Tang Jie, Yao Dan, Zhou Huizhen, Du Lianming, Daroch Maurycy
School of Food and Bioengineering, Chengdu University, Chengdu 610106, China.
School of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Road, Shenzhen 518055, China.
Plants (Basel). 2022 Apr 13;11(8):1060. doi: 10.3390/plants11081060.
Morphologically similar to Synechococcus, a large number of Parasynechococcus strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 Synechococcus-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as Parasynechococcus-like strains and showing considerably intragenus genetic divergence among the subclades identified. Further, bioinformatics analysis disclosed diversified patterns of distribution, abundance, density, and diversity of microsatellites (SSRs) and compound microsatellites (CSSRs) in genomes of these Parasynechococcus-like strains. Variations of SSRs and CSSRs were observed amongst phylotypes and subclades. Both SSRs and CSSRs were in particular unequally distributed among genomes. Dinucleotide SSRs were the most widespread, while the genomes showed two patterns in the second most abundant repeat type (mononucleotide or trinucleotide SSRs). Both SSRs and CSSRs were predominantly observed in coding regions. These two types of microsatellites showed positive correlation with genome size (p < 0.01) but negative correlation with GC content (p < 0.05). Additionally, the motif (A)n, (AG)n and (AGC)n was a major one in the corresponding category. Meanwhile, distinctive motifs of CSSRs were found in 39 genomes. This study characterizes SSRs and CSSRs in genomes of Parasynechococcus-like strains and will be useful as a prerequisite for future studies regarding their distribution, function, and evolution. Moreover, the identified SSRs may facilitate fast acclimation of Parasynechococcus-like strains to fluctuating environments and contribute to the extensive distribution of Parasynechococcus species in global marine environments.
许多类聚球藻菌株在形态上与聚球藻相似，因此被错误分类，导致对其遗传多样性的极度低估。在本研究中，使用16S rRNA系统发育和基因组方法相结合的方式对80株类聚球藻菌株进行了重新评估，鉴定出54株类副聚球藻菌株，并显示出在所鉴定的亚分支之间存在相当大的属内遗传差异。此外，生物信息学分析揭示了这些类副聚球藻菌株基因组中微卫星（SSRs）和复合微卫星（CSSRs）的分布、丰度、密度和多样性的多样化模式。在不同的系统发育型和亚分支中观察到了SSRs和CSSRs的变异。SSRs和CSSRs在基因组中尤其分布不均。二核苷酸SSRs最为普遍，而基因组在第二丰富的重复类型（单核苷酸或三核苷酸SSRs）上呈现出两种模式。SSRs和CSSRs主要出现在编码区域。这两种类型的微卫星与基因组大小呈正相关（p < 0.01），但与GC含量呈负相关（p < 0.05）。此外，基序（A）n、（AG）n和（AGC）n是相应类别中的主要基序。同时，在39个基因组中发现了CSSRs的独特基序。本研究对类副聚球藻菌株基因组中的SSRs和CSSRs进行了表征，将作为未来关于它们的分布、功能和进化研究的前提条件。此外，所鉴定的SSRs可能有助于类副聚球藻菌株快速适应波动的环境，并有助于副聚球藻物种在全球海洋环境中的广泛分布。
