Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes

Abstract

Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.

Pangenomic analysis of Wolbachia provides insight into the evolution of host adaptation and cytoplasmic incompatibility factor genes

“…So, we speculate that extensive gene fractionation occurred during the evolutionary history of arthropod-infecting Wolbachia strain genomes, which promoted the retention of genes that are essential for survival and host adaptation. In contrast, nematode-infecting Wolbachia strains have established long-lasting mutualistic relationships with their specific hosts (Darby et al, 2012;Godel et al, 2012), leading to a stable state of the genome that may lead to the loss of large numbers of genes (Gerth et al, 2014) or to form species-specific novel genes (Weyandt et al, 2022), as recently reported in another Wolbachia study.…”

Wolbachia springs eternal: symbiosis in Collembola is associated with host ecology

“…The contigs obtained from the sequencing of the six Wolbachia -positive samples were highly similar between themselves. Thus, to increase the coverage of the assembly, the authors decided to pool the 192 contigs and named the final assembly w Tex [ 23 ]. Regarding the hosts of w Tex, two genera might be associated this pool: Helicotylenchus spp.…”

“…Usually, an outgroup should be selected from outside the studied phylum, but the other Rickettsiales are too phylogenetically distant. Inferring Wolbachia phylogenies with Anaplasma and Ehrlichia might generate long-branch attraction artefacts and multiple polytomies [3,5,8,10,23,32,33,35,36,48,[58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74]. This is why more than half of the produced topologies of Wolbachia do not use an outgroup (electronic supplementary material, table S4).…”

“…Wolbachia is essential for enabling embryonic development and supporting adult survival, consistent with their location in the female germline and somatic hypodermal cords. However, most of the time the nature of the association is often undefined and in particular it is not established for plant nematodes [23] and poorly understood for springtails, although a link to parthenogentic reproduction has been suggested [24][25][26][27].…”

“…One issue is that phylogenetic analysis methods are prone to long-branch attraction artefacts and therefore the origin of infection remains unresolved. The most recent comprehensive phylogeny suggests that L (in plant nematodes), M (aphids) and E (Collembola and mites) are sister clades to all the other Wolbachia supergroups [23]. Regarding supergroup E, 29 species of Collembola have been tested for Wolbachia up to now and 13 are infected [35][36][37][38][39].…”