差异表达。具有差异表达模式的细胞色素 P450 同源基因经历了亚功能化和/或新功能化，以适应潮间带。除了 WGD，藤壶中还发生了与潮间带适应相关的平行进化。
本研究揭示了藤壶基因组中的一个古老的 WGD 事件，该事件可能与 Thoracican 藤壶的起源和多样化有关，并可能有助于它们的潮间带固着生活方式的适应性进化。
