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.

This study emerged from the genomes published by Dong et al. (2025) and for which some vouchers are in CONN.

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, X. Zhou, J. Wu, J. Li, Y. Yao, R. Hu, T. Zhao, J.C. Villarreal A., L. Dirick, L. Liu, M. Ignatov, M. Jin, J. Ruan, Y. He, H. Wang, B. Xu, R. Rozzi, 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, S. Rensing, J. Huang, M. Long, 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

Vouchers for some of the specimens used for genome extraction and sequencing are deposited in CONN.

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.

Summer Rayne Oakes visited the UBC and composed three videos featuring our amazing plants and plant experts. The videos are part of her extensive series on YouTube whose “mission is to bring people closer to plants by bringing plants closer to them through engaging, entertaining, and educational content.”

Enjoy.

UConn’s ORCHID GREENHOUSE Tour — Ep. 418 https://youtu.be/NOHs8sZt2KQ?si=yz67PDy5LCqdSQjy

CONOPHYTUM & MESEMB Tour at UConn — Ep. 419 https://youtu.be/o9iGVSyCCJ0?si=2pI9QluropaxCcvU

ANT PLANT Tour at UConn Conservatory — Ep. 420 https://youtu.be/LhvQiDckWBY?si=To3nrV9oDCiG3J3z

Former herbarium curator Dr. Robert Capers published the discovery of Apopellia endiviifolia for North America. A voucher is in the CONN herbarium.

Favreau M., L. L. Forrest, R. Capers & J. C. Villarreal A. 2025. Apopellia endiviifolia (Dicks.) Nebel & D.Quandt confirmed in North America. Evansia 42(2): 34. pdf.

Abstract reads: Specimens morphologically identified as the liverwort Apopellia endiviifolia have been collected in Quebec, Canada, for over 20 years. Their identity as this species is herein confirmed by DNA sequence data, and the species range is extended to the United States, in Maine and Vermont.

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. 

The voucher is this species added to the flora of Uganda is in the CONN herbarium.

Graham, M.R., N. Kaur, C.S. Jones, K.  Lamour & B. A. Connolly. 2025. A phoenix in the greenhouse: characterization and phylogenomics of complete chloroplast genomes sheds light on the putatively extinct-in-the-wild Solanum ensifolium (Solanaceae). BMC Plant Biology 25: 320. pdf

Abstract reads:

Background: The genus Solanum is a diverse group of flowering plants with significant economic importance. Within this genus, the subgenus Leptostemonum, comprising spiny solanums, is particularly noteworthy due to its high species diversity and endemism. Solanum ensifolium, a member of this subgenus, is a critically endangered species endemic to Puerto Rico and known locally as erubia. The species survives in greenhouses and botanical gardens and is thought to be extinct in the wild, but with reintroduction efforts in progress. Despite its conservation status, genomic data for S. ensifolium remains scarce, limiting our understanding of its evolutionary history and potential adaptations.
Results: The S. ensifolium chloroplast genome (155,295 bp) exhibits a typical quadripartite structure and encodes 151 genes, including 95 protein-coding genes involved in photosynthesis, transcription, translation, and other essential cellular functions. Gene content and genome organization are similar to those observed in closely related Solanum species. Comparative genomic analysis of the annotated genome with that of closely related Solanum species revealed differences in nucleotide diversity between the large single-copy (LSC) and small single-copy regions (SSC), and the inverted repeat (IR) regions. Additionally, phylogenetic analyses confirmed placement of S. ensifolium within the Leptostemonum subgenus, affirming its suspected close relationship with S. crotonoides and S. aturense. Furthermore, of the three individuals of S. ensifolium for which chloroplast genomes were obtained, no genetic variation was observed.
Conclusions:  The availability of the S. ensifolium chloroplast genome provides insights into its evolutionary history and conservation needs. Comparative genomics uncovered evolutionary differences in Solanum chloroplast genomes, including nucleotide diversity and structural variations. Phylogenetic analyses confirmed the close relationship between S. ensifolium and other Leptostemonum species. These findings enhance our understanding of this critically endangered species’ evolution, guiding effective conservation strategies like using chloroplast variation to assess genetic diversity for ex situ conservation and reintroduction programs. The uniformity of the chloroplast genome in S. ensifolium may reveal that this species has undergone a genetic bottleneck. To prevent inbreeding depression and maintain evolutionary adaptability, efforts should be made to generate and preserve as much genetic diversity as possible.

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

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.

Kirbis A., N. Rahmatpour, S. Dong, J. Yu, L. Waser, H. Huang, N. van Gessel, M. Waller, R. Reski, D. Lang, S. A. Rensing, E. M. Temsch, J. L. Wegrzyn, B. Goffinet, Y. Liu & P. Szövényi. 2025. Comparative analysis of the Funaria hygrometrica genome suggests greater collinearity in mosses than in seed plants. Communication Biology 8: 330. pdf

The voucher for this collaborative genome study is in CONN!

Abstract reads: Mosses, the largest lineage of seed-free plants, have smaller and less variable genome sizes than flowering plants. Nevertheless, whether this difference results from divergent genome dynamics is poorly known. Here, we use newly generated chromosome-scale genome assemblies for Funaria hygrometrica and comparative analysis with other moss and seed plant genomes to investigate moss genome dynamics. Although someaspects of moss genome dynamics are seed plant-like, such as the mechanism of genome size change and de novo gain/loss of genes, moss genomes retain higher synteny, and collinearity over evolutionary time than seed plant genomes. Furthermore, transposable elements and genes are more evenly distributed along chromosomes in mosses than in seed plants, a feature shared with other sequenced seed-free plant genomes. Overall, our findings support the hypothesis that large-scale genome structure and dynamics of mosses and seed plants differ. In particular, our data suggest a lower rate of gene order reshuffling along chromosomes in mosses compared to seed plants.Wespeculate that such lower rate of structural genomic variation and unique chromosome structure in mosses may contribute to their relatively smaller and less variable genome sizes.

Lee, Y.J. & Z. Lei. 2024. A new cicada species of the genus Kosemia Matsumura (Hemiptera: Cicadidae: Cicadettinae) from Xinjiang, China. Journal of Insect Biodiversity 57(1): 13–18. pdf

Abstract reads: Kosemia brevis sp. nov. (Hemiptera: Cicadidae: Cicadettinae: Cicadettini) is described from Xinjiang, China. This species is morphologically closest to Kosemia yezoensis (Matsumura, 1898) as its forewing median vein and cubitus anterior vein are fused at the base. However, the new species can be distinguished from K. yezoensis by the size and color of the anal styles. Its body is much smaller but plump, and its forewing is comparatively short, compared to K. yezoensis.