TY - JOUR A1 - Hellemans, S. A1 - Rocha, M. M. A1 - Wang, M. A1 - Romero Arias, J. A1 - Aanen, D. K. A1 - Bagnères, A.-G. A1 - Buček, A. A1 - Carrijo, T. F. A1 - Chouvenc, T. A1 - Cuezzo, C. A1 - Constantini, J. P. A1 - Constantino, R. A1 - Dedeine, F. A1 - Deligne, J. A1 - Eggleton, P. A1 - Evans, T. A. A1 - Hanus, R. A1 - Harrison, Mark C. A1 - Harry, M. A1 - Josens, G. A1 - Jouault, C. A1 - Kalleshwaraswamy, C. M. A1 - Kaymak, E. A1 - Korb, J. A1 - Lee, C.-Y. A1 - Legendre, F. A1 - Li, H.-F. A1 - Lo, N. A1 - Lu, T. A1 - Matsuura, K. A1 - Maekawa, K. A1 - McMahon, Dino Peter A1 - Mizumoto, N. A1 - Oliveira, D. E. A1 - Poulsen, M. A1 - Sillam-Dussès, D. A1 - Su, N.-Y. A1 - Tokuda, G. A1 - Vargo, E. L. A1 - Ware, J. L. A1 - Šobotník, J. A1 - Scheffrahn, R. H. A1 - Cancello, E. A1 - Roisin, Y. A1 - Engel, M. S. A1 - Bourguignon, T. T1 - Genomic data provide insights into the classification of extant termites N2 - The higher classification of termites requires substantial revision as the Neoisoptera, the most diverse termite lineage, comprise many paraphyletic and polyphyletic higher taxa. Here, we produce an updated termite classification using genomic-scale analyses. We reconstruct phylogenies under diverse substitution models with ultraconserved elements analyzed as concatenated matrices or within the multi-species coalescence framework. Our classification is further supported by analyses controlling for rogue loci and taxa, and topological tests. We show that the Neoisoptera are composed of seven family-level monophyletic lineages, including the Heterotermitidae Froggatt, Psammotermitidae Holmgren, and Termitogetonidae Holmgren, raised from subfamilial rank. The species-rich Termitidae are composed of 18 subfamily-level monophyletic lineages, including the new subfamilies Crepititermitinae, Cylindrotermitinae, Forficulitermitinae, Neocapritermitinae, Protohamitermitinae, and Promirotermitinae; and the revived Amitermitinae Kemner, Microcerotermitinae Holmgren, and Mirocapritermitinae Kemner. Building an updated taxonomic classification on the foundation of unambiguously supported monophyletic lineages makes it highly resilient to potential destabilization caused by the future availability of novel phylogenetic markers and methods. The taxonomic stability is further guaranteed by the modularity of the new termite classification, designed to accommodate as-yet undescribed species with uncertain affinities to the herein delimited monophyletic lineages in the form of new families or subfamilies. KW - Termite KW - Taxonomy KW - Evolution PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-608276 DO - https://doi.org/10.1038/s41467-024-51028-y VL - 15 IS - 1 SP - 1 EP - 17 PB - Springer Science and Business Media LLC AN - OPUS4-60827 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Bucek, A. A1 - Sobotnik, J. A1 - He, Shulin A1 - Shi, M. A1 - McMahon, Dino Peter A1 - Holmes, E.C. A1 - Roisin, Y. A1 - Lo, N. A1 - Bourguignon, T. T1 - Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies N2 - Termitidae comprises 80% of all termite species that play dominant decomposer roles in Tropical cosystems. Two major events during Termite evolution were the loss of cellulolytic gut protozoans in the ancestor of Termitidae and the subsequent gain in the termitid subfamily Macrotermitinae of fungal symbionts cultivated externally in ‘‘combs’’ constructed within the nest. How these symbiotic transitions occurred remains unresolved. Phylogenetic analyses of mitochondrial data previously suggested that Macrotermitinae is the earliest branching termitid lineage, followed soon after by Sphaerotermitinae, which cultivates bacterial symbionts on combs inside its nests. This has led to the hypothesis that comb building was an important evolutionary step in the loss of gut protozoa in ancestral termitids. We sequenced genomes and transcriptomes of 55 termite species and reconstructed phylogenetic trees from up to 4,065 orthologous genes of 68 species. We found strong support for a novel sister-group relationship between the bacterial comb-building Sphaerotermitinae and fungus comb-building Macrotermitinae. This key finding indicates that comb building is a derived trait within Termitidae and that the creation of a comb-like ‘‘external rumen’’ involving bacteria or fungi may not have driven the loss of protozoa from ancestral termitids, as previously hypothesized. Instead, associations with gut prokaryotic symbionts, combined with dietary shifts from wood to other plant-based substrates, may have played a more important role in this symbiotic transition. Our phylogenetic tree provides a platform for future studies of comparative termite evolution and the evolution of symbiosis in this taxon. KW - Molecular clock KW - Fungiculture KW - Gut symbionts KW - Insect evolution KW - Isoptera PY - 2019 DO - https://doi.org/10.1016/j.cub.2019.08.076 VL - 29 IS - 21 SP - 3728 EP - 3734.e4 PB - Elsevier Ltd. AN - OPUS4-49647 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Liu, Cong A1 - Aumont, Cédric A1 - Mikhailova, Alina A. A1 - Audisio, Tracy A1 - Hellemans, Simon A1 - Weng, Yi-Ming A1 - He, Shulin A1 - Clitheroe, Crystal A1 - Wang, Zongqing A1 - Haifig, Ives A1 - Sillam-Dussès, David A1 - Buček, Aleš A1 - Tokuda, Gaku A1 - Šobotník, Jan A1 - Harrison, Mark C. A1 - McMahon, Dino P. A1 - Bourguignon, Thomas T1 - Unravelling the evolution of wood-feeding in termites with 47 high-resolution genome assemblies N2 - Termites are a lineage of social cockroaches abundant in tropical ecosystems where they are key decomposers of organic matter. Despite their ecological significance, only a handful of reference-quality termite genomes have been sequenced, which is insufficient to unravel the genetic mechanisms that have contributed to their ecological success. Here, we perform sequencing and hybrid assembly of 45 taxonomically and ecologically diverse termites and two cockroaches, resulting in haplotype-merged genome assemblies of 47 species, 22 of which were near-chromosome level. Next, we examine the link between termite dietary evolution and major genomic events. We find that Termitidae, which include ~80% of described termite species, have larger genomes with more genes and a higher proportion of transposons than other termites. Our analyses identify a gene number expansion early in the evolution of Termitidae, including an expansion of the repertoire of CAZymes, the genes involved in lignocellulose degradation. Notably, this expansion of genomes and gene repertoires coincided with the origin of soil-feeding in Termitidae and remained unchanged in lineages that secondarily reverted to a wood-based diet. Overall, our sequencing effort multiplies the number of available termite genomes by six and provides insights into the genome evolution of an ancient lineage of social insects. KW - Comparative genomics KW - Entomology KW - Genome evolution KW - Phylogenetics PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-651719 DO - https://doi.org/10.1038/s41467-025-65969-5 SN - 2041-1723 VL - 16 SP - 1 EP - 14 PB - Springer Science and Business Media LLC AN - OPUS4-65171 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Liu, Cong A1 - Hellemans, Simon A1 - Weng, Yi-Ming A1 - Mikhailova, Alina A. A1 - Aumont, Cédric A1 - Buček, Aleš A1 - Šobotník, Jan A1 - Harrison, Mark C. A1 - McMahon, Dino P. A1 - Bourguignon, Thomas T1 - Robust termite phylogenies built using transposable element composition and insertion events N2 - Phylogenetic trees are typically reconstructed using conserved sequence alignments. Other genomic elements, such as transposable elements (TEs), make up a large fraction of eukaryotic genomes but are ignored for phylogenetic reconstruction, despite potentially containing phylogenetic information, which could be used to resolve nodes that remain contentious. Here, we reconstructed accurate phylogenetic trees of 45 termites and two cockroaches using two types of characters derived from the TE landscape: (1) genome-wide presence and absence of 37,966 TE families and (2) presence/absence data of 37,966 TE families in the flanking regions of orthologous ultraconserved elements (UCEs), which was a proxy for TE insertions. The topologies of our TE-based phylogenetic trees were largely congruent with phylogenetic trees inferred from alignments of UCEs and single-copy orthologous genes, only differing for a few nodes variably reconstructed in other phylogenetic analyses. Notably, trees based on genome-wide TE family composition were more accurate than trees inferred from mitochondrial genome alignments, and trees based on TE family composition in regions flanking UCEs achieved comparable accuracy with trees inferred from single-copy orthologous gene alignments. Our results demonstrate that the TE landscape is phylogenetically informative, representing an additional set of markers for robust phylogenetic reconstructions, with potential use to resolve ambiguous nodes in the tree of life. KW - Comparative genomics KW - Genome evolution KW - Insects KW - Isoptera KW - Mitogenomes KW - Molecular markers KW - Phylogenomics KW - Transposons PY - 2025 DO - https://doi.org/10.1016/j.cub.2025.10.019 SN - 0960-9822 VL - 35 IS - 22 SP - 1 EP - 10 PB - Elsevier Inc. AN - OPUS4-64737 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Liu, Cong A1 - Hellemans, Simon A1 - Kinjo, Yukihiro A1 - Mikhailova, Alina A A1 - Aumont, Cédric A1 - Weng, Yi-Ming A1 - Buček, Aleš A1 - Husnik, Filip A1 - Šobotník, Jan A1 - Harrison, Mark C A1 - McMahon, Dino P A1 - Bourguignon, Thomas T1 - Recurrent horizontal gene transfers across diverse termite genomes N2 - Horizontal gene transfer (HGT), the transmission of genetic material across species, is an important innovation source in prokaryotes. In contrast, its significance is unclear in many eukaryotes, including insects. Here, we used high-quality genomes of 45 termites and two cockroaches to investigate HGTs from non-metazoan organisms across blattodean genomes. We identified 289 genes and 2,494 pseudogenes classified into 168 orthologous groups originating from an estimated 281 HGT events. Wolbachia represented the primary HGT source, while termite gut bacteria and the cockroach endosymbiont Blattabacterium did not contribute meaningfully to HGTs. Most horizontally acquired genes descended from recent and species-specific HGTs, experienced frequent duplications and pseudogenizations, and accumulated substitutions faster than synonymous sites of native protein-coding genes. Genes frequently transferred horizontally to termite genomes included mobile genetic elements and genetic information processing genes. Our results indicate that termites continuously acquired genes through HGT, and that most horizontally acquired genes are specific to restricted lineages. Overall, genes acquired by HGT by termites and cockroaches seemed generally non-functional and bound to be lost. KW - Phylogenomics KW - Isoptera KW - Comparative genomics PY - 2026 DO - https://doi.org/10.1093/evolut/qpag003 SN - 0014-3820 SP - 1 EP - 14 PB - Oxford University Press (OUP) AN - OPUS4-65418 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -