Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach

Abstract

 Consent to participate (Not applicable) Consent for publication (Not applicable)  Availability of data and materialThe whole genome sequence data obtained in this study was deposited at DDBJ/EMBL/GenBank under BioProject Accession: PRJDB11924.  Code availability (Not applicable) Author Contributions Chunqi Jiang conceived, designed and performed the experiments, analyzed the data, visualized the data, drafted and reviewed the manuscript. Mami Tanaka and Sayo Nishikawa performed the experiments, reviewed the manuscript.

Taxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.

“…spongicola compared to the other Amphritea species ( Fig 1 ). This observation triggered further assessments of PT3 T using molecular phylogenetic network and genomic approaches, which are frequently used in Vibrionaceae taxonomy [ 11 , 30 ].…”

“…Even after the description of A. pacifica [6], two distinct lineages based on 16S gene sequences in the genus Amphritea have never been discussed yet, but the finding of PT3 T showed phylogenetically more cohesion of the strain to A. ceti and A. spongicola compared to the other Amphritea species (Fig 1). This observation triggered further assessments of PT3 T using molecular phylogenetic network and genomic approaches, which are frequently used in Vibrionaceae taxonomy [11,30].…”

The pan‐genome of Splendidus clade species in the familyVibrionaceae: Insights into evolution, adaptation, and pathogenicity

“…The molecular phylogenetic analysis was performed using multilocus sequence analysis (MLSA) according to Sawabe et al (2013). Split decomposition analysis using the concatenated sequence was performed using Split-sTree 4.14.8 with a neighbour net drawing and a Jukes-Cantor correction (Jiang et al, 2022). The sequences were aligned with MUSCLE (Edgar, 2004), and the phylogenetic tree was constructed using MEGA-X v10.1.8 (Kumar et al, 2018) with 1000 bootstraps using Maximum Likelihood (ML) method and General Time Reversible model (Nei & Kumar, 2000).…”

“…(B) The Maximum Likelihood (ML) rooted tree for the Splendidus clade, constructed by MEGA-X v10.1.8 with 1,000 bootstraps, E. coli K12 MG1655 and V. cholerae ATCC 14035 T as outgroups. Reference sequence data was obtained from Jiang et al (2022) and effective tool for delineating new species and clades in Vibrionaceae, because of the higher gene resolution (Jiang et al, 2022). According to the 8-HKGs MLSA of 195 Vibrionaceae, the Splendidus clade showed two main evolutionary directions; V. fortis and V. pelagius in one direction with 'V.…”

Editorial: Molecular Adaptations of Vibrionaceae to Changing Environments, Volume II

“…The family Vibrionaceae contains a broad spectrum of bacterial genera that are ubiquitous in aquatic ecosystems worldwide (Jiang et al, 2022). Due to their presence in different environments (i.e., water, sediments, aquatic organisms), the bacteria need to adapt to the prevailing conditions found in specific habitats (Sakib et al, 2018;Ceccarelli et al, 2019).…”