Yu J., Y. Cai, Y. Zhu, Y. Zeng, S. Dong, K. Zhang, S. Wang, L. Li, B. Goffinet, H. Liu & Y. Liu. 2022. Chromosome-level genome assemblies of two Hypnales mosses reveal high intergeneric synteny. Genome Biology and Evolution 14: evac020. pdf  Google scholar

Abstract reads: Mosses compose one of the three lineages of bryophytes. Today, about 13,000 species of mosses are recognized from across the globe, and at least a third of this diversity composes the Hypnales, a lineage characterized by an early rapid radiation. We sequenced and de novo assembled the genomes of two hypnalean mosses, namely Entodon seductrix and Hypnum curvifolium, based on the 10x genomics and Hi-C data. The genome assemblies of E. seductrix and H. curvifolium comprise 348.4 Mb and 262.0 Mb, respectively, estimated by k-mer analyses to represent 93.3% and 97.2% of their total genome size. Both genomes were assembled at the chromosome-level, with scaffold N50 of 30.0 Mb and 20.7 Mb, respectively. The annotated genome of E. seductrix comprises 25,801 protein-coding genes and that of H. curvifolium 29,077, estimated to represent 96.8% and 97.2%, respectively, of the total gene spaces based on BUSCO assessment. For both genomes, most contigs were anchored to the largest 11 pseudomolecules, corresponding to the 11 chromosomes of the two species, and each with a putative sex-related chromosome characterized by low gene density. The chromosomes of E. seductrix and H. curvifolium are highly syntenic, suggests limited architectural shifts occurred following the rapid radiation of the Hypnales. We compared their genomic features to the model moss Physcomitrium patens. The hypnalean moss genomes lack signatures of recent whole genome duplication (WGD). The presented high-quality moss genomes provide new resources for comparative genomics to potentially unveil the genomic evolution of derived moss lineages.

Widhelm T.J., F. Grewe, B. Goffinet, M. Wedin, T. Goward, L.F. Coca, I. Distefano, A. Košuthová & H.T. Lumbsch. 2021. Phylogenomic reconstruction addressing the Peltigeralean backbone (Lecanoromycetes, Ascomycota). Fungal Diversity
110: 59–73. pdf  Google scholar

Abstract reads: Rapid radiations in Fungi are only beginning to be studied with phylogenomic data. The evolutionary history of the lichenized fungal order Peltigerales has not been well resolved, particularly for the Collematineae. Here, we used concatenation and coalescent-based species tree methods to reconstruct the phylogeny of the Peltigerales based on sequences of 125 nuclear single-copy exon sequences among 60 samples, representing 58 species. Despite uneven, lineage-specific missing data and significant topological incongruence of individual exon trees, the resulting phylogenies were concordant and successfully resolved the phylogenetic relationships of the Peltigerales. Relationships in the Collematineae were defined by short branches and lower nodal support than in other parts of the tree, due in part to conflicting signal in exon trees, suggesting rapid diversification events in the early evolution of the suborder. Using tree distance measures, we were able to identify a minimum subset of exons that could reconstruct phylogenetic relationships in Peltigerales with higher support than the 125-exon dataset. Comparisons between the minimum and complete datasets in species tree inferences, bipartition analyses, and divergence time estimations displayed similar results, although the minimum dataset was characterized by higher levels of error in estimations of divergence times. Contrasting our inferences from the complete and minimum datasets to those derived from few nuclear and mitochondrial loci reveal that our topology is concordant with topologies reconstructed using the nuclear large subunit and mitochondrial small subunit ribosomal DNA markers, but the target capture datasets had much higher support values. We demonstrated how target capture approaches can effectively decipher ancient rapid radiations in cases where well resolved individual exon trees are sufficiently sampled and how to identify subsets of loci that are appropriate for fungal order-level phylogenetics.

Antoine Simon, who graduated from the University of Liège, Belgium, is joining our lab for a year, based on a fellowship from the Belgian American Educational Foundation. Antoine’s research focuses on lichenized fungi and their symbiotic partners, their evolution and diversification, and interactions.

Antoine has stayed at UCONN twice before as part of his Master’s thesis and doctoral dissertation projects.

 

Abstract reads: Phylogenetic turnover has emerged as a powerful tool to identify the mechanisms by which biological communities assemble. When significantly structured along environmental gradients, phylogenetic turnover evidences phylogenetic niche conservatism, a critical principle explaining patterns of species distributions at different spatio–temporal scales. Here, we quantify the contribution of geographic and macroclimatic drivers to explain patterns of phylogenetic turnover in an entire phylum of land plants, namely liverworts. We further determine whether climatic niche conservatism has constrained the distribution of liverworts in the course of their evolutionary history. Two datasets, one insular, focused on 60 archipelagos and including 2346 species, and the second global, including 6334 species in 451 oceanic and continental operational geographic units (OGUs) worldwide, were assembled. Phylogenetic turnover among OGUs was quantified through π_st statistics. π_st-through-time profiles were generated at 1 Myr intervals along the phylogenetic time-scale and used to compute the correlation between πst, current geographic distance and macroclimatic variation with Mantel tests based on Moran spectral randomization to control for spatial autocorrelation. The contribution of macroclimatic variation to phylogenetic turnover was about fourtimes higher than that of geographic distance, a pattern that was consistently observed in island and global geographic settings, and with datasets including or excluding species-poor OGUs. The correlation between phylogenetic turnover and geographic distance rapidly decayed at increasing phylogenetic depth, whereas the relationship with macroclimatic variation remained constant until 100 Mya. Our analyses reveal that changes in the phylogenetic composition among liverwort floras across the globe are primarily shaped by macroclimatic variation. They demonstrate the relevance of macroclimatic niche conservatism for the assembly of liverwort floras over very large spatial and evolutionary time scales, which may explain why such a pervasive biodiversity pattern as the increase of species richness towards the tropics also applies to organisms with high dispersal capacities.

 

Frangedakis E., F. Guzman-Chavez, M. Rebmann, K. Markel, Y. Yu, A. Perraki, S. Wai Tse, Y. Liu, J. Rever, S. Sauret-Gueto, B. Goffinet, H. Schneider & J. Haseloff. 2021. A system for rapid genome engineering and hyper-expression in plastids. ACS Synthetic Biology 10: 1651–1666. pdf Google scholar

Abstract reads: Chloroplasts are attractive platforms for synthetic biology applications since they are capable of driving very high levels of transgene expression, if mRNA production and stability are properly regulated. However, plastid transformation is a slow process and currently limited to a few plant species. The liverwort Marchantia polymorpha is a simple model plant that allows rapid transformation studies; however, its potential for protein hyperexpression has not been fully exploited. This is partially due to the fact that chloroplast post-transcriptional regulation is poorly characterized in this plant. We have mapped patterns of transcription in Marchantiachloroplasts. Furthermore, we have obtained and compared sequences from 51 bryophyte species and identified putative sites for pentatricopeptide repeat protein binding that are thought to play important roles in mRNA stabilization. Candidate binding sites were tested for their ability to confer high levels of reporter gene expression in Marchantia chloroplasts, and levels of protein production and effects on growth were measured in homoplastic transformed plants. We have produced novel DNA tools for protein hyperexpression in this facile plant system that is a test-bed for chloroplast engineering.

I am delighted to share the news that Kris Anderson was awarded the Stanley Greene Award from the International Association of Bryologists in support of her project entitled “Experimentally testing the fundamental assumption that shifts in ploidy facilitate shifts in sexuality in a dioicous moss.” Congratulations. Looking forward to the outcome. Good luck.

Zach is mentioned in this article in The Chronicle about the discovery of Teloschistes chrysophthalmus and other  species in Connecticut.

The original publication is:

Frye H.A., Z. Muscavitch & B. Goffinet. 2021. Discovery of epiphytic lichens in Connecticut suggest novel introduction and reintroduction via horticultural practices. The Bryologist 124: 191–197. https://doi.org/10.1639/0007-2745-124.2.191

 

Patel N., R. Medina, M. Johnson & B. Goffinet. 2021. Karyotypic diversity and cryptic speciation: Have we vastly underestimated moss species diversity? Bryophyte Diversity and Evolution 43: 150–163. https://doi.org/10.11646/bde.43.1.12

Abstract reads: Karyotypic diversity is critical to catalyzing change in the evolution of all plants. By resulting in meiotic incompatibility among sets of homologous chromosomes, polyploidy and aneuploidy may facilitate reproductive isolation and the potential for speciation. Across plants, karyotypic variants in the form of allopolyploids receive greater taxonomic attention relative to autopolyploids and aneuploids. In particular, the prevalence and significance of autopolyploidy and aneuploidy in bryophytes is little understood. Using Fritsch’s 1991 compendium of bryophyte karyotypes with augmentation from karyological studies published since, we have quantified the prevalence of karyotypic variants among ~1500 extant morphological species of mosses. We assessed the phylogenetic distribution of karyological data, the frequency of autopolyploidy and aneuploidy, and the methodological correlates with karyotypic diversity. At least two ploidy levels were recorded from 17% of species potentially increasing current taxonomic diversity of mosses to over 15,000 species. We find that for a given species, the number of unique karyotypes recorded is correlated with the number of populations sampled. The evidence suggests that cytological diversity likely underlies yet undescribed species diversity in mosses, and that intensive karyological sampling is a needed tool for its discovery.

 

Cole T.C.H., H.H. Hilger, J.B. Bachelier, B. Goffinet, P.F. Stevens, N.M. Shiyan, S.L. Zhygalova & S.L. Mosyakin. Spanning the Globe – The Plant Phylogeny Poster (PPP) Project. Ukrainian Botanical Journal: Short Communication 78(3): 235–241. https://doi.org/10.15407/ukrbotj78.03.235

Abstract reads: Historically, wallcharts and posters created by botanical illustrators, often highly skilled artists, have played an important role in teaching botany at the university level. Large-scale panels and posters can visualize complex interrelationships and entire stories in a clear and appealing overview in graphs, tables, and diagrams. Carrying this concept of educational tools into the electronic era, the Plant Phylogeny Poster project uses this approach for displaying evolutionary relationships in systematic botany. The Angiosperm Phylogeny Poster (APP) displays, as phylogenetically arranged clades, the orders and families of flowering plants (with orders hyperlinked to APweb, Stevens, 2001–onwards), the Tracheophyte Phylogeny Poster (TPP) families and genera of ferns and gymnosperms, and the Bryophyte Phylogeny Poster (BPP) orders and families of liverworts, mosses, and hornworts. The portfolio currently also includes about 30 posters on individual orders and families of angiosperms. Each group within these evolutionary trees is matched with essentially relevant morphological features, biogeographic occurrences, and other information in compactly condensed text blocks. All posters are freely available online, some in more than 30 languages, coauthored by a team of more than 130 botanists. The posters are regularly updated, current literature is cited. The project is expanding steadily and rapidly.

Rafael Medina, a former postdoc in our lab, lead-authored the paper: Medina, R., M.G. Johnson, Y. Liu, N.J. Wickett, A.J. Shaw & B. Goffinet. 2019. “Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma” and published in the Journal of Systematics and Evolution 57: 404–417 in 2019. https://doi.org/10.1111/jse.12516

In 2019, this publication earned the Special issue paper award from the Journal of Systematics and Evolution.

In 2021, the journal awarded him, for this publication, the “JSE Outstanding Paper by Young Investigators Award”, which will be announced in the latest issue of 2021.

Rafa is now a faculty member at the University of Madrid.

 

Congratulations Rafa.