1
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Świsłowski P, Domagała PJ, Rajfur M. The Genetic Diversity of Pleurozium schreberi: A Preliminary Study Based on the atpB-rbcL. PLANTS (BASEL, SWITZERLAND) 2023; 12:3487. [PMID: 37836227 PMCID: PMC10574878 DOI: 10.3390/plants12193487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
Pleurozium schreberi is a common and widespread species that has been the object of many studies, and its biology and ecology are well known. However, genetic studies on this species are limited or even absent. Because of the lack of any data about the genetic diversity of the moss species P. schreberi in Poland, the present paper describes the results of the studies carrying out for the first time this kind of research based on the atpB-rbcL spacer sequences of chloroplast DNA. A total of 35 specimens of P. schreberi from 19 locations in Poland were sampled. Total genomic DNA was extracted, amplified, and sequenced, and all obtained sequences were analyzed. Our findings suggest the low genetic diversity of P. schreberi in Poland. We detected four different haplotypes, shared between different populations.
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Affiliation(s)
- Paweł Świsłowski
- Institute of Biology, University of Opole, Oleska St. 22, 45-052 Opole, Poland; (P.J.D.); (M.R.)
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2
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Zhao J, Pu X, Li W, Li M. Characterization and evolutionary diversification of the phospholipase D gene family in mosses. Front Genet 2022; 13:1015393. [PMID: 36313445 PMCID: PMC9607936 DOI: 10.3389/fgene.2022.1015393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Plant phospholipase D (PLD) exerts important roles in various biological processes, such as intracellular signaling and morphological development. Our knowledge about early land plant PLDs is still underdeveloped. In this study, we identified 84 PLD genes in six mosses, i.e., Physcomitrella patens, Ceratodon purpureus, Fontinalis antipyretica, Pleurozium schreberi, Sphagnum magellanicum, and Sphagnum fallax. These PLDs were classified into four clades (I–IV). We showed that PLD underwent rapid expansion in mosses. A total of six conserved domains and two core HKD motifs were detected. Structure analysis uncovered that the moss PLDs from within a clade generally exhibited similar exon-intron organization. Cis-elements prediction and expression analyses indicated that P. patens PLDs had key roles in stress responsiveness and plant development. Particularly, about half of the P. patens PLDs (e.g., PpPLD1, PpPLD2, and PpPLD5) were differentially expressed under biotic and abiotic stresses. We also determined the expression pattern of P. patens PLD genes in various tissues and at different stages of development. Although the moss, clubmoss, liverwort, and fern PLDs evolved largely under functional constraints, we found episodic positive selection in the moss PLDs, e.g., C. purpureus PLD2 and P. patens PLD11. We infer that the evolutionary force acting on the PLDs may have facilitated moss colonization of land. Our work provides valuable insights into the diversification of moss PLD genes, and can be used for future studies of their functions.
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Affiliation(s)
- Jinjie Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Xinyuan Pu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Wenfei Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, Yunnan, China
| | - Meng Li
- Yunnan Academy of Tobacco Science, Kunming, Yunnan, China
- *Correspondence: Meng Li,
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3
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Fernandez-Pozo N, Haas FB, Gould SB, Rensing SA. An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4291-4305. [PMID: 35148385 DOI: 10.1093/jxb/erac052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes are useful models for the study of plant evolution, development, plant-fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Subtropical and Mediterranean Fruit Crops, Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-CSIC-UMA), Málaga, Spain
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Sven B Gould
- Evolutionary Cell Biology, Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
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4
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Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4306-4322. [PMID: 35437589 DOI: 10.1093/jxb/erac127] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.
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Affiliation(s)
- Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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5
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Bowles AMC, Paps J, Bechtold U. Water-related innovations in land plants evolved by different patterns of gene cooption and novelty. THE NEW PHYTOLOGIST 2022; 235:732-742. [PMID: 35048381 PMCID: PMC9303528 DOI: 10.1111/nph.17981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/25/2021] [Indexed: 05/26/2023]
Abstract
The origin of land plants and their descendants was marked by the evolution of key adaptations to life in terrestrial environments such as roots, vascular tissue and stomata. Though these innovations are well characterized, the evolution of the genetic toolkit underlying their development and function is poorly understood. We analysed molecular data from 532 species to investigate the evolutionary origin and diversification of genes involved in the development and regulation of these adaptations. We show that novel genes in the first land plants led to the single origin of stomata, but the stomatal closure of seed plants resulted from later gene expansions. By contrast, the major mechanism leading to the origin of vascular tissue was cooption of genes that emerged in the first land plants, enabling continuous water transport throughout the ancestral vascular plant. In turn, new key genes in the ancestors of plants with true leaves and seed plants led to the emergence of roots and lateral roots. The analysis highlights the different modes of evolution that enabled plants to conquer land, suggesting that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history.
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Affiliation(s)
- Alexander M. C. Bowles
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Geographical SciencesUniversity of BristolUniversity RoadBristolBS8 1RLUK
| | - Jordi Paps
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Ulrike Bechtold
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- Present address:
Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
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6
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Qiao X, Zhang S, Paterson AH. Pervasive genome duplications across the plant tree of life and their links to major evolutionary innovations and transitions. Comput Struct Biotechnol J 2022; 20:3248-3256. [PMID: 35782740 PMCID: PMC9237934 DOI: 10.1016/j.csbj.2022.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 01/09/2023] Open
Abstract
Whole-genome duplication (WGD) has occurred repeatedly during plant evolution and diversification, providing genetic layers for evolving new functions and phenotypes. Advances in long-read sequencing technologies have enabled sequencing and assembly of over 1000 plant genomes spanning nearly 800 species, in which a large set of ancient WGDs has been uncovered. Here, we review the recently reported WGDs that occurred in major plant lineages and key evolutionary positions, and highlight their contributions to morphological innovation and adaptive evolution. Current gaps and challenges in integrating enormous volumes of sequenced plant genomes, accurately inferring WGDs, and developing web-based analysis tools are emphasized. Looking to the future, ambitious genome sequencing projects and global efforts may substantially recapitulate the plant tree of life based on broader sampling of phylogenetic diversity, reveal much of the timetable of ancient WGDs, and address the biological significance of WGDs in plant adaptation and radiation.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605, USA,Corresponding author.
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7
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Pucker B, Irisarri I, de Vries J, Xu B. Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. QUANTITATIVE PLANT BIOLOGY 2022; 3:e5. [PMID: 37077982 PMCID: PMC10095996 DOI: 10.1017/qpb.2021.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/24/2021] [Accepted: 12/21/2021] [Indexed: 05/03/2023]
Abstract
Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.
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Affiliation(s)
- Boas Pucker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
- Author for correspondence: Boas Pucker E-mail:
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Göttingen, Germany
- Department of Applied Bioinformatics, Göttingen Center for Molecular Biosciences (GZMB), University of Goettingen, Göttingen, Germany
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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8
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de Vries S, de Vries J. Evolutionary genomic insights into cyanobacterial symbioses in plants. QUANTITATIVE PLANT BIOLOGY 2022; 3:e16. [PMID: 37077989 PMCID: PMC10095879 DOI: 10.1017/qpb.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 05/03/2023]
Abstract
Photosynthesis, the ability to fix atmospheric carbon dioxide, was acquired by eukaryotes through symbiosis: the plastids of plants and algae resulted from a cyanobacterial symbiosis that commenced more than 1.5 billion years ago and has chartered a unique evolutionary path. This resulted in the evolutionary origin of plants and algae. Some extant land plants have recruited additional biochemical aid from symbiotic cyanobacteria; these plants associate with filamentous cyanobacteria that fix atmospheric nitrogen. Examples of such interactions can be found in select species from across all major lineages of land plants. The recent rise in genomic and transcriptomic data has provided new insights into the molecular foundation of these interactions. Furthermore, the hornwort Anthoceros has emerged as a model system for the molecular biology of cyanobacteria-plant interactions. Here, we review these developments driven by high-throughput data and pinpoint their power to yield general patterns across these diverse symbioses.
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Affiliation(s)
- Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
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9
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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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10
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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11
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Stuart RK, Pederson ERA, Weyman PD, Weber PK, Rassmussen U, Dupont CL. Bidirectional C and N transfer and a potential role for sulfur in an epiphytic diazotrophic mutualism. THE ISME JOURNAL 2020; 14:3068-3078. [PMID: 32814866 PMCID: PMC7784912 DOI: 10.1038/s41396-020-00738-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/09/2020] [Accepted: 08/05/2020] [Indexed: 01/23/2023]
Abstract
In nitrogen-limited boreal forests, associations between feathermoss and diazotrophic cyanobacteria control nitrogen inputs and thus carbon cycling, but little is known about the molecular regulators required for initiation and maintenance of these associations. Specifically, a benefit to the cyanobacteria is not known, challenging whether the association is a nutritional mutualism. Targeted mutagenesis of the cyanobacterial alkane sulfonate monooxygenase results in an inability to colonize feathermosses by the cyanobacterium Nostoc punctiforme, suggesting a role for organic sulfur in communication or nutrition. Isotope probing paired with high-resolution imaging mass spectrometry (NanoSIMS) demonstrated bidirectional elemental transfer between partners, with carbon and sulfur both being transferred to the cyanobacteria, and nitrogen transferred to the moss. These results support the hypothesis that moss and cyanobacteria enter a mutualistic exosymbiosis with substantial bidirectional material exchange of carbon and nitrogen and potential signaling through sulfur compounds.
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Affiliation(s)
- Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
| | - Eric R A Pederson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Philip D Weyman
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
- Zymergen Inc., Emeryville, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Ulla Rassmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
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12
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Yu J, Li L, Wang S, Dong S, Chen Z, Patel N, Goffinet B, Chen H, Liu H, Liu Y. Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta). GIGABYTE 2020; 2020:gigabyte8. [PMID: 36824590 PMCID: PMC9631980 DOI: 10.46471/gigabyte.8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/13/2020] [Indexed: 11/09/2022] Open
Abstract
Mosses comprise one of three lineages forming a sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to, and colonization of, land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss that is widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo-assembled its genome using the 10X Genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO Viridiplantae odb10 dataset. The newly generated F. antipyretica genome is the third moss genome, and the second seedless aquatic plant genome, to be sequenced and assembled to date.
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Affiliation(s)
- Jin Yu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Shanshan Dong
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
| | - Ziqiang Chen
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130012, China
| | - Nikisha Patel
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Hongfeng Chen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen & China National GeneBank, Shenzhen 518083, China,Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China, Corresponding author. E-mail:
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13
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Kirbis A, Waller M, Ricca M, Bont Z, Neubauer A, Goffinet B, Szövényi P. Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica. FRONTIERS IN PLANT SCIENCE 2020; 11:747. [PMID: 32587596 PMCID: PMC7299128 DOI: 10.3389/fpls.2020.00747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 05/03/2023]
Abstract
Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators.
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Affiliation(s)
- Alexander Kirbis
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Mariana Ricca
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Zoe Bont
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
- *Correspondence: Péter Szövényi,
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