Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae

Abstract

The families Paracoccaceae and Roseobacteraceae comprise metabolically, phenotypically and genotypically diverse members, and their descriptions rely heavily on 16S rRNA gene analysis. Hundreds of genera have been reported within the two families and misclassifications have been a reoccurring problem, even when the taxonomies have been established based on genome-scale phylogenetic reconstructions. In this study, we conducted a comprehensive phylotaxonomic assessment of the families Paracoccaceae and Roseobacteraceae based on four ubiquitous gene sets, bac120 (120 genes in Bacteria), rhodo268 (268 genes in ‘ Rhodobacteraceae ’, defined in this study), rp1 (16 ribosomal protein genes in Prokaryote) and rp2 (23 ribosomal protein genes in Prokaryote), using two tree-inferring applications and two approaches (supermatrix and consensus). The results suggested that the four supermatrix trees based on bac120 and rhodo268 shared a high proportion of common nodes (>88.4 %) and the topology was reproducible among all the trees within most of the genera. The evolutionary distance (ED) analysis showed significant overlapping between the intergeneric and intrageneric comparisons, implying that the proposal of some genera seemed to be unnecessary. In addition, the bac120 gene set and the FastTree program were found to be the most cost-effective way to conduct phylogenomic analysis of the families Paracoccaceae and Roseobacteraceae . An ED threshold of 0.21–0.23 based on either bac120 or rhodo268 was proposed as one standard for later genus delimitation in these families. A comprehensive phylogenetic framework is presented in this study and the proposed genus definition will help to establish a more reasonable taxonomy in the families Paracoccaceae and Roseobacteraceae .

Ruegeria marisflavi sp. nov. and Ruegeria aquimaris sp. nov., isolated from seawater of the Yellow Sea

“…Genome-based phylogeny of the supermatrix approach from protein sequences of the bac120 gene set (120 single-copy genes prevalent in Bacteria ) was reconstructed by using EasyCGTree version 4.1 (https://github.com/zdf1987/EasyCGTree4) [3, 33]. The bac120 tree indicated that strains WL0004 T and XHP0148 T clustered together with R. marina CGMCC 1.9108 T and were close to the cluster formed by R. alba 1NDH52C T and R. pomeroyi DSS-3 T ().…”

“…Genome annotation was conducted by the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) [26]. The genomes of strains WL0004 T and XHP0148 T were both reported in our previous study [3]. The complete 16S rRNA gene sequences of strains WL0004 T and XHP0148 T were predicted from the two genomes using program barrnap (version 0.9; https://github.com/tseemann/barrnap).…”

“…The genus Ruegeria was first proposed by Uchino et al in 1998 [1]. It currently belongs to the family Roseobacteraceae [2,3] within the class Alphaproteobacteria [4]. According to the List of Prokaryotic names with Standing in Nomenclature server (https://lpsn.dsmz.de/genus/ruegeria, accessed on 28 November 2023) [5], the genus Ruegeria contains 21 validly published and correctly named child taxa.…”

“…In this study, two novel bacteria, designated as WL0004 T and XHP0148 T , were isolated from a seawater sample. The genome-based taxonomic status of the two strains were described in a recent phylotaxonomic assessment study of the family Roseobacteraceae and suggested that these two strains should be classified as representing two novel species in the genus Ruegeria [3]. This study aimed to further demonstrate the taxonomic status of strains WL0004 T and XHP0148 T through a polyphasic taxonomy approach.…”

Actomonas aquatica gen. nov., sp. nov., a marine lineage in the phylum Verrucomicrobiota with genetic potential for carbon and nitrogen fixation

“…To conduct phylogenomic analysis, genomic informations of type strains in the phylum Verrucomicrobiota were collected using Python (www.python.org) and Perl (www.perl.org) scripts (https://github.com/zdf1987/Usefull_Scripts) introduced in our previous study [37]. The assembly accession numbers were used to retrieve genomic data sets from the RefSeq and GenBak (if not available in RefSeq) databases (on 1 December 2023) through Batch Entrez (www.ncbi.nlm.nih.gov/sites/batchentrez), because genome records collected in RefSeq are all annotated using NCBI PGAP [20].…”