Han Shiyun, Zhang Sijia, Ge Wen, Yang Jianke, Peng Hui, Gao Jinming, Zhang Mengsa, Xiao Yingying, Du Dongsheng, Kan Xianzhao
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences, Anhui Normal University Wuhu China.
Anhui Rural Revitalization Collaborative Technology Service Center Wuhu Institute of Technology Wuhu Anhui China.
Ecol Evol. 2025 Jul 7;15(7):e71739. doi: 10.1002/ece3.71739. eCollection 2025 Jul.
UCYN-A is a phenomenal diazotrophic cyanobacterium with significant ecological importance. UCYN-A1 and UCYN-A2 are the two most abundant ecotypes. Recently, the striking discovery of nitroplast, a novel N-fixing organelle in cultured /UCYN-A2 endosymbiont, indicated the possibility that UCYN-A2 has evolved beyond endosymbiosis to an early phase of organellogenesis. This study addresses the following critical question: What evolutionary heterogeneity has emerged between UCYN-A1 and UCYN-A2? To investigate this issue, we comprehensively compared a total of seven genomes from UCYN-A2 and UCYN-A1. Under similar genome organizations, GC content, and gene composition, we still detected abundant genetic differences, including group-unique orthogroups, ANI below 85%, and 577 UCYN-A2-unique INDELs in single-copy orthologous genes (SCOGs). Moreover, we also focused on the orthologous genes of 40 metabolic-pathway genes in nitroplast. In addition to high-informative SNPs and INDELs possessing distinct interlineage differences, we traced abundant codon usage "signatures" that serve as lineage-unique molecular markers. Most notably, we successfully established a strain-level identification map for UCYN-A strains using codon aversion motifs, which represents the first case study of this approach in bacteria. In summary, all the comparative results reported here collectively indicate that UCYN-A1 and UCYN-A2 have evolved remarkable genomic heterogeneities. Furthermore, the findings of this work will definitely promote our current understanding of codon aversion and the evolution of UCYN-A.
UCYN - A是一种具有重要生态意义的非凡固氮蓝细菌。UCYN - A1和UCYN - A2是两种最丰富的生态型。最近，在培养的UCYN - A2内共生体中惊人地发现了一种新型固氮细胞器——硝化质体，这表明UCYN - A2可能已经从内共生进化到细胞器形成的早期阶段。本研究解决了以下关键问题：UCYN - A1和UCYN - A2之间出现了哪些进化异质性？为了研究这个问题，我们全面比较了来自UCYN - A2和UCYN - A1的总共七个基因组。在相似的基因组组织、GC含量和基因组成情况下，我们仍然检测到大量的遗传差异，包括群体独特的直系同源组、ANI低于85%，以及单拷贝直系同源基因（SCOGs）中577个UCYN - A2独特的插入缺失。此外，我们还关注了硝化质体中40个代谢途径基因的直系同源基因。除了具有明显谱系间差异的高信息性单核苷酸多态性（SNPs）和插入缺失外，我们还追踪到大量作为谱系独特分子标记的密码子使用“特征”。最值得注意的是，我们成功地利用密码子偏好基序建立了UCYN - A菌株的菌株水平鉴定图谱，这代表了该方法在细菌中的首个案例研究。总之，这里报道的所有比较结果共同表明UCYN - A1和UCYN - A2已经进化出显著的基因组异质性。此外，这项工作的发现必将促进我们目前对密码子偏好和UCYN - A进化的理解。
