Large-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade

Abstract

Rickettsia are intracellular bacteria originally described as arthropod borne pathogens that are emerging as a diverse group of often biologically important, non-pathogenic symbionts of invertebrates and microeukaryotes. However, sparse genomic resources for symbiotic strains and for the sister genus (Candidatus Megaira) inhibit our understanding of Rickettsia evolution and biology. Here, we present the first closed genomes of Ca. Megaira from an alga (Mesostigma viride), and Torix Rickettsia from midge (Culicoides impunctatus) and bed bug (Cimex lectularius) hosts. Additionally, we sequenced and constructed draft genomes for Ca. Megaira from another alga (Carteria cerasiformis), Transitional group Rickettsia from tsetse fly (Glossina morsitans submorsitans), and Torix Rickettsia from a spider mite (Bryobia graminum). We further extract 22 draft genomes from arthropod genome sequencing projects, including 1 Adalia, 4 Transitional, 1 Spotted Fever, 7 Torix, 7 Belli and the first Rhyzobius and Meloidae Rickettsia group genomes. We used new and existing Rickettsia genomes to estimate the phylogeny and metabolic potential across groups and reveal transitions in genomic properties. These data reveal Torix as unique amongst currently described Rickettsia, with highly distinct and diverse accessory genomes. We confirm the presence of a third subclade of Torix, previously only known from gene marker sequences. Further, Torix share an intact pentose phosphate pathway with Ca. Megaira, not observed in other Rickettsia. Considering the distinctness and diversity of Torix, we propose that the group be named Candidatus Tisiphia. The wide host range of Ca. Tisiphia symbionts necessitates onward research to understand the biological and physiological bases of Ca. Tisiphia-host interactions.

Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common

“…Previous studies have delimited multiple cif clades denominated as Type I to IV and a proposed Type V comprising homologues carrying additional domains on the C-terminal part of the cifB protein. cif homologues have also been reported in other Rickettsiales , some of them carried by plasmids (Gillespie et al 2018; Davison et al 2021; Martinez et al 2021; Takano et al 2021). We investigated the evolutionary origin of the cif genes located on Wolbachia -associated plasmid sequences and found that they group with Type V homologues (Figure 6), which is consistent with the length and predicted domains of their cifB protein (Figure 5).…”

Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common

“…Previous studies have delimited multiple cif clades denominated as Type I to IV and a proposed Type V comprising homologues carrying additional domains on the C-terminal part of the cifB protein. cif homologues have also been reported in other Rickettsiales , some of them carried by plasmids [ 33 , 34 , 48 , 49 ]. We investigated the evolutionary origin of the cif genes located on Wolbachia -associated plasmid sequences and found that they group with Type V homologues ( Fig 6 ), which is consistent with the length and predicted domains of their cifB protein ( Fig 5 ).…”