Dirick L., Y. Liu, S. Dong, J. Yu, L. Ouerdane, C. Curie & B. Goffinet. Independent horizontal microbial gene transfers with replacement in plants. 2025. Nature Communications 16: 8339.

Abstract reads: The evolution of land plants is marked by major innovations enhancing their vegetative and reproductive fitness. Despite their extensive adaptations to terrestrial habitats, plants rely on ecological interactions with microbes for various physiological processes. Beyond their role as critical partners in the conquest of, and diversification on land, fungi and bacteria also serve as sources of genetic tools. Analyses of the gene space of land plant model organisms suggest that such transfers are unique and ancient. However here, using genomic data spanning the diversity of mosses, we demonstrate that a metallophore-synthesis gene was acquired independently from distinct microbial donors by at least five plant lineages. Furthermore we find that the first NAS gene acquired by mosses was later replaced by another fungal copy, transferred to another major moss lineage. Such a complex history of acquisition of a gene may reflect a more general pattern of highly dynamic gene exchange across the tree of life.

Dong S., S. Wang, L. Li, J. Yu, Y. Zhang, J.-Y. Xue, H. Chen, J. Ma, Y. Zeng, Y. Cai, W. Huang, J. Li, Y. Yao, R. Hu, T. Zhao, J.C. Villarreal A., L. Dirick, L. Liu, M. Ignatov, J. Ruan, Y. He, H. Wang, B. Xu, J. Wegrzyn, D. W. Stevenson, K. S. Renzaglia, H. Chen, L. Zhang, S. Zhang, R. Mackenzie, J. Moreno, M. Melkonian, T. Wei, Y. Gu, X. Xu, M. Long, J. Huang, S. Rensing, B. Goffinet, J. L. Bowman, Y. Van de Peer, H. Liu, and Y. Liu. 2025. Bryophytes hold a larger gene family space than vascular plants. Nature Genetics 2025. pdf

Abstract reads: After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes’ rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.

 

 

The American Bryological and Lichenological Society announced the awards for the best papers published in The Bryologist in 2024 (Volume 127) and awarded the SULLIVANT AWARD (for the best bryological paper) to our checklist: Buck W.R. & B. Goffinet. 2024. A new checklist of the mosses of the continental United States and Canada. The Bryologist 127: 484–549.  pdf  Google Scholar

Atwood, J., WR. Buck & B. Goffinet. 2025. Bryomyces, a genus described from foliar moss gemmae, is an earlier name for Plenogemma (Orthotrichaceae). Novon 33: 115–121.

Abstract reads: Bryomyces Miq. and Phragmidiolum Müll. Hal., originally described as genera of endophytic bryophilous ascomycetes, refer instead to foliar moss gemmae based on a comparative assessment of their published illustrations with bryophyte specimens and relevant bryological literature. Phragmidiolum and Plenogemma Plášek, Sawicki & Ochyra are morphologically congeneric with Bryomyces, the latter of which has priority. The new combination B. phyllanthus (Brid.) J. J. Atwood, W. R. Buck & Goffinet is proposed. Bryomyces elegans Miq., Phragmidiolum apicale Müll. Hal., and Ulota phyllantha Brid. [≡ Plenogemma phyllantha (Brid.) Sawicki, Plášek & Ochyra] are new synonyms of that species. Bryomyces montagneanus Miq. is a new synonym of Calymperes androgynum Mont. [= Syrrhopodon rigidus Hook. & Grev.], whereas B. muelleri Miq., Phragmidiolum ramosum Müll. Hal., and Phragmidiolum sparsum Müll. Hal. are new synonyms of Orthotrichum lyellii Hook. & Taylor [≡ Pulvigera lyellii (Hook. & Taylor) Plášek, Sawicki & Ochyra]. Lectotypes are designated for B. montagneanus, Phragmidiolum, Phragmidiolum apicale, and Phragmidiolum ramosum, while a neotype is designated for B. elegans.

Milis A., P. Mäder, M. De Haan, P. Ballings, I. Van Der Beeten, B. Goffinet & A. Vanderpoorten. 2025. Time to spice-up paleoecological records with bryophyte spores. Trends in Plant Sciences in press

Abstract reads: Paleovegetation reconstructions rely virtually exclusively on inferences from vascular plants, particularly pollen grains, ignoring other components of the land flora. Artificial intelligence (AI) opens the door to the identification of other microfossils, particularly bryophyte spores, which offer a new, higher magnification lens to characterize past climatic environments.

Finally, the study first completed by Nasim Rahmatpour for her Ph.D. and then picked up by former postdoc Niki Patel and current Ph.D. student Vidya Vuruputoor is now published in the New Phytologist! Amazing study highlighting the “Immediate premeiotic transcriptomic effects following nonchemically induced whole genome duplication in the moss Funaria hygrometrica” pdf  Congratulations to all and thank you to our collaborators, Drs. Yang Liu, Shanshan Dong and Peter Szövényi.

 

Patel N.*, V. Vuruputoor*, N. Rahmatpour, Y. Liu, P. Szövényi, B. Goffinet & J. Wegrzyn. 2025. Induced whole genome duplication triggers immediate shifts in gene expression in an emerging moss model. New Phytologist 247: 24–32.

Brenden Thomson earned his MSc degree having completed his thesis on the phylogenetic diversity of Physcomitrium (Bryopsida) win North America. Well done and congratulations.

Crystal Zhu, graduated this weekend, with honors and as UConn Scholar. She earned the Connecticut State Museum of Natural History Award for outstanding scholarship and original research concentrating on the natural history, behavior, or overall biology of a focal organism for her honors’ thesis “Unveiling and Illustrating the Diversity of Lichen-Forming Fungal Species in Chile”. Congratulations. She will pursue her interests in lichens, right here starting in the fall.

 

Goffinet, B. & T. Pócs. 2025. Reporting Rhachithecium perpusillum H. Rob. new to Uganda. In Ellis M. Alataş, Sk. N. Ali, D. J. Alvarez, A. M. Aponte Rojas e, J. J. Atwood f, N. Batan g, H. Bednarek-Ochyra, M. J. Cano, Ž. L. Cimerman, T. Colotti, M. J. F. Costa, E. Enkhjargal, H. Erata, P. Erzberger, B. Espinoza-Prieto, M. Evangelista-dos-Santos, T. Ezer, L. Fatková, V. E. Fedosov ,R. Gabriel, L. Gil, B. Goffinet, A. Graulich, Yu-Chwen Hsu, T. Kiebacher, J. M. Kocjan, S. S. Krajšek, S. Kubešová, J. Kučera, J. Larraín, E. Lavocat-Bernard, Y. Mamontov, P. M. Mir-Rosselló, C. P. Morales, R. Natcheva, M. A. Negritto, Juan D. Ospino-C, M. Paul, B. Papp, T. Pócs, E. Rodríguez-Quiel, M. Rogošić, K. Ramírez-Roncallo, A. A. Roque, A. D. Sabovljević, M. S. Sabovljević, A. Schäfer-Verwimp, V. Šegota, C. Sérgio, P. H. Sette-de-Souza, D. Singh, P. Širka, A. Sotiaux, G. M. Suárez, D. Ya. Tubanova, Kuei-Yu Yao & G. Winter. New national and regional bryophyte records, 79. Journal of Bryology 46: 295–318.

Coca L.F., H.T. Lumbsch, J.A. Mercado-Díaz, T. Widhelm, B. Goffinet, P. Kirika & R. Lücking. 2025. Diversity, phylogeny, and historical biogeography of the genus Coccocarpia (lichenized Ascomycota: Peltigerales) in the tropics. Molecular Phylogenetics and Evolution 206: 108312. pdf  Google Scholar

Abstract reads Coccocarpia Pers. currently comprises 28 mostly broadly distributed tropical species of fungi associated with cyanobacteria. Three of these taxa, C. erythroxyli, C. palmicola, and C. pellita, are presumably pantropical to subcosmopolitan, with broad morphological variation across their range. This study provides the first global phylogeny of the genus, to test current species concepts and infer distribution patterns, based on samples from Colombia, Puerto Rico, Gabon, Kenya, Thailand, Fiji, and Hawaii. We also estimate divergence times within the clade and provide a first reconstruction of its biogeographic history. Based on phylogenetic reconstructions inferred from maximum likelihood and Bayesian approaches of four molecular markers (mtSSU, nuLSU, ITS, RPB2), Coccocarpia was recovered as monophyletic. However, the currently accepted taxa are largely polyphyletic entities and the underlying diversity in this genus is much higher than currently understood. Different methods for species delimitation boundaries came to agree on a scenario involving more than 150 species in the available, albeit still small, dataset. This suggests that with broader sampling, Coccocarpia may indeed represent a hyper-diverse genus, potentially containing over 200 species. The phylogeny is geographically structured: one clade is exclusive to the Paleotropics, one to the Neotropics, and one is pantropical. Coccocarpia likely emerged during the Late Cretaceous (90 ± 10 Mya) in the tropical regions of Australasia-Oceania, initially colonizing Oceania, and Asia and subsequently the Neotropics. The three main clades diverged between the Late Cretaceous and the Paleocene, with significant diversification in the Oligocene, during which the neotropical clade gave rise to morphological novelties, including the epiphylla and stellata clades.