The first hornwort genome is now published, filling a major gap in the survey of genomes of major lineages of land  plants. This project was led by collaborators of the Chinese Academy of Sciences, Beijing, China.

Zhang J., X.-X. Fu, R.-Q. Li, X. Zhao, Y. Liu, M.-H. Li, A. Zwaenepoel, H. Ma, B. Goffinet, Y.-L. Guan, J.-Y. Xue, Y.-Y. Liao, Q.-F. Wang, Q.-H. Wang,Q.-H. Wang, J.-Y. Wang, G.-Q. Zhang, Z.-W. Wang, Y. Jia, M.-Z. Wang, S.-S. Dong, J.-F. Yang, Y.-N. Jiao, Y.-L. Guo, H.-Z. Kong, A.-M. Lu, S.-Z. Zhang, Y. Van de Peer, Z.-J. Liu & Z.-D. Chen. 2020. The hornwort genome and early land plant evolution. Nature Plants (2020). pdf  or here.

 

Abstract reads: Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.

Former EEB undergraduate Nicholas Russo, now a graduate student at UCLA, published his study of birds eating mosses in sub-Antarctic  Chile: Russo N.J., M. Robertson, R. MacKenzie, B. Goffinet & J.E. Jimenez. 2020. Evidence of targeted consumption of mosses by birds in sub-Antarctic South America. Austral Ecology 45: 399–403.pdf

Abstract reads: Bryophyte consumption is uncommon among bird species globally and is often presumed incidental. We sought to determine whether herbivorous bird species of the high Andes, including the white-bellied seedsnipe (Attagis malouinus) and Chloephaga geese (C. picta and C. poliocephala), consume bryophytes, and if so, how frequently. We collected 26 seedsnipe and 22 goose droppings from alpine and sub-alpine habitats of Navarino Island, Chile and examined their contents for bryophyte diaspores. We detected bryophyte fragments in 84.6% and 90.9% of seedsnipe and Chloephaga goose faecal samples, respectively. We also extracted DNA from three bryophyte fragments isolated from goose droppings and sequenced three chloroplast loci for each sample. We inferred through a barcoding analysis that at least one species of Chloephaga goose consumes Polytrichum strictum and Notoligotrichum trichodon. The composition of 11 collected goose droppings was >50% Polytrichaceae bryophyte fragments, suggesting that at least one Chloephaga goose species foraged deliberately on moss species of this family. These new observations suggest that bryophytes are part of the diet of some high Andean birds and that birds might disperse bryophytes internally – via endozoochory – in the sub-Antarctic.

Bernard Goffinet and William R. Buck have updated the on-line classification of extant mosses integrating most generic and supra generic taxa described to 2019. The classification now accommodates 969 genera!

Dong S., C. Zhao, S. Zhang, L. Zhang, H. Wu, R. Zhu, Y. Jia, B. Goffinet & Y. Liu. 2020. Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination. BMC Genomics 20: 953. pdf

Abstract reads: Background: In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available mt genomes of 18 liverwort accessions representing nine genera and five orders are syntenous except for Gymnomitrion concinnatum whose genome is characterized by two rearrangements. Here, we expanded the number of assembled liverwort mt genomes to 47, broadening the sampling to 31 genera and 10 orders spanning much of the phylogenetic breadth of liverworts to further test whether the evolution of the liverwort mitogenome is overall static. Results: Liverwort mt genomes range in size from 147 Kb in Jungermanniales (clade B) to 185 Kb in Marchantiopsida, mainly due to the size variation of intergenic spacers and number of introns. All newly assembled liverwort mt genomes hold a conserved set of genes, but vary considerably in their intron content. The loss of introns in liverwort mt genomes might be explained by localized retroprocessing events. Liverwort mt genomes are strictly syntenous in genome structure with no structural variant detected in our newly assembled mt genomes. However, by screening the paired-end reads, we do find rare cases of recombination, which means multiple concurrent genome structures may exist in the vegetative tissues of liverworts. Our phylogenetic analyses of the nuclear encoded double stand break repair protein families revealed liverwort-specific subfamilies expansions. Conclusions: The low repeat recombination level, selection, along with the intensified nuclear surveillance, might together shape the structural evolution of liverwort mt genomes.

Dong S., C. Zhao, S. Zhang, H. Wu, W. Mu, T. Wei, N. Li, H. Liu, J. Cui, R. Zhu, B. Goffinet & Y. Liu. 2020. The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity. Genome Biology and Evolution 11: 3233–3239. pdf

Abstract reads: RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here, we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded pentatricopeptide repeat (PPR) proteins in the transcriptome assemblies of these taxa.We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059 PPR protein sequences. The abundance of organellar RNA editing sites varies greatly among liverwort lineages, genes, and codon positions, and shows strong positive correlations with the GC content of protein-coding genes, and the diversity of the PLS class of nuclear PPR proteins.

 

The Art of Organisms Living in the Extreme

The American Bryological and Lichenological Society awarded Dong S., J.-Y. Xue, S. Zhang, L. Zhang, H. Wu, Z. Chen, B. Goffinet & Yang Liu the Sullivan award for best paper on bryology published in the Bryologist in 2018 (volume 121) for their article entitled “Complete mitochondrial genome sequence of Anthoceros angustus: conservative evolution of mitogenome in hornworts” and published in The Bryologist 121: 14–22. https://doi.org/10.1639/0007-2745-122.1.130

The editors of the Journal of Systematics and Evolution awarded the Special Issue Paper Award to Medina, R., M. G. Johnson, Y. Liu, N.J. Wickett, A.J. Shaw & B. Goffinet for their article entitled “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

Undergraduate research and work opportunities

In Evolutionary Biology Fall 2019

As part of a study funded by the National Science Foundation focused on the evolutionary significance of whole genome duplication in plants (we use mosses as model systems) we seek to fill TWO POSITIONS with BIO or EEB majors interested in evolutionary biology (see advertisement: Undergraduate research and work opportunities):

1. Maintain cultures of mosses: we establish and propagate cultures of mosses for genome analysis, reproduction biology experiments and morphological study
2. Process DNA sample (extraction, amplification and sequencing) for phylogenetic analysis

Prerequisites: BIOL 1108 or BIOL 1110

Number of hours weekly: 6-8

Open for credit (1 credit = 3 hours) or compensation 

Deadline for application: Sept 6, 2019

Contact bernard.goffinet@uconn.edu.

Subject line: bryology position

The Goffinet Lab (see http://bryology.eeb.uconn.edu):

We study the evolution and systematics of plants with a focus on mosses, liverworts, and hornworts, and also of fungi, namely those establishing permanent symbiotic associations, called lichens. Past undergrads have done projects addressing a variety of questions and acquiring experience in DNA extraction, amplification and sequencing, estimating genome size via flow cytometry, analysis of morphological traits, assessing phenotypic signatures following genome duplication, sterile cultures techniques for moss propagation, and lichen barcoding.

The evo-devo model species Physcomitrella patens has a new name!

Medina, R., M. G. Johnson, Y. Liu, N.J. Wickett, A.J. Shaw & B. Goffinet. 2019. Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on nuclear targeted exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma. Journal of Systematics and Evolution 57: 404–417. pdf

Abstract reads: Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with reduced architectures. The Funariaceae are a cosmopolitan and diverse lineage of mostly annual mosses, and exhibit variable sporophyte complexities, spanning from long, exerted, operculate capsules with two rings of well‐developed teeth, to capsules immersed among maternal leaves, lacking a differentiated line of dehiscence (i.e., inoperculate) and without peristomes. The family underwent a rapid diversification, and the relationships of taxa with reduced sporophytes remain ambiguous. Here, we infer the relationships of five taxa with highly reduced sporophytes based on 648 nuclear loci (exons complemented by their flanking regions), based on inferences from concatenated data and concordance analysis of single gene trees. Physcomitrellopsis is resolved as nested within one clade of Entosthodon. Physcomitrella s. l., is resolved as a polyphyletic assemblage and, along with its putative relative Aphanorrhegma, nested within Physcomitrium. We propose a new monophyletic delineation of Physcomitrium, which accommodates species of Physcomitrella and Aphanorrhegma. The monophyly of Physcomitrium s. l. is supported by a small plurality of exons, but a majority of trees inferred from exons and their adjacent non‐coding regions.

Widhelm T.J., F. Grewe, J. P. Huang, J. Mercado, B. Goffinet, R. Lücking, I. Schmitt, B. Moncada, R. Mason-Gamer & H. T. Lumbsch. 2019. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Scientific Reports 9: 8968. pdf

Abstract reads: In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.