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 - 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 - 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 - Teixeira, M.M. A1 - Moreno, L.F. A1 - Stielow, B.J. A1 - Muszewska, A. A1 - Hainaut, M. A1 - Gonzaga, L. A1 - Abouelleil, A. A1 - Patan, J.S.L. A1 - Priest, M. A1 - Souza, R. A1 - Ferreira, K.S. A1 - Zeng, Q. A1 - da Cunha, M.M.L. A1 - Gladki, A. A1 - Barker, B. A1 - Vicente, V.A. A1 - de Souza, E.M. A1 - Almeida, S. A1 - Henrissat, B. A1 - Vasconelos, A.T.R. A1 - Deng, S. A1 - Vogelmayr, H. A1 - Moussa, T.A.A. A1 - Gorbushina, Anna A1 - Felipe, M.S.S. A1 - Cuomo, C.A. A1 - de Hoog, G.S. T1 - Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota) N2 - The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sexrelated genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi. KW - Black yeast KW - Comparative genomics KW - Chaetothyriales KW - Ecology KW - Evolution KW - Herpotrichiellaceae KW - Phylogeny PY - 2017 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-408720 DO - https://doi.org/10.1016/j.simyco.2017.01.001 SN - 1872-9797 VL - 86 IS - 1 SP - 1 EP - 28 PB - Elsevier CY - Amsterdam AN - OPUS4-40872 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -