Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.
Universidad Autónoma de Baja California. Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico.
Sci Rep. 2017 Jun 15;7(1):3564. doi: 10.1038/s41598-017-02845-3.
Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.
细菌是生命中遗传多样性最丰富的王国。虽然在描述这种多样性方面已经取得了很大的进展，但仍然难以确定界定具有类似物种特性的细菌群体的系统发育和生态特征。与物种划分相关的一个主要挑战是，并非所有共享基因都具有相同的进化历史，因此基因座的选择会对系统发育重建产生重大影响。在这里，我们分析了 119 株海洋放线菌属 Salinispora 的基因组，该属目前由三个命名物种组成，它们共享 99%的 16S rRNA 基因序列同一性。虽然 63%的核心基因组显示出重组的证据，但这对种水平的系统基因组分辨率没有影响。然而，重组确实模糊了种内关系和生物地理分辨率。全基因组平均核苷酸同一性为 Salinispora 的多样性提供了一个新的视角，揭示了多达七个新的物种。直系同源群分布模式揭示了划定候选分类群的遗传基础，并深入了解与细菌物种相关的遗传凝聚水平。
