Diversity of Cardinium Endosymbiont Genomes from Plant-Parasitic Nematodes

<i>Cardinium</i> endosymbionts are obligate intracellular bacteria found in a wide range of invertebrate hosts. In this study, we generated ten new <i>Cardinium</i> genomes from plant-parasitic nematodes of the genera <i>Amplimerlinius</i>, <i>Bursaphelenchus</i>, <i>Cactodera</i>, <i>Ditylenchus</i>, <i>Globodera</i>, <i>Meloidoderita</i>, and <i>Rotylenchus</i>, revealing their broad ecological and phylogenetic distribution. Using an expanded set of genes, we clarified the relationship between previously defined <i>Cardinium</i> groups B and F from nematodes, showing that they are closely related and likely share a single evolutionary origin within nematode-associated <i>Cardinium</i>. Among the newly assembled <i>Cardinium</i> genomes obtained in this study, two genomes originating from strains associated with wood-inhabiting <i>Bursaphelenchus</i> species exhibited remarkable genome reduction, with estimated sizes of approximately 695 kb. Functional annotation of <i>Cardinium</i> genomes indicated an absence of or a reduction in several central metabolic pathways, including the biotin biosynthetic pathway. A complete biotin pathway was found only in <i>D. weischeri</i>, and this pathway is only partially encoded in <i>Cactodera</i> sp. The <i>polA</i> gene, which encodes DNA polymerase I, showed partial loss in several <i>Cardinium</i> strains. Phylogenetic and comparative genomic analyses provided strong evidence that several carbohydrate, glycerophospholipid, and biotin metabolism genes in these endosymbionts have been acquired through horizontal gene transfer. Future research that integrates high-quality genome assemblies with functional analyses of host-symbiont interactions will be essential to elucidate how metabolic dependency, genome reduction, and horizontal gene transfer collectively shape the evolution and ecological diversification of <i>Cardinium</i> across nematode hosts.