Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis

Authors: MACHADO, RICARDO - University Of Neuchatel; MULLER, ARTHUR - University Of Neuchatel; HILTMANN, ALEXANDRE - University Of Neuchatel; BHAT, AASHAQ HUSSAIN - University Of Neuchatel; PUŽA, VLADIMÍR - Czech Academy Of Sciences; MALAN, ANTOINETTE - Stellenbosch University; CASTANEDA-ALVAREZ, CARLOS - Universidad De Chile; SAN-BLAS, ERNESTO - O'Higgins University; DUNCAN, LARRY - University Of Florida; Shapiro Ilan, David; KARIMI, JAVAD - Ferdowsi University Of Mashhad; LALRAMLIANA - Pachhunga University College; BAIMEY, HUGUES - University Of Parakou

Submitted to: Molecular Phylogenetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/4/2025
Publication Date: 1/6/2025
Citation: Machado, R.A., Muller, A., Hiltmann, A., Bhat, A., Puža, V., Malan, A.P., Castaneda-Alvarez, C., San-Blas, E., Duncan, L.W., Shapiro Ilan, D.I., Karimi, J., Lalramliana, Baimey, H. 2025. Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis. Molecular Phylogenetics and Evolution. 204. https://doi.org/10.1016/j.ympev.2025.108284.
DOI: https://doi.org/10.1016/j.ympev.2025.108284

Interpretive Summary: Entomopathogenic nematodes, also known as beneficial nematodes, are small round worms that are used as natural bio-pesticides. These nematodes only attack and reproduce in insects and do not harm humans or the environment. There are two genera (kinds) of beneficial nematodes used in biological pest control: the heterorhabditids and steinernematids. There are about 20 species of heterorhabditids and roughly 100 species of steinernematids. The phylogenetic (evolutionary) relationships among these nematode species is not well understood. This study implemented a broad whole genome study of the Heterorhabditis genus to elucidate evolutionary relationships. All heterorhabditid species were included in the study. Results shed new light on the relationships among entomopathogenic nematodes in the heterorhabditid group. The improved phylogenetic understanding will result in improved application in biological pest control.

Technical Abstract: Recent multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species within the most derived clades of the nematode genus Heterorhabditis. In addition, conflicting tree topologies are often obtained using different gene markers. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes. Robust, well-resolved, and highly congruent phylogenetic relationships were reconstructed using both whole nuclear and mitochondrial genomes. Similarly, whole ribosomal operon sequences proved valuable for phylogenomic reconstructions, though they have limited value to discriminate closely related species, especially within the most derived clades. Among all the evaluated genes, two mitochondrial genes, the cytochrome c oxidase subunit I (cox-1) and the NADH dehydrogenase subunit 4 (nad-4), and two housekeeping genes, the fanconi-associated nuclease 1 (fan-1) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (ppfr-1), provided the most robust phylogenetic reconstructions. Similarly, whole ribosomal operon sequences were generally useful to reconstruct phylogenetic relationships, but the resolution of closely related species, particularly of the most derived clade, was low. According to our findings, whole nuclear and/or mitochondrial genomes are strongly recommended for reconstructing phylogenetic relationships of the genus Heterorhabditis. However, when nuclear and/or mitochondrial genomes are not available, a combination of nuclear and mitochondrial genes can be used instead. However, under these circumstances, sequences of multiple conspecific isolates in a genus-wide phylogenetic context should be analysed to avoid artefactual species over-splitting driven by the high intraspecific sequence divergency of mitochondrial genes and to avoid artefactual species lumping driven by the low interspecific sequence divergency of some nuclear genes. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of an important group of biological control agents and advances our efforts to develop more tools that are compatible with sustainable and eco-friendly agricultural practices.