Phylogenomic Analysis Substantiates the gyrB Gene as a Powerful Molecular Marker to Efficiently Differentiate the Most Closely Related Genera Myxococcus, Corallococcus, and Pyxidicoccus

作者：Yang Liu, Tao Pei, Shuoxing Yi, Juan Du, Xianjiao Zhang, Xiaoqin Deng, Qing Yao, Ming‐Rong Deng, Honghui Zhu · 发表于：Frontiers in Microbiology · 年份：2021 · DOI：10.3389/fmicb.2021.763359 · 被引用次数：26 · 研究领域：Genomics and Phylogenetic Studies、Protist diversity and phylogeny、Marine Sponges and Natural Products

Rapid and accurate strain identification of the most closely related genera Myxococcus , Corallococcus , and Pyxidicoccus can enhance the efficiency of the mining of novel secondary metabolites through dereplication. However, the commonly used 16S rRNA gene sequencing cannot accurately differentiate members of the three genera above, and the whole-genome sequencing is unable to rapidly and inexpensively provide species assignation toward a large number of isolates. To overcome the limitations, the gyrB gene was investigated as a candidate genetic marker for exploring the phylogenetic relationships of bacteria within the three genera and for developing the gyrB -based typing method. Here, the bacterial phylogeny and species affiliations of the three genera were determined based on the phylogenomic reconstruction and the analysis of digital DNA–DNA hybridization values among 90 genomes, further confirming nine novel taxa and assigning over one-third of genomes to defined species. The phylogenetic relationships of these strains based on the gyrB gene sequences were congruent with those based on their genome sequences, allowing the use of the gyrB gene as a molecular marker. The gyrB gene-specific primers for the PCR-amplification and sequencing of bacteria within the three genera were designed and validated for 31 isolates from our group collection. The gyrB -based taxonomic tool proved to be able to differentiate closely related isolates at the species level. Based on the newly...