Phylogenomics of Haloarchaea: The Controversy of the Genera .

The haloarchaeal genera and were described almost simultaneously by two different research groups and some strains studied separately were described as different species of these genera. Furthermore, the description of additional species were assigned to either or , mainly on the basis of the phylogenetic comparative analysis of single genes (16S rRNA gene and more recently gene), but these species were not adequately separated or assigned to the corresponding genus. Some studies suggested that the species of these two genera should be unified into a single genus, while other studies indicated that the genera should remain but some of the species should be reassigned. In this study, we have sequenced or collected the genomes of the type strains of species of and and we have carried out a comparative genomic analysis in order to clarify the controversy related to these two genera. The phylogenomic analysis based on the comparison of 525 translated single-copy orthologous genes and the Overall Genome Relatedness Indexes (i.e., AAI, POCP, ANI, and dDDH) clearly indicate that the species , , , , , , and should be transferred to the genus , as , , , , , , and , respectively. On the contrary, the species , , and will remain as the only representative species of the genus . Besides, the species should be reclassified as a member of the genus , as . At the species level, and should be considered as a later heterotypic synonyms of the species () and () , respectively. Synteny analysis and phenotypic features also supported those proposals.