Goffinet, B. 2024. Reporting Rutenbergia madagassa Geheeb & Hampe new to the Comoros. In Ellis L.T., O.M. Afonina, M. Alataş, H.B. M. Alia, J. Alvarez, A.M. Aponte Rojas, J.J. Atwood, G. Bacilliere, N. Batan, V. Biberdžić, M.A. Bruggeman-Nannenga, L.V. Campos, M.J. Cano, L.F. Coca, I.V. Czernyadjeva, S. de Faria Lopes, Q. Dejonghe, S. Dragićević, H. Erata, B. Espinoza-Prieto, P. Erzberger, T. Ezer, L.L. Forrest, B. Goffinet, O.A. Gonçalves, A. Graulich, V. Hugonnot, S. Huttunen, M.S. Ignatov, E.A. Ignatova, J.A. Jiménez, S. Kumara, I. Kuusisto, E. Yu Kuzminac, D.G. Longt, X-Y. Ma, A.S. Maciel-Silva, C.N. Manju, B. Mufeed, F. Müller, M.B. Nosova, R. Ochyra, M. F. Oliveira, M.S. Özkaya, F. Pépin, V. Plášek, M. Puglisi, C. Reeb, R. Romanov, M.S. Sajitha, T. Saha, P.O. Santos, C.Shakira, Y.-M. Shu, J. B. Silvaa, D. Singh, G.M. Suáre, N. Taşçi, M. Tossou, D. Ya. Tubanova, J. Uribe-M, A. Schäfer-Verwimp, P.M. Vineesha, R. Virtanen, Y.-H. Wu & T.-X. Zheng. 2024. New national and regional bryophyte records, 76. Journal of Bryology 46: 51–74. pdf

Vuruputoor V.S., A. Starovoitov, Y. Cai, Y. Liu, N. Rahmatpour, T. Hedderson, N. Wilding, J.L. Wegrzyn & B. Goffinet. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana. G3: Genes, Genomes, Genetics 14(7): jkae104. pdf  Google Scholar

Abstract reads:  The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single- Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events. 

Zach has received a 2024 Evolutionary, Ecological, and Conservation Genomics (EECG) Research Award ($6,000) from the American Genetics Association for his project “Unveiling the mysteries of fog lichens: Phylogenomic insights into the phenotypic diversity of a niche-specific radiation. Congratulations!

Crystal (Zhu) was awarded a Summer Undergraduate Research Fellowship from the UConn Office of Undergraduate Research for her project “More than meets the eye: Unveiling the diversity of lichen-forming fungal species in Chile using DNA barcoding”.  The project focuses on Lobarioideae (Peltigerales) and primarily the genus Pseudocyphellaria. The award consists of a stipend and funds to cover research expenses. Congratulations. 

The SURF program is jointly sponsored by the Office of Undergraduate Research, the Provost’s Office, the Office of the Vice President for Research, the Honors Program, donors to the university, and the Deans of the Schools and Colleges.

Crystal will be traveling to subantarctic Chile in May to see the various species in the Nothofagus forests on Navarino Island and near Punta Arenas.

Bechteler J., G. Peñaloza-Bojacá, D. Bell, G. Burleigh, S. F. McDaniel, E. C. Davis, E. B. Sessa, A. Bippus, D. Christine Cargill, S. Chantanoarrapint, I. Draper, L. Endara, L. L. Forrest, R. Garilleti, S. W. Graham, S. Huttunen, J. Jauregui Lazo, F. Lara, J. Larraín, L. R. Lewis, D. G. Long, D. Quandt, K. Renzaglia, A. Schäfer-Verwimp, G. Ee Lee, A. S. Pinilla, M. von Konrat, C. E. Zartman, M. Regina Pereira, B. Goffinet & J. C. Villarreal. 2023. Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. American Journal of Botany 110: e16249. pdf GoogleScholar

Abstract reads: 
Premise: Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns and processes of diversification across bryophytes remain unclear.

Methods: Using the GoFlag probe set we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.

Results: The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology.

Conclusions: We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.

Patel N., R. Medina, L.D. Williams, O. Lemieux, B. Goffinet & M.G. Johnson. Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes. Evolution 77: 2561–2575. pdf

Abstract reads: Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. Here, we test a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called Homologizer, in the family Funariaceae. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of Physcomitrium eurystomum and of one population of P. collenchymatum. We also reveal that hybridization gave rise to P. immersum, as well as to yet unrecognized lineages sharing the phenotype of P. pyriforme, and P. sphaericum. Our findings demonstrate the utility of our approach when working with polyploid genomes, and its value in identifying progenitor species using target capture data.

Hu R., X. Li, Y. Hu, R. Zhang, Q. Lv, M. Zhang, X. Sheng, F. Zhao, Z. Chen, Y. Ding, H. Yuan, X. Wu, S. Xing, X. Yan, F. Bao, P. Wan, L. Xiao, X. Wang, W. Xiao, E.L. Decker, N. van Gessel, H. Renault, G. Wiedemann, N.A. Horst, F.B. Haas, P.K.I. Wilhelmsson, K. Ullrich, E. Neumann, B. Lv, C. Liang, H. Du, H. Lu, Q. Gao, Z. Cheng, H. You, P. Xin, J. Chu, C.-H. Huang, Y. Liu, S. Dong, L. Zhang, F. Chen, L. Deng, F. Duan, W. Zhao, K. Li, Z. Li, X. Li, H. Cui, Y. Zhang, C. Ma, R. Zhu, Y. Jia, M. Wang, M. Hasebe, J. Fu, B. Goffinet, H. Ma, S.A. Rensing, R. Reski, Y. He. 2023. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet. Cell 186: 3558–3576.  pdf

The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010–2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.

Abstract reads: Physcomitrium pygmaeum is an ephemeral moss described in 1871 from a single collection from Utah, currently considered conspecific with Physcomitrium pyriforme. The interpretation of the taxon has been problematic due to its rarity in the field, the elusiveness of the type material, and an extremely scattered and inconsistent collection record. Here we present a comprehensive description and assessment of the taxon following the identification of the original material and lectotype designation, the examination of all existing herbarium specimens to the best of our knowledge, the collection of fresh material in Nevada, and the molecular barcoding of the latter using four plastid and two nuclear loci. Available information, albeit scant, suggests that this member of the North American bryoflora should be considered critically endangered following IUCN criteria.