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Lesch E, Stempel MS, Dressnandt V, Oldenkott B, Knoop V, Schallenberg-Rüdinger M. Conservation of the moss RNA editing factor PPR78 despite the loss of its known cytidine-to-uridine editing sites is explained by a hidden extra target. THE PLANT CELL 2024; 36:727-745. [PMID: 38000897 PMCID: PMC10896298 DOI: 10.1093/plcell/koad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/27/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023]
Abstract
Cytidine (C)-to-uridine (U) RNA editing in plant organelles relies on specific RNA-binding pentatricopeptide repeat (PPR) proteins. In the moss Physcomitrium patens, all such RNA editing factors feature a C-terminal DYW domain that acts as the cytidine deaminase for C-to-U conversion. PPR78 of Physcomitrium targets 2 mitochondrial editing sites, cox1eU755SL and rps14eU137SL. Remarkably, the latter is edited to highly variable degrees in different mosses. Here, we aimed to unravel the coevolution of PPR78 and its 2 target sites in mosses. Heterologous complementation in a Physcomitrium knockout line revealed that the variable editing of rps14eU137SL depends on the PPR arrays of different PPR78 orthologues but not their C-terminal domains. Intriguingly, PPR78 has remained conserved despite the simultaneous loss of editing at both known targets among Hypnales (feather mosses), suggesting it serves an additional function. Using a recently established RNA editing assay in Escherichia coli, we confirmed site-specific RNA editing by PPR78 in the bacterium and identified 4 additional off-targets in the bacterial transcriptome. Based on conservation profiles, we predicted ccmFNeU1465RC as a candidate editing target of PPR78 in moss mitochondrial transcriptomes. We confirmed editing at this site in several mosses and verified that PPR78 targets ccmFNeU1465RC in the bacterial editing system, explaining the conservation and functional adaptation of PPR78 during moss evolution.
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Affiliation(s)
- Elena Lesch
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Maike Simone Stempel
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Vanessa Dressnandt
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Bastian Oldenkott
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Volker Knoop
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
| | - Mareike Schallenberg-Rüdinger
- IZMB-Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn D-53115, Germany
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2
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Filippova IP, Makhutova ON, Guseynova VE, Gladyshev MI. Fatty Acid Profiles of Some Siberian Bryophytes and Prospects of Their Use in Chemotaxonomy. Biomolecules 2023; 13:biom13050840. [PMID: 37238711 DOI: 10.3390/biom13050840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/09/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The composition of fatty acids (FAs) in gametophyte samples of 20 Siberian bryophyte species from four orders of mosses and four orders of liverworts collected in relatively cold months (April and/or October) was examined. FA profiles were obtained using gas chromatography. Thirty-seven FAs were found, from 12:0 to 26:0; they included mono-, polyunsaturated (PUFAs) and rare FAs, such as 22:5n-3 and two acetylenic FAs, 6a,9,12-18:3 and 6a,9,12,15-18:4 (dicranin). Acetylenic FAs were found in all examined species of the Bryales and Dicranales orders, dicranin being the predominant FA. The role of particular PUFAs in mosses and liverworts is discussed. Multivariate discriminant analysis (MDA) was performed to determine whether FAs can be used in the chemotaxonomy of bryophytes. Based on the MDA results, FA composition is related to the taxonomic status of species. Thus, several individual FAs were identified as chemotaxonomic markers at the level of bryophyte orders. These were 18:3n-3; 18:4n-3; 6a,9,12-18:3; 6a,9,12,15-18:4; 20:4n-3 and EPA in mosses and 16:3n-3; 16:2n-6; 18:2n-6; 18:3n-3 and EPA in liverworts. These findings indicate that further research into bryophyte FA profiles can shed light on phylogenetic relationships within this group of plants and the evolution of their metabolic pathways.
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Affiliation(s)
- Irina P Filippova
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
| | - Olesia N Makhutova
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
- Institute of Biophysics, Krasnoyarsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Valeriya E Guseynova
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
| | - Michail I Gladyshev
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodny av., Krasnoyarsk 660041, Russia
- Institute of Biophysics, Krasnoyarsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
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3
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Abstract
Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and likely enabled adaptation under harsh conditions. Besides genomic data, transcriptome data have been widely employed to detect WGDs, due to their efficient accessibility to the gene space of a species. Age distributions based on synonymous substitutions (so-called KS age distributions) for paralogs assembled from transcriptome data have identified numerous WGDs in plants, paving the way for further studies on the importance of WGDs for the evolution of seed and flowering plants. However, it is still unclear how transcriptome-based age distributions compare to those based on genomic data. In this chapter, we implemented three different de novo transcriptome assembly pipelines with two popular assemblers, i.e., Trinity and SOAPdenovo-Trans. We selected six plant species with published genomes and transcriptomes to evaluate how assembled transcripts from different pipelines perform when using KS distributions to detect previously documented WGDs in the six species. Further, using genes predicted in each genome as references, we evaluated the effects of missing genes, gene family clustering, and de novo assembled transcripts on the transcriptome-based KS distributions. Our results show that, although the transcriptome-based KS distributions differ from the genome-based ones with respect to their shapes and scales, they are still reasonably reliable for unveiling WGDs, except in species where most duplicates originated from a recent WGD. We also discuss how to overcome some possible pitfalls when using transcriptome data to identify WGDs.
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Affiliation(s)
- Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
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4
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Slimp M, Williams LD, Hale H, Johnson MG. On the potential of Angiosperms353 for population genomic studies. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311419. [PMID: 34336401 PMCID: PMC8312745 DOI: 10.1002/aps3.11419] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 05/11/2023]
Abstract
PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)-typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens.
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Affiliation(s)
- Madeline Slimp
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Lindsay D. Williams
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Haley Hale
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech University2901 Main StreetLubbockTexas79409USA
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5
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Carey SB, Jenkins J, Lovell JT, Maumus F, Sreedasyam A, Payton AC, Shu S, Tiley GP, Fernandez-Pozo N, Healey A, Barry K, Chen C, Wang M, Lipzen A, Daum C, Saski CA, McBreen JC, Conrad RE, Kollar LM, Olsson S, Huttunen S, Landis JB, Burleigh JG, Wickett NJ, Johnson MG, Rensing SA, Grimwood J, Schmutz J, McDaniel SF. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. SCIENCE ADVANCES 2021; 7:7/27/eabh2488. [PMID: 34193417 PMCID: PMC8245031 DOI: 10.1126/sciadv.abh2488] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/14/2021] [Indexed: 05/19/2023]
Abstract
Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.
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Affiliation(s)
- Sarah B Carey
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Florian Maumus
- Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam C Payton
- Department of Biology, University of Florida, Gainesville, FL, USA
- RAPiD Genomics, Gainesville, FL, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Jordan C McBreen
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Leslie M Kollar
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA-CIFOR, Madrid, Spain
| | - Sanna Huttunen
- Department of Biology and Biodiversity Unit, University of Turku, Turku, Finland
| | - Jacob B Landis
- L.H. Bailey Hortorium and Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, USA
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Stefan A Rensing
- Plant Cell Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg im Breisgau, Germany
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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6
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Szövényi P, Gunadi A, Li FW. Charting the genomic landscape of seed-free plants. NATURE PLANTS 2021; 7:554-565. [PMID: 33820965 DOI: 10.1038/s41477-021-00888-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 05/02/2023]
Abstract
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
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Affiliation(s)
- Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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7
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High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae. Mol Phylogenet Evol 2020; 154:106965. [PMID: 32956800 DOI: 10.1016/j.ympev.2020.106965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
A new paradigm has slowly emerged regarding the diversification of bryophytes, with inferences from molecular data highlighting a dynamic evolution of their genome. However, comparative studies of expressed genes among closely related taxa is so far missing. Here we contrast the dimensions of the vegetative transcriptome of Funaria hygrometrica and Physcomitrium pyriforme against the genome of their relative, Physcomitrium (Physcomitrella) patens. These three species of Funariaceae share highly conserved vegetative bodies, and are partially sympatric, growing on mineral soil in mostly temperate regions. We analyzed the vegetative gametophytic transcriptome of F. hygrometrica and P. pyriforme and mapped short reads, transcripts, and proteins to the genome and gene space of P. patens. Only about half of the transcripts of F. hygrometrica map to their ortholog in P. patens, whereas at least 90% of those of P. pyriforme align to loci in P. patens. Such divergence is unexpected given the high morphological similarity of the gametophyte but reflects the estimated times of divergence of F. hygrometrica and P. pyriforme from P. patens, namely 55 and 20 mya, respectively. The newly sampled transcriptomes bear signatures of at least one, rather ancient, whole genome duplication (WGD), which may be shared with one reported for P. patens. The transcriptomes of F. hygrometrica and P. pyriforme reveal significant contractions or expansions of different gene families. While transcriptomes offer only an incomplete estimate of the gene space, the high number of transcripts obtained suggest a significant divergence in gene sequences, and gene number among the three species, indicative of a rather strong, dynamic genome evolution, shaped in part by whole, partial or localized genome duplication. The gene ontology of their specific and rapidly-evolving protein families, suggests that the evolution of the Funariaceae may have been driven by the diversification of metabolic genes that may optimize the adaptations to environmental conditions, a hypothesis well in line with ecological patterns in the genetic diversity and structure in seed plants.
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8
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Carey SB, Jenkins J, Lovell JT, Maumus F, Sreedasyam A, Payton AC, Shu S, Tiley GP, Fernandez-pozo N, Barry K, Chen C, Wang M, Lipzen A, Daum C, Saski CA, Mcbreen JC, Conrad RE, Kollar LM, Olsson S, Huttunen S, Landis JB, Burleigh JG, Wickett NJ, Johnson MG, Rensing SA, Grimwood J, Schmutz J, Mcdaniel SF. The Ceratodon purpureus genome uncovers structurally complex, gene rich sex chromosomes.. [PMID: 0 DOI: 10.1101/2020.07.03.163634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
AbstractNon-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration1,2. The correlation between suppressed recombination and degeneration is clear in animal XY systems1,2, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions3,4. Here we test for degeneration in the bryophyte UV sex chromosome system through genomic comparisons with new female and male chromosome-scale reference genomes of the moss Ceratodon purpureus. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.
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9
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Godden GT, Kinser TJ, Soltis PS, Soltis DE. Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints. Genome Biol Evol 2020; 11:3393-3408. [PMID: 31687761 PMCID: PMC7145710 DOI: 10.1093/gbe/evz239] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. Although mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7–18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the nonuniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.
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Affiliation(s)
- Grant T Godden
- Florida Museum of Natural History, University of Florida
| | - Taliesin J Kinser
- Florida Museum of Natural History, University of Florida.,Department of Biology, University of Florida
| | | | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida.,Department of Biology, University of Florida
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10
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Bainard JD, Newmaster SG, Budke JM. Genome size and endopolyploidy evolution across the moss phylogeny. ANNALS OF BOTANY 2020; 125:543-555. [PMID: 31777923 PMCID: PMC7102977 DOI: 10.1093/aob/mcz194] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 11/27/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Compared with other plant lineages, bryophytes have very small genomes with little variation across species, and high levels of endopolyploid nuclei. This study is the first analysis of moss genome evolution over a broad taxonomic sampling using phylogenetic comparative methods. We aim to determine whether genome size evolution is unidirectional as well as examine whether genome size and endopolyploidy are correlated in mosses. METHODS Genome size and endoreduplication index (EI) estimates were newly generated using flow cytometry from moss samples collected in Canada. Phylogenetic relationships between moss species were reconstructed using GenBank sequence data and maximum likelihood methods. Additional 1C-values were compiled from the literature and genome size and EI were mapped onto the phylogeny to reconstruct ancestral character states, test for phylogenetic signal and perform phylogenetic independent contrasts. KEY RESULTS Genome size and EI were obtained for over 50 moss taxa. New genome size estimates are reported for 33 moss species and new EIs are reported for 20 species. In combination with data from the literature, genome sizes were mapped onto a phylogeny for 173 moss species with this analysis, indicating that genome size evolution in mosses does not appear to be unidirectional. Significant phylogenetic signal was detected for genome size when evaluated across the phylogeny, whereas phylogenetic signal was not detected for EI. Genome size and EI were not found to be significantly correlated when using phylogenetically corrected values. CONCLUSIONS Significant phylogenetic signal indicates closely related mosses have more similar genome sizes and EI values. This study supports that DNA content in mosses is defined by small genomes that are highly endopolyploid, suggesting strong selective pressure to maintain these features. Further research is needed to understand the functional significance of DNA content evolution in mosses.
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Affiliation(s)
- Jillian D Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-food Canada, Swift Current, SK, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Steven G Newmaster
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Jessica M Budke
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
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11
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Cerbin S, Wai CM, VanBuren R, Jiang N. GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals. Genome Biol Evol 2020; 11:3181-3193. [PMID: 31633753 PMCID: PMC6839031 DOI: 10.1093/gbe/evz230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2019] [Indexed: 02/06/2023] Open
Abstract
Transposable elements represent the largest components of many eukaryotic genomes and different genomes harbor different combinations of elements. Here, we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla. Further searching for related sequences to the conserved DDE region uncovered the presence of this superfamily of elements in fish, coral, sea anemone, and other animal species. However, this element appears restricted to Bryophytes and Lycophytes in plants. This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100-150 bp terminal inverted repeats. Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons, the most abundant component in plant genomes. A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla. Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes, which contrasts to the compact genome size of about 100 Mb. Nevertheless, a considerable portion of GingerRoot elements was found to carry gene fragments, suggesting the capacity of duplicating gene sequences is unlikely attributed to the proximity to genes. Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments, indicating they are preferentially retained in gene-poor regions. This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase, suggesting the possibility of de novo formation of Gypsy-like elements in plants.
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Affiliation(s)
- Stefan Cerbin
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
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12
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Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss. G3-GENES GENOMES GENETICS 2019; 9:2791-2797. [PMID: 31285273 PMCID: PMC6723128 DOI: 10.1534/g3.119.400279] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The pleurocarpous feather moss Pleurozium schreberi is a ubiquitous moss species which plays a fundamental role in many terrestrial ecosystems, for instance within the boreal forest, the Earth's largest terrestrial biome, this species plays a significant role in driving ecosystem nitrogen and carbon inputs and fluxes. By hosting dinitrogen (N2)-fixing cyanobacteria, the moss-cyanobacteria symbiosis constitutes the main nitrogen input into the ecosystem and by the high productivity and the low decomposability of the moss litter, P schreberi contributes significantly to build-up soil organic matter, and therefore long-term C sequestration. Knowledge on P. schreberi genome will facilitate the development of 'omics' and system's biology approaches to gain a more complete understanding of the physiology and ecological adaptation of the moss and the mechanisms underpinning the establishment of the symbiosis. Here we present the de novo assembly and annotation of P. schreberi genome that will help investigating these questions. The sequencing was performed using the HiSeq X platform with Illumina paired-end and mate-pair libraries prepared with CTAB extracted DNA. In total, the assembled genome was approximately 318 Mb, while repetitive elements account for 28.42% of the genome and 15,992 protein-coding genes were predicted from the genome, of which 84.23% have been functionally annotated. We anticipate that the genomic data generated will constitute a significant resource to study ecological and evolutionary genomics of P. schreberi, and will be valuable for evo-devo investigations as well as our understanding of the evolution of land plants by providing the genome of a pleurocarpous moss.
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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Phylogenet Evol 2019; 134:12-23. [DOI: 10.1016/j.ympev.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/28/2023]
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Tiley GP, Barker MS, Burleigh JG. Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications. Genome Biol Evol 2018; 10:2882-2898. [PMID: 30239709 PMCID: PMC6225891 DOI: 10.1093/gbe/evy200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “Ks plots.” For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention rates following WGD on inferring WGDs from Ks plots. Our simulations reveal limitations of Ks plot analyses. Strict interpretations of mixture model analyses often overestimate the number of WGD events, and Ks plot analyses typically fail to detect WGDs when ≤10% of the duplicated genes are retained following the WGD. However, WGDs can accurately be characterized over an intermediate range of Ks. The simulation results are supported by empirical analyses of transcriptomic data, which also suggest that biases in gene retention likely affect our ability to detect ancient WGDs. Although our results indicate mixture model results should be interpreted with great caution, using node-averaged Ks estimates and applying more appropriate mixture models can improve the accuracy of detecting WGDs.
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Affiliation(s)
- George P Tiley
- Department of Biology, University of Florida.,Department of Biology, Duke University
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona
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15
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Monitoring of elements in mosses by instrumental neutron activation analysis and total X-ray fluorescence spectrometry. J Radioanal Nucl Chem 2018. [DOI: 10.1007/s10967-018-5896-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Parks MB, Nakov T, Ruck EC, Wickett NJ, Alverson AJ. Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). AMERICAN JOURNAL OF BOTANY 2018; 105:330-347. [PMID: 29665021 DOI: 10.1002/ajb2.1056] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/18/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and primary productivity motivate comparisons to angiosperms, whose genomes have been inordinately shaped by whole-genome duplication (WGD). WGDs have been linked to speciation, increased rates of lineage diversification, and identified as a principal driver of angiosperm evolution. We synthesized a large but scattered body of evidence that suggests polyploidy may be common in diatoms as well. METHODS We used gene counts, gene trees, and distributions of synonymous divergence to carry out a phylogenomic analysis of WGD across a diverse set of 37 diatom species. KEY RESULTS Several methods identified WGDs of varying age across diatoms. Determining the occurrence, exact number, and placement of events was greatly impacted by uncertainty in gene trees. WGDs inferred from synonymous divergence of paralogs varied depending on how redundancy in transcriptomes was assessed, gene families were assembled, and synonymous distances (Ks) were calculated. Our results highlighted a need for systematic evaluation of key methodological aspects of Ks-based approaches to WGD inference. Gene tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades. CONCLUSIONS Our results suggest that WGD has played a major role in the evolution of diatom genomes. We outline challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the impact of genome duplication in a group that likely harbors substantial genomic diversity.
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Affiliation(s)
- Matthew B Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Teofil Nakov
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR, 72701, USA
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, SCEN 601, Fayetteville, AR, 72701, USA
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17
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Medina R, Johnson M, Liu Y, Wilding N, Hedderson TA, Wickett N, Goffinet B. Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae. Mol Phylogenet Evol 2017; 120:240-247. [PMID: 29222063 DOI: 10.1016/j.ympev.2017.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/02/2017] [Accepted: 12/04/2017] [Indexed: 11/19/2022]
Abstract
Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.
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Affiliation(s)
- Rafael Medina
- University of Connecticut, Ecology and Evolutionary Biology, 75 N Eagleville Rd., Storrs, 06269 CT, USA; Augustana College, Department of Biology, 639 38th St. Rock, Island, 61201 IL, USA.
| | - Matthew Johnson
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022 USA; Texas Tech University, Department of Biological Sciences, 2901 Main Street, Lubbock, 79409 TX, USA
| | - Yang Liu
- University of Connecticut, Ecology and Evolutionary Biology, 75 N Eagleville Rd., Storrs, 06269 CT, USA; Key Laboratory of Southern Subtropical Plant Diversity, Shenzhen Fairy Lake Botanical Garden, Shenzhen 518004, China
| | - Nicholas Wilding
- University of La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410 Saint-Pierre, France; Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, 7701 Rondebosch, South Africa
| | - Terry A Hedderson
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, 7701 Rondebosch, South Africa
| | - Norman Wickett
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022 USA
| | - Bernard Goffinet
- University of Connecticut, Ecology and Evolutionary Biology, 75 N Eagleville Rd., Storrs, 06269 CT, USA.
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Coudert Y, Bell NE, Edelin C, Harrison CJ. Multiple innovations underpinned branching form diversification in mosses. THE NEW PHYTOLOGIST 2017; 215:840-850. [PMID: 28470778 PMCID: PMC5697605 DOI: 10.1111/nph.14553] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/27/2017] [Indexed: 05/22/2023]
Abstract
Broad-scale evolutionary comparisons have shown that branching forms arose by convergence in vascular plants and bryophytes, but the trajectory of branching form diversification in bryophytes is unclear. Mosses are the most species-rich bryophyte lineage and two sub-groups are circumscribed by alternative reproductive organ placements. In one, reproductive organs form apically, terminating growth of the primary shoot (gametophore) axis. In the other, reproductive organs develop on very short lateral branches. A switch from apical to lateral reproductive organ development is proposed to have primed branching form diversification. Moss gametophores have modular development and each module develops from a single apical cell. Here we define the architectures of 175 mosses by the number of module classes, branching patterns and the pattern in which similar modules repeat. Using ancestral character state reconstruction we identify two stages of architectural diversification. During a first stage there were sequential changes in the module repetition pattern, reproductive organ position, branching pattern and the number of module classes. During a second stage, vegetative changes occurred independently of reproductive fate. The results pinpoint the nature of developmental change priming branching form diversification in mosses and provide a framework for mechanistic studies of architectural diversification.
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Affiliation(s)
- Yoan Coudert
- School of Biological SciencesUniversity of BristolLife Sciences Building24 Tyndall AvenueBristolBS8 1TQUK
- Institute of Systematics, Evolution and BiodiversityCNRSNatural History Museum ParisUPMC Sorbonne UniversityEPHE57 rue Cuvier75005ParisFrance
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
| | - Neil E. Bell
- Royal Botanic Garden Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
| | - Claude Edelin
- UMR 3330UMIFRE 21French Institute of PondicherryCNRS11 Saint Louis StreetPondicherry605001India
| | - C. Jill Harrison
- School of Biological SciencesUniversity of BristolLife Sciences Building24 Tyndall AvenueBristolBS8 1TQUK
- Department of Plant SciencesUniversity of CambridgeDowning StreetCambridgeCB2 3EAUK
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