Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov.

Abstract

The genera Convivina , Fructobacillus , Leuconostoc , Oenococcus and Weissella , which formed the family Leuconostocaceae , have recently been merged within the family Lactobacillaceae . Using genome sequences for 47 of the 52 named species from these genera, we report here comprehensive phylogenomic and comparative analyses on protein sequences from these species using multiple approaches. In a phylogenomic tree based on concatenated sequences of 498 core proteins from these five genera, and in a 16S rRNA gene tree, members of the genera Fructobacillus , Leuconostoc and Oenococcus formed distinct strongly supported clades. In contrast, Weissella species grouped into two distinct unrelated clades designated as the ‘ Weissella main clade’ and ‘ Weissella clade 2’. The presence of these clades is also seen in a matrix of pairwise average amino acid identity based on core protein sequences. In parallel, comparative genomic studies on protein sequences from Leuconostocaceae genomes have identified 46 conserved signature indels (CSIs) in diverse proteins that are unique characteristics of the different observed species clades. Of these identified CSIs, five, five and 13 CSIs are uniquely present in members of the genera Fructobacillus , Leuconostoc and Oenococcus , respectively. We also report here six and five CSIs that are exclusively present in the species from the Weissella main clade and Weissella clade 2, respectively, providing independent evidence supporting their distinctness from each other. The remaining 12 identified CSIs are commonly shared by some or all of the species from the genera Convivina , Fructobacillus and Leuconostoc , clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera Fructobacillus , Leuconostoc and Oenococcus as well as the two Weissella species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus Weissella be limited to only the species from the Weissell a main clade, whereas the species forming Weissella clade 2 should be transferred to a new genus Periweissella gen. nov.