Zeng Xiangjian, Zhao Wenqi, Kanika Nusrat Hasan, Dong Yue, Hou Xin, Chen Xiaowen, Wang Jun, Wang Chenghui
Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shannghai, China.
National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
Genome Biol Evol. 2025 Jul 3;17(7). doi: 10.1093/gbe/evaf115.
Transposable elements (TEs) are pivotal in driving genome evolution, playing a significant role in generating genetic diversity, modulating genome size, and inducing chromosome structural changes. Despite extensive research in model species, studies on TE evolution and structure in crustaceans are notably limited. This study offers an in-depth analysis of TEs diversity and its impact on representative crustacean genomes' genome structure and function. Our results revealed substantial variation in TE content among crustacean species, with levels ranging from 16.19% in Daphnia pulex to a high of 63.36% in Procambarus clarkii. Notably, species with larger genomes, such as P. clarkii and Homarus americanus, show a higher proportion of TEs, which implies that TE proliferation may be a major factor in the expansion of genome size. Analysis of sequence divergence across multiple TE subfamilies reveals 2 distinct peaks, suggesting that most crustacean species may have experienced at least 2 separate periods of TE expansion. The second peak, characterized by divergence rates between 0% and 5%, indicates a more recent episode of TE proliferation and implies potential ongoing activity. Phylogenetic signal analysis revealed distinct evolutionary dynamics among TEs: terminal inverted repeat (TIR) transposon elements initially contracted then expanded, long terminal repeat retrotransposon (LTR) and short interspersed nuclear element (SINE) elements consistently expanded, with TIRs evolving at significantly lower rates. Chronological analysis of LTR transposons in crustaceans revealed the recent proliferation of Bel-Pao, Copia, and Ty3 subfamilies, with species-specific patterns of diversification. Furthermore, the molt stage-specific expression of TEs in Eriocheir sinensis and Penaeus vannamei throughout the molting process suggests that TEs may play a role in regulating this periodic event. Generally, these results deepen our understanding of the role of TEs in crustacean genome evolution and hint at their possible involvement in regulating biological processes within these species.
转座元件（TEs）在推动基因组进化方面起着关键作用，在产生遗传多样性、调节基因组大小以及诱导染色体结构变化中发挥着重要作用。尽管在模式物种中进行了广泛研究，但关于甲壳类动物转座元件进化和结构的研究明显有限。本研究深入分析了转座元件的多样性及其对代表性甲壳类动物基因组的基因组结构和功能的影响。我们的结果显示，甲壳类物种之间转座元件含量存在显著差异，范围从蚤状溞的16.19%到克氏原螯虾的高达63.36%。值得注意的是，基因组较大的物种，如克氏原螯虾和美洲螯龙虾，其转座元件比例更高，这意味着转座元件增殖可能是基因组大小扩张的主要因素。对多个转座元件亚家族的序列分歧分析揭示了2个不同的峰值，表明大多数甲壳类物种可能经历了至少2个独立的转座元件扩张时期。第二个峰值的特征是分歧率在0%至5%之间，表明转座元件增殖的较近期事件，并暗示可能仍在进行活动。系统发育信号分析揭示了转座元件之间不同的进化动态：末端反向重复（TIR）转座子元件最初收缩然后扩张，长末端重复逆转录转座子（LTR）和短散在核元件（SINE）元件持续扩张，而TIRs的进化速率显著较低。对甲壳类动物LTR转座子的年代分析揭示了Bel - Pao、Copia和Ty3亚家族的近期增殖，具有物种特异性的多样化模式。此外，中华绒螯蟹和凡纳滨对虾在整个蜕皮过程中转座元件的蜕皮阶段特异性表达表明，转座元件可能在调节这一周期性事件中发挥作用。总体而言，这些结果加深了我们对转座元件在甲壳类动物基因组进化中作用的理解，并暗示它们可能参与调节这些物种内的生物过程。
