Phylogenomic and comparative genomic analyses of species: identification of molecular signatures specific for the genera , and and proposal for a novel genus gen. nov. Open Access

Abstract

The genera , , , and , which formed the family , have recently been merged within the family . 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 , and formed distinct strongly supported clades. In contrast, species grouped into two distinct unrelated clades designated as the ‘ main clade’ and ‘ 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 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 , and , respectively. We also report here six and five CSIs that are exclusively present in the species from the main clade and 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 , and , clarifying their interrelationships. The identified CSIs provide novel and reliable means for the identification/circumscription of members of the genera , and as well as the two species clades in molecular terms. Based on the strong phylogenetic and molecular evidence presented here, we propose that the genus be limited to only the species from the a main clade, whereas the species forming clade 2 should be transferred to a new genus gen. nov.

Funding
This study was supported by the:
  • Natural Sciences and Engineering Research Council of Canada (Award RGPIN-2019-06397)
    • Principle Award Recipient: RadheyS. Gupta
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2022-03-23
2024-03-28
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