Coutinho Felipe, Tschoeke Diogo Antonio, Thompson Fabiano, Thompson Cristiane
Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ) , Rio de Janeiro , Brazil.
PeerJ. 2016 Jan 14;4:e1522. doi: 10.7717/peerj.1522. eCollection 2016.
Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages.
聚球藻是全球初级生产力的最重要贡献者之一。此前已对该分类单元的多个菌株的基因组进行了测序，以了解这些高度多样化的微生物的生理学和生态学。在此，我们展示了一项聚球藻基因组的比较研究。为此，我们开发了GenTaxo，这是一个用Perl编写的程序，用于基于平均核苷酸同一性、平均氨基酸同一性和二核苷酸特征进行基因组分类，结果表明所分析的菌株在基因组内容上截然不同。系统发育基因组重建表明聚球藻分为两个进化枝（即聚球藻和新属副聚球藻），证实了这实际上是一个多系群的证据。通过将蛋白质编码基因聚类到同源组中，我们能够追踪海洋和淡水聚球藻的泛基因组和核心基因组，并确定区分这些谱系的基因型特征。
