School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China.
BMC Genomics. 2024 Apr 10;25(1):356. doi: 10.1186/s12864-024-10280-8.
Centromeres play a crucial and conserved role in cell division, although their composition and evolutionary history in green algae, the evolutionary ancestors of land plants, remains largely unknown.
We constructed near telomere-to-telomere (T2T) assemblies for two Trebouxiophyceae species, Chlorella sorokiniana NS4-2 and Chlorella pyrenoidosa DBH, with chromosome numbers of 12 and 13, and genome sizes of 58.11 Mb and 53.41 Mb, respectively. We identified and validated their centromere sequences using CENH3 ChIP-seq and found that, similar to humans and higher plants, the centromeric CENH3 signals of green algae display a pattern of hypomethylation. Interestingly, the centromeres of both species largely comprised transposable elements, although they differed significantly in their composition. Species within the Chlorella genus display a more diverse centromere composition, with major constituents including members of the LTR/Copia, LINE/L1, and LINE/RTEX families. This is in contrast to green algae including Chlamydomonas reinhardtii, Coccomyxa subellipsoidea, and Chromochloris zofingiensis, in which centromere composition instead has a pronounced single-element composition. Moreover, we observed significant differences in the composition and structure of centromeres among chromosomes with strong collinearity within the Chlorella genus, suggesting that centromeric sequence evolves more rapidly than sequence in non-centromeric regions.
This study not only provides high-quality genome data for comparative genomics of green algae but gives insight into the composition and evolutionary history of centromeres in early plants, laying an important foundation for further research on their evolution.
着丝粒在细胞分裂中起着至关重要且保守的作用，尽管其在绿藻（陆地植物的进化祖先）中的组成和进化历史在很大程度上仍是未知的。
我们构建了两个绿藻Treubouxiophyceae 物种，即 Chlorella sorokiniana NS4-2 和 Chlorella pyrenoidosa DBH 的近端粒到端粒（T2T）组装体，它们的染色体数分别为 12 和 13，基因组大小分别为 58.11 Mb 和 53.41 Mb。我们使用 CENH3 ChIP-seq 鉴定和验证了它们的着丝粒序列，发现与人类和高等植物一样，绿藻的着丝粒 CENH3 信号显示出低甲基化的模式。有趣的是，尽管两种物种的着丝粒组成有很大差异，但它们主要由转座元件组成。绿藻属内的物种显示出更多样化的着丝粒组成，主要成分包括 LTR/Copia、LINE/L1 和 LINE/RTEX 家族的成员。这与包括 Chlamydomonas reinhardtii、Coccomyxa subellipsoidea 和 Chromochloris zofingiensis 在内的绿藻形成鲜明对比，在这些绿藻中，着丝粒组成则具有明显的单一元件组成。此外，我们观察到在 Chlorella 属内具有强共线性的染色体之间，着丝粒的组成和结构存在显著差异，这表明着丝粒序列的进化速度比非着丝粒区域的序列更快。
本研究不仅为绿藻的比较基因组学提供了高质量的基因组数据，还深入了解了早期植物着丝粒的组成和进化历史，为进一步研究它们的进化奠定了重要基础。
