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Dorrell RG, Nef C, Altan-Ochir S, Bowler C, Smith AG. Presence of vitamin B 12 metabolism in the last common ancestor of land plants. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230354. [PMID: 39343018 PMCID: PMC11439496 DOI: 10.1098/rstb.2023.0354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 10/01/2024] Open
Abstract
Vitamin B12, also known as cobalamin, is an essential organic cofactor for methionine synthase (METH), and is only synthesized by a subset of bacteria. Plants and fungi have an alternative methionine synthase (METE) that does not need B12 and are typically considered not to utilize it. Some algae facultatively utilize B12 because they encode both METE and METH, while other algae are dependent on B12 as they encode METH only. We performed phylogenomic analyses of METE, METH and 11 further proteins involved in B12 metabolism across more than 1600 plant and algal genomes and transcriptomes (e.g. from OneKp), demonstrating the presence of B12-associated metabolism deep into the streptophytes. METH and five further accessory proteins (MTRR, CblB, CblC, CblD and CblJ) were detected in the hornworts (Anthocerotophyta), and two (CblB and CblJ) were identified in liverworts (Marchantiophyta) in the bryophytes, suggesting a retention of B12-metabolism in the last common land plant ancestor. Our data further show more limited distributions for other B12-related proteins (MCM and RNR-II) and B12 dependency in several algal orders. Finally, considering the collection sites of algae that have lost B12 metabolism, we propose freshwater-to-land transitions and symbiotic associations to have been constraining factors for B12 availability in early plant evolution. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Richard G. Dorrell
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative—UMR 7238, Sorbonne Université, 4 place Jussieu, 75005 Paris, France
| | - Charlotte Nef
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS,INSERM, Université PSL, Paris75005, France
| | - Setsen Altan-Ochir
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS,INSERM, Université PSL, Paris75005, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS,INSERM, Université PSL, Paris75005, France
| | - Alison G. Smith
- Department of Plant Sciences, University of Cambridge, CambridgeCB2 3EA, UK
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2
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Kunz CF, de Vries S, de Vries J. Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230358. [PMID: 39343031 DOI: 10.1098/rstb.2023.0358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 10/01/2024] Open
Abstract
Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes. This article is part of the theme issue 'The evolution of plant metabolism'.
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Affiliation(s)
- Cäcilia F Kunz
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen , Goettingen 37077, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen , Goettingen 37077, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen , Goettingen 37077, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen , Goettingen 37077, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettingen , Goettingen 37077, Germany
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3
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Kumazawa M, Ifuku K. Unraveling the evolutionary trajectory of LHCI in red-lineage algae: Conservation, diversification, and neolocalization. iScience 2024; 27:110897. [PMID: 39386759 PMCID: PMC11462038 DOI: 10.1016/j.isci.2024.110897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/21/2024] [Accepted: 09/04/2024] [Indexed: 10/12/2024] Open
Abstract
Red algae and the secondary symbiotic algae that engulfed a red alga as an endosymbiont are called red-lineage algae. Several photosystem (PS) I-light-harvesting complex I (LHCI) structures have been reported from red-lineage algae-two red algae Cyanidioschyzon merolae (Cyanidiophyceae) and Porphyridium purpureum (Rhodophytina), a diatom, and a Cryptophyte. Here, we clarified the orthologous relation of LHCIs by combining a detailed phylogenetic analysis and the structural information of PSI-LHCI. We found that the seven Lhcr groups in LHCI are conserved in Rhodophytina; furthermore, during both genome reduction in Cyanidioschyzonales and endosymbiosis leading to Cryptophyta, some LHCIs were lost and replaced by existing or differentiated LHCIs. We denominate "neolocalization" to these examples of flexible reorganization of LHCIs. This study provides insights into the evolutionary process of LHCIs in red-lineage algae and clarifies the need for both molecular phylogeny and structural information to elucidate the plausible evolutionary history of LHCI.
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Affiliation(s)
- Minoru Kumazawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Kentaro Ifuku
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan
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4
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Bierenbroodspot MJ, Pröschold T, Fürst-Jansen JMR, de Vries S, Irisarri I, Darienko T, de Vries J. Phylogeny and evolution of streptophyte algae. ANNALS OF BOTANY 2024; 134:385-400. [PMID: 38832756 PMCID: PMC11341676 DOI: 10.1093/aob/mcae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of probably >5000 species of streptophyte algae that form a paraphyletic grade next to land plants. Here, we focus on the deep divergences that gave rise to the diversity of streptophytes, hence particularly on the streptophyte algae. Phylogenomic efforts have not only clarified the position of streptophyte algae relative to land plants, but recent efforts have also begun to unravel the relationships and major radiations within streptophyte algal diversity. We illustrate how new phylogenomic perspectives have changed our view on the evolutionary emergence of key traits, such as intricate signalling networks that are intertwined with multicellular growth and the chemodiverse hotbed from which they emerged. These traits are key for the biology of land plants but were bequeathed from their algal progenitors.
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Affiliation(s)
- Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Thomas Pröschold
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Research Department for Limnology, University of Innsbruck, Mondseestr. 9, 5310 Mondsee, Austria
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- Section of Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Department of Experimental Phycology and Culture Collection of Algae, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstraße 1, 37077 Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
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5
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Bonchuk AN, Georgiev PG. C2H2 proteins: Evolutionary aspects of domain architecture and diversification. Bioessays 2024; 46:e2400052. [PMID: 38873893 DOI: 10.1002/bies.202400052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2-type zinc finger domains that specifically bind to DNA. Few well-studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks.
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Affiliation(s)
- Artem N Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel G Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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Bowles AMC, Williams TA, Donoghue PCJ, Campbell DA, Williamson CJ. Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land. THE NEW PHYTOLOGIST 2024. [PMID: 38840553 DOI: 10.1111/nph.19860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK
| | - Douglas A Campbell
- Department of Biology, Mount Allison University, Sackville, NB, E4L 1H3, Canada
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7
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Puginier C, Libourel C, Otte J, Skaloud P, Haon M, Grisel S, Petersen M, Berrin JG, Delaux PM, Dal Grande F, Keller J. Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae. Nat Commun 2024; 15:4452. [PMID: 38789482 PMCID: PMC11126685 DOI: 10.1038/s41467-024-48787-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.
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Affiliation(s)
- Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Juergen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Pavel Skaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800, Praha 2, Czech Republic
| | - Mireille Haon
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Sacha Grisel
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Malte Petersen
- High Performance Computing & Analytics Lab, University of Bonn, Friedrich-Hirzebruch-Allee 8, 53115, Bonn, Germany
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Department of Biology, University of Padova, Padua, Italy.
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
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8
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Rey Redondo E, Xu Y, Yung CCM. Genomic characterisation and ecological distribution of Mantoniella tinhauana: a novel Mamiellophycean green alga from the Western Pacific. Front Microbiol 2024; 15:1358574. [PMID: 38774501 PMCID: PMC11106453 DOI: 10.3389/fmicb.2024.1358574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Mamiellophyceae are dominant marine algae in much of the ocean, the most prevalent genera belonging to the order Mamiellales: Micromonas, Ostreococcus and Bathycoccus, whose genetics and global distributions have been extensively studied. Conversely, the genus Mantoniella, despite its potential ecological importance, remains relatively under-characterised. In this study, we isolated and characterised a novel species of Mamiellophyceae, Mantoniella tinhauana, from subtropical coastal waters in the South China Sea. Morphologically, it resembles other Mantoniella species; however, a comparative analysis of the 18S and ITS2 marker genes revealed its genetic distinctiveness. Furthermore, we sequenced and assembled the first genome of Mantoniella tinhauana, uncovering significant differences from previously studied Mamiellophyceae species. Notably, the genome lacked any detectable outlier chromosomes and exhibited numerous unique orthogroups. We explored gene groups associated with meiosis, scale and flagella formation, shedding light on species divergence, yet further investigation is warranted. To elucidate the biogeography of Mantoniella tinhauana, we conducted a comprehensive analysis using global metagenomic read mapping to the newly sequenced genome. Our findings indicate this species exhibits a cosmopolitan distribution with a low-level prevalence worldwide. Understanding the intricate dynamics between Mamiellophyceae and the environment is crucial for comprehending their impact on the ocean ecosystem and accurately predicting their response to forthcoming environmental changes.
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Affiliation(s)
| | | | - Charmaine Cheuk Man Yung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
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K. Raval P, MacLeod AI, Gould SB. A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms. PLoS Biol 2024; 22:e3002608. [PMID: 38713727 PMCID: PMC11135702 DOI: 10.1371/journal.pbio.3002608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 05/29/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander I. MacLeod
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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10
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Guiry MD. How many species of algae are there? A reprise. Four kingdoms, 14 phyla, 63 classes and still growing. JOURNAL OF PHYCOLOGY 2024; 60:214-228. [PMID: 38245909 DOI: 10.1111/jpy.13431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
To date (1 November 2023), the online database AlgaeBase has documented 50,589 species of living algae and 10,556 fossil species here referred to four kingdoms (Eubacteria, Chromista, Plantae, and Protozoa), 14 phyla, and 63 classes. The algae are the third most speciose grouping of plant-like organisms after the flowering plants (≈382,000 species) and fungi (≈170,000 species, including lichens) but are the least well defined of all the botanical groupings. Priority is given to phyla and class names that are familiar to phycologists and that are nomenclaturally valid. The most species-rich phylum is the Heterokontophyta to which 18 classes are referred with 21,052 living species and which is dominated by the diatoms in three classes with 18,673 species (16,427 living; 2239 fossil). The next most species-rich phyla are the red algae (7276 living), the green algae (6851 living), the blue-green algae (Cyanobacteria, 5723 living), the charophytes (4950 living, including the Charophyceae, 511 species living, and the Zygnematophyceae, 4335 living species), Dinoflagellata (2956 living, including the Dinophyceae, 2828 extant), and haptophytes (Haptophyta 1722 species, 517 living).
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Affiliation(s)
- Michael D Guiry
- AlgaeBase, Ryan Institute, University of Galway, University Road, Galway, Ireland
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11
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Liu M, Yu J, Yang M, Cao L, Chen C. Adaptive evolution of chloroplast division mechanisms during plant terrestrialization. Cell Rep 2024; 43:113950. [PMID: 38489264 DOI: 10.1016/j.celrep.2024.113950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/12/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Despite extensive research, the origin and evolution of the chloroplast division machinery remain unclear. Here, we employ recently sequenced genomes and transcriptomes of Archaeplastida clades to identify the core components of chloroplast division and reconstruct their evolutionary histories, respectively. Our findings show that complete division ring structures emerged in Charophytes. We find that Glaucophytes experienced strong selection pressure, generating diverse variants adapted to the changing terrestrial environments. By integrating the functions of chloroplast division genes (CDGs) annotated in a workflow developed using large-scale multi-omics data, we further show that dispersed duplications acquire more species-specific functions under stronger selection pressures. Notably, PARC6, a dispersed duplicate CDG, regulates leaf color and plant growth in Solanum lycopersicum, demonstrating neofunctionalization. Our findings provide an integrated perspective on the functional evolution of chloroplast division machinery and highlight the potential of dispersed duplicate genes as the primary source of adaptive evolution of chloroplast division.
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Affiliation(s)
- Moyang Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Yu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Yang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingyan Cao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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12
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Dhabalia Ashok A, Freitag JN, Irisarri I, de Vries S, de Vries J. Sequence similarity networks bear out hierarchical relationships of green cytochrome P450. PHYSIOLOGIA PLANTARUM 2024; 176:e14244. [PMID: 38480467 DOI: 10.1111/ppl.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Land plants have diversified enzyme families. One of the most prominent is the cytochrome P450 (CYP or CYP450) family. With over 443,000 CYP proteins sequenced across the tree of life, CYPs are ubiquitous in archaea, bacteria, and eukaryotes. Here, we focused on land plants and algae to study the role of CYP diversification. CYPs, acting as monooxygenases, catalyze hydroxylation reactions crucial for specialized plant metabolic pathways, including detoxification and phytohormone production; the CYPome consists of one enormous superfamily that is divided into clans and families. Their evolutionary history speaks of high substrate promiscuity; radiation and functional diversification have yielded numerous CYP families. To understand the evolutionary relationships within the CYPs, we employed sequence similarity network analyses. We recovered distinct clusters representing different CYP families, reflecting their diversified sequences that we link to the prediction of functionalities. Hierarchical clustering and phylogenetic analysis further elucidated relationships between CYP clans, uncovering their shared deep evolutionary history. We explored the distribution and diversification of CYP subfamilies across plant and algal lineages, uncovering novel candidates and providing insights into the evolution of these enzyme families. This identified unexpected relationships between CYP families, such as the link between CYP82 and CYP74, shedding light on their roles in plant defense signaling pathways. Our approach provides a methodology that brings insights into the emergence of new functions within the CYP450 family, contributing to the evolutionary history of plants and algae. These insights can be further validated and implemented via experimental setups under various external conditions.
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Affiliation(s)
- Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jella N Freitag
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettinzgen, Goettingen, Germany
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13
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Zhang Z, Diao R, Sun J, Liu Y, Zhao M, Wang Q, Xu Z, Zhong B. Diversified molecular adaptations of inorganic nitrogen assimilation and signaling machineries in plants. THE NEW PHYTOLOGIST 2024; 241:2108-2123. [PMID: 38155438 DOI: 10.1111/nph.19508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Plants evolved sophisticated machineries to monitor levels of external nitrogen supply, respond to nitrogen demand from different tissues and integrate this information for coordinating its assimilation. Although roles of inorganic nitrogen in orchestrating developments have been studied in model plants and crops, systematic understanding of the origin and evolution of its assimilation and signaling machineries remains largely unknown. We expanded taxon samplings of algae and early-diverging land plants, covering all main lineages of Archaeplastida, and reconstructed the evolutionary history of core components involved in inorganic nitrogen assimilation and signaling. Most components associated with inorganic nitrogen assimilation were derived from the ancestral Archaeplastida. Improvements of assimilation machineries by gene duplications and horizontal gene transfers were evident during plant terrestrialization. Clusterization of genes encoding nitrate assimilation proteins might be an adaptive strategy for algae to cope with changeable nitrate availability in different habitats. Green plants evolved complex nitrate signaling machinery that was stepwise improved by domains shuffling and regulation co-option. Our study highlights innovations in inorganic nitrogen assimilation and signaling machineries, ranging from molecular modifications of proteins to genomic rearrangements, which shaped developmental and metabolic adaptations of plants to changeable nutrient availability in environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zilong Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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14
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Feng H, Tan J, Deng Z. Decoding plant adaptation: deubiquitinating enzymes UBP12 and UBP13 in hormone signaling, light response, and developmental processes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:721-732. [PMID: 37904584 DOI: 10.1093/jxb/erad429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 11/01/2023]
Abstract
Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge of these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators such as receptor kinases and transcription factors during phytohormone and developmental signaling.
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Affiliation(s)
- Hanqian Feng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Jinjuan Tan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
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15
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Feng S, Liu Z, Chen H, Li N, Yu T, Zhou R, Nie F, Guo D, Ma X, Song X. PHGD: An integrative and user-friendly database for plant hormone-related genes. IMETA 2024; 3:e164. [PMID: 38868516 PMCID: PMC10989150 DOI: 10.1002/imt2.164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/19/2023] [Accepted: 12/17/2023] [Indexed: 06/14/2024]
Abstract
Plant Hormone Gene Database (PHGD) database platform construction pipeline. First, we collected all reported hormone-related genes in the model plant Arabidopsis thaliana, and combined with the existing experimental background, mapped the hormone-gene interaction network to provide a blueprint. Next, we collected 469 high-quality plant genomes. Then, bioinformatics was used to identify hormone-related genes in these plants. Finally, these genetic data were programmed to be stored in a database and a platform website PHGD was built. PHGD was divided into eight modules, namely Home, Browse, Search, Resources, Download, Tools, Help, and Contact. We provided data resources and platform services to facilitate the study of plant hormones.
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Affiliation(s)
- Shuyan Feng
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
| | - Zhuo Liu
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
| | - Huilong Chen
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Nan Li
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
| | - Tong Yu
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
| | - Rong Zhou
- Department of Food ScienceAarhus UniversityAarhusDenmark
| | - Fulei Nie
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
| | - Di Guo
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
| | - Xiao Ma
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
- College of Horticultural Science & Technology, Hebei NormalUniversity of Science & TechnologyQinhuangdaoHebeiChina
| | - Xiaoming Song
- School of Life Sciences/LibraryNorth China University of Science and TechnologyTangshanHebeiChina
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16
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Bowles AMC, Williamson CJ, Williams TA, Donoghue PCJ. Cryogenian Origins of Multicellularity in Archaeplastida. Genome Biol Evol 2024; 16:evae026. [PMID: 38333966 PMCID: PMC10883732 DOI: 10.1093/gbe/evae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
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17
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Ponce de León I. Evolution of immunity networks across embryophytes. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102450. [PMID: 37704543 DOI: 10.1016/j.pbi.2023.102450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
Land plants (embryophytes), including vascular (tracheophytes) and non-vascular plants (bryophytes), co-evolved with microorganisms since descendants of an algal ancestor colonized terrestrial habitats around 500 million years ago. To cope with microbial pathogen infections, embryophytes evolved a complex immune system for pathogen perception and activation of defenses. With the growing number of sequenced genomes and transcriptome datasets from algae, bryophytes, tracheophytes, and available plant models, comparative analyses are increasing our understanding of the evolution of molecular mechanisms underpinning immune responses in different plant lineages. In this review, recent progress on plant immunity networks is highlighted with emphasis on the identification of key components that shaped immunity against pathogens in bryophytes compared to angiosperms during plant evolution.
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Affiliation(s)
- Inés Ponce de León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600, Montevideo, Uruguay.
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18
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Jian J, Wu Z, Silva-Núñez A, Li X, Zheng X, Luo B, Liu Y, Fang X, Workman CT, Larsen TO, Hansen PJ, Sonnenschein EC. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168042. [PMID: 37898203 DOI: 10.1016/j.scitotenv.2023.168042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKS) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Overlap with repeats and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.
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Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Arisbe Silva-Núñez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Tecnologico de Monterrey, School of Engineering and Science, Monterrey, Nuevo León, Mexico
| | - Xiaohui Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Bei Luo
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yun Liu
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Per Juel Hansen
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Department of Biosciences, Swansea University, Swansea, United Kingdom.
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19
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MacLeod AI, Knopp MR, Gould SB. A mysterious cloak: the peptidoglycan layer of algal and plant plastids. PROTOPLASMA 2024; 261:173-178. [PMID: 37603062 PMCID: PMC10784329 DOI: 10.1007/s00709-023-01886-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/23/2023] [Indexed: 08/22/2023]
Abstract
The plastids of algae and plants originated on a single occasion from an endosymbiotic cyanobacterium at least a billion years ago. Despite the divergent evolution that characterizes the plastids of different lineages, many traits such as membrane organization and means of fission are universal-they pay tribute to the cyanobacterial origin of the organelle. For one such trait, the peptidoglycan (PG) layer, the situation is more complicated. Our view on its distribution keeps on changing and little is known regarding its molecular relevance, especially for land plants. Here, we investigate the extent of PG presence across the Chloroplastida using a phylogenomic approach. Our data support the view of a PG layer being present in the last common ancestor of land plants and its remarkable conservation across bryophytes that are otherwise characterized by gene loss. In embryophytes, the occurrence of the PG layer biosynthetic toolkit becomes patchier and the availability of novel genome data questions previous predictions regarding a functional coevolution of the PG layer and the plastid division machinery-associated gene FtsZ3. Furthermore, our data confirm the presence of penicillin-binding protein (PBP) orthologs in seed plants, which were previously thought to be absent from this clade. The 5-7 nm thick, and seemingly unchanged, PG layer armoring the plastids of glaucophyte algae might still provide the original function of structural support, but the same can likely not be said about the only recently identified PG layer of bryophyte and tracheophyte plastids. There are several issues to be explored regarding the composition, exact function, and biosynthesis of the PG layer in land plants. These issues arise from the fact that land plants seemingly lack certain genes that are believed to be crucial for PG layer production, even though they probably synthesize a PG layer.
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Affiliation(s)
- Alexander I MacLeod
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany.
| | - Michael R Knopp
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, 40225, Düsseldorf, Germany
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20
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Domozych DS, LoRicco JG. The extracellular matrix of green algae. PLANT PHYSIOLOGY 2023; 194:15-32. [PMID: 37399237 PMCID: PMC10762512 DOI: 10.1093/plphys/kiad384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
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Affiliation(s)
- David S Domozych
- Department of Biology, Skidmore College, Saratoga Springs, NY 12866, USA
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21
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Groussman RD, Blaskowski S, Coesel SN, Armbrust EV. MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Sci Data 2023; 10:926. [PMID: 38129449 PMCID: PMC10739892 DOI: 10.1038/s41597-023-02842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.
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Affiliation(s)
- R D Groussman
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
| | - S Blaskowski
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Molecular Engineering & Sciences Building 3946 W Stevens Way NE, Seattle, WA, 98195, USA
| | - S N Coesel
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA
| | - E V Armbrust
- School of Oceanography, University of Washington, Benjamin Hall IRB, Room 306 616 NE Northlake Place, Seattle, WA, 98105, USA.
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22
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Glass SE, McCourt RM, Gottschalk SD, Lewis LA, Karol KG. Chloroplast genome evolution and phylogeny of the early-diverging charophycean green algae with a focus on the Klebsormidiophyceae and Streptofilum. JOURNAL OF PHYCOLOGY 2023; 59:1133-1146. [PMID: 37548118 DOI: 10.1111/jpy.13359] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 08/08/2023]
Abstract
The Klebsormidiophyceae are a class of green microalgae observed globally in both freshwater and terrestrial habitats. Morphology-based classification schemes of this class have been shown to be inadequate due to the simple morphology of these algae, the tendency of morphology to vary in culture versus field conditions, and rampant morphological homoplasy. Molecular studies revealing cryptic diversity have renewed interest in this group. We sequenced the complete chloroplast genomes of a broad series of taxa spanning the known taxonomic breadth of this class. We also sequenced the chloroplast genomes of three strains of Streptofilum, a recently discovered green algal lineage with close affinity to the Klebsormidiophyceae. Our results affirm the previously hypothesized polyphyly of the genus Klebsormidium as well as the polyphyly of the nominal species in this genus, K. flaccidum. Furthermore, plastome sequences strongly support the status of Streptofilum as a distinct, early-diverging lineage of charophytic algae sister to a clade comprising Klebsormidiophyceae plus Phragmoplastophyta. We also uncovered major structural alterations in the chloroplast genomes of species in Klebsormidium that have broad implications regarding the underlying mechanisms of chloroplast genome evolution.
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Affiliation(s)
- Sarah E Glass
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, New York, New York, USA
| | - Richard M McCourt
- Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, USA
| | - Stephen D Gottschalk
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Kenneth G Karol
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
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23
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Rapin MN, Murray L, Sadler IH, Bothwell JH, Fry SC. Same but different - pseudo-pectin in the charophytic alga Chlorokybus atmophyticus. PHYSIOLOGIA PLANTARUM 2023; 175:e14079. [PMID: 38148229 PMCID: PMC10953000 DOI: 10.1111/ppl.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 12/28/2023]
Abstract
All land-plant cell walls possess hemicelluloses, cellulose and anionic pectin. The walls of their cousins, the charophytic algae, exhibit some similarities to land plants' but also major differences. Charophyte 'pectins' are extractable by conventional land-plant methods, although they differ significantly in composition. Here, we explore 'pectins' of an early-diverging charophyte, Chlorokybus atmophyticus, characterising the anionic polysaccharides that may be comparable to 'pectins' in other streptophytes. Chlorokybus 'pectin' was anionic and upon acid hydrolysis gave GlcA, GalA and sulphate, plus neutral sugars (Ara≈Glc>Gal>Xyl); Rha was undetectable. Most Gal was the l-enantiomer. A relatively acid-resistant disaccharide was characterised as β-d-GlcA-(1→4)-l-Gal. Two Chlorokybus 'pectin' fractions, separable by anion-exchange chromatography, had similar sugar compositions but different sulphate-ester contents. No sugars were released from Chlorokybus 'pectin' by several endo-hydrolases [(1,5)-α-l-arabinanase, (1,4)-β-d-galactanase, (1,4)-β-d-xylanase, endo-polygalacturonase] and exo-hydrolases [α- and β-d-galactosidases, α-(1,6)-d-xylosidase]. 'Driselase', which hydrolyses most land-plant cell wall polysaccharides to mono- and disaccharides, released no sugars except traces of starch-derived Glc. Thus, the Ara, Gal, Xyl and GalA of Chlorokybus 'pectin' were not non-reducing termini with configurations familiar from land-plant polysaccharides (α-l-Araf, α- and β-d-Galp, α- and β-d-Xylp and α-d-GalpA), nor mid-chain residues of α-(1→5)-l-arabinan, β-(1→4)-d-galactan, β-(1→4)-d-xylan or α-(1→4)-d-galacturonan. In conclusion, Chlorokybus possesses anionic 'pectic' polysaccharides, possibly fulfilling pectic roles but differing fundamentally from land-plant pectin. Thus, the evolution of land-plant pectin since the last common ancestor of Chlorokybus and land plants is a long and meandering path involving loss of sulphate, most l-Gal and most d-GlcA; re-configuration of Ara, Xyl and GalA; and gain of Rha.
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Affiliation(s)
- Marie N. Rapin
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's BuildingsEdinburghUK
| | - Lorna Murray
- EastChem School of Chemistry, The University of EdinburghEdinburghUK
| | - Ian H. Sadler
- EastChem School of Chemistry, The University of EdinburghEdinburghUK
| | | | - Stephen C. Fry
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's BuildingsEdinburghUK
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24
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Wegner L, Porth ML, Ehlers K. Multicellularity and the Need for Communication-A Systematic Overview on (Algal) Plasmodesmata and Other Types of Symplasmic Cell Connections. PLANTS (BASEL, SWITZERLAND) 2023; 12:3342. [PMID: 37765506 PMCID: PMC10536634 DOI: 10.3390/plants12183342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
In the evolution of eukaryotes, the transition from unicellular to simple multicellular organisms has happened multiple times. For the development of complex multicellularity, characterized by sophisticated body plans and division of labor between specialized cells, symplasmic intercellular communication is supposed to be indispensable. We review the diversity of symplasmic connectivity among the eukaryotes and distinguish between distinct types of non-plasmodesmatal connections, plasmodesmata-like structures, and 'canonical' plasmodesmata on the basis of developmental, structural, and functional criteria. Focusing on the occurrence of plasmodesmata (-like) structures in extant taxa of fungi, brown algae (Phaeophyceae), green algae (Chlorophyta), and streptophyte algae, we present a detailed critical update on the available literature which is adapted to the present classification of these taxa and may serve as a tool for future work. From the data, we conclude that, actually, development of complex multicellularity correlates with symplasmic connectivity in many algal taxa, but there might be alternative routes. Furthermore, we deduce a four-step process towards the evolution of canonical plasmodesmata and demonstrate similarity of plasmodesmata in streptophyte algae and land plants with respect to the occurrence of an ER component. Finally, we discuss the urgent need for functional investigations and molecular work on cell connections in algal organisms.
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Affiliation(s)
- Linus Wegner
- Institute of Botany, Justus-Liebig University, D-35392 Giessen, Germany
| | | | - Katrin Ehlers
- Institute of Botany, Justus-Liebig University, D-35392 Giessen, Germany
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25
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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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26
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Chakraborty P, Biswas A, Dey S, Bhattacharjee T, Chakrabarty S. Cytochrome P450 Gene Families: Role in Plant Secondary Metabolites Production and Plant Defense. J Xenobiot 2023; 13:402-423. [PMID: 37606423 PMCID: PMC10443375 DOI: 10.3390/jox13030026] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by the active participation of CYPs in several biosynthetic and detoxifying pathways. There are immense potentialities for using CYPs as a candidate for developing agricultural crop species resistant to biotic and abiotic stressors. This review provides an overview of the plant CYP families and their functions to plant secondary metabolite production and defense against different biotic and abiotic stresses.
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Affiliation(s)
- Panchali Chakraborty
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
| | - Ashok Biswas
- Annual Bast Fiber Breeding Laboratory, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
- Department of Horticulture, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Susmita Dey
- Annual Bast Fiber Breeding Laboratory, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
- Department of Plant Pathology and Seed Science, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tuli Bhattacharjee
- Department of Chemistry, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Swapan Chakrabarty
- College of Forest Resources and Environmental Sciences, Michigan Technological University, Houghton, MI 49931, USA
- College of Computing, Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
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27
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Permann C, Pichrtová M, Šoljaková T, Herburger K, Jouneau P, Uwizeye C, Falconet D, Marechal E, Holzinger A. 3D-reconstructions of zygospores in Zygnema vaginatum (Charophyta) reveal details of cell wall formation, suggesting adaptations to extreme habitats. PHYSIOLOGIA PLANTARUM 2023; 175:e13988. [PMID: 37616005 PMCID: PMC10953328 DOI: 10.1111/ppl.13988] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/25/2023]
Abstract
The streptophyte green algal class Zygnematophyceae is the immediate sister lineage to land plants. Their special form of sexual reproduction via conjugation might have played a key role during terrestrialization. Thus, studying Zygnematophyceae and conjugation is crucial for understanding the conquest of land. Moreover, sexual reproduction features are important for species determination. We present a phylogenetic analysis of a field-sampled Zygnema strain and analyze its conjugation process and zygospore morphology, both at the micro- and nanoscale, including 3D-reconstructions of the zygospore architecture. Vegetative filament size (26.18 ± 1.07 μm) and reproductive features allowed morphological determination of Zygnema vaginatum, which was combined with molecular analyses based on rbcL sequencing. Transmission electron microscopy (TEM) depicted a thin cell wall in young zygospores, while mature cells exhibited a tripartite wall, including a massive and sculptured mesospore. During development, cytological reorganizations were visualized by focused ion beam scanning electron microscopy (FIB-SEM). Pyrenoids were reorganized, and the gyroid cubic central thylakoid membranes, as well as the surrounding starch granules, degraded (starch granule volume: 3.58 ± 2.35 μm3 in young cells; 0.68 ± 0.74 μm3 at an intermediate stage of zygospore maturation). Additionally, lipid droplets (LDs) changed drastically in shape and abundance during zygospore maturation (LD/cell volume: 11.77% in young cells; 8.79% in intermediate cells, 19.45% in old cells). In summary, we provide the first TEM images and 3D-reconstructions of Zygnema zygospores, giving insights into the physiological processes involved in their maturation. These observations help to understand mechanisms that facilitated the transition from water to land in Zygnematophyceae.
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Affiliation(s)
| | - Martina Pichrtová
- Department of Botany, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tereza Šoljaková
- Department of Botany, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Klaus Herburger
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Institute of Biological Sciences, University of RostockRostockGermany
| | - Pierre‐Henri Jouneau
- Laboratoire Modélisation et Exploration des MatériauxIRIG, CEA, Univ. Grenoble AlpesGrenobleFrance
| | - Clarisse Uwizeye
- Laboratoire de Physiologie Cellulaire et VégétaleCEA, CNRS, INRAE, Univ. Grenoble AlpesGrenobleFrance
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et VégétaleCEA, CNRS, INRAE, Univ. Grenoble AlpesGrenobleFrance
| | - Eric Marechal
- Laboratoire de Physiologie Cellulaire et VégétaleCEA, CNRS, INRAE, Univ. Grenoble AlpesGrenobleFrance
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28
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Barcytė D. Extremophilic red algae reordered. JOURNAL OF PHYCOLOGY 2023; 59:441-443. [PMID: 37313841 DOI: 10.1111/jpy.13328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
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29
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McCourt RM, Lewis LA, Strother PK, Delwiche CF, Wickett NJ, de Vries J, Bowman JL. Green land: Multiple perspectives on green algal evolution and the earliest land plants. AMERICAN JOURNAL OF BOTANY 2023; 110:e16175. [PMID: 37247371 DOI: 10.1002/ajb2.16175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 05/31/2023]
Abstract
Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step-by-step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.
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Affiliation(s)
- Richard M McCourt
- Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, 19118, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Paul K Strother
- Department of Earth and Environmental Sciences, Boston College Weston Observatory, 381 Concord Road, Weston, MA, 02493, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Norman J Wickett
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA
| | - Jan de Vries
- Göttingen Center for Molecular Biosciences, Department of Applied Bioinformatics, University of Göttingen Goldschmidtstr. 1, Göttingen, 37077, Germany
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
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30
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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31
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Julca I, Tan QW, Mutwil M. Toward kingdom-wide analyses of gene expression. TRENDS IN PLANT SCIENCE 2023; 28:235-249. [PMID: 36344371 DOI: 10.1016/j.tplants.2022.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Gene expression data for Archaeplastida are accumulating exponentially, with more than 300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The gene expression data stem from thousands of experiments that capture gene expression in various organs, tissues, cell types, (a)biotic perturbations, and genotypes. Advances in software tools make it possible to process all these data in a matter of weeks on modern office computers, giving us the possibility to study gene expression in a kingdom-wide manner for the first time. We discuss how the expression data can be accessed and processed and outline analyses that take advantage of cross-species analyses, allowing us to generate powerful and robust hypotheses about gene function and evolution.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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32
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Leterme S, Bastien O, Aiese Cigliano R, Amato A, Michaud M. Phylogenetic and Structural Analyses of VPS13 Proteins in Archaeplastida Reveal Their Complex Evolutionary History in Viridiplantae. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231211976. [PMID: 38033810 PMCID: PMC10683392 DOI: 10.1177/25152564231211976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. VPS13 folds into a long hydrophobic tunnel, allowing lipid transport, decorated by distinct domains involved in protein localization and regulation. Whereas VPS13 organization and function have been extensively studied in yeast and mammals, information in organisms originating from primary endosymbiosis is scarce. In the higher plant Arabidopsis thaliana, four paralogs, AtVPS13S, X, M1, and M2, were identified, AtVPS13S playing a role in the regulation of root growth, cell patterning, and reproduction. In this work, we performed phylogenetic, as well as domain and structural modeling of VPS13 proteins in Archaeplastida in order to understand their general organization and evolutionary history. We confirmed the presence of human VPS13B orthologues in some phyla and described two new VPS13 families presenting a particular domain arrangement: VPS13R in Rhodophytes and VPS13Y in Chlorophytes and Streptophytes. By focusing on Viridiplantae, we were able to draw the evolutionary history of these proteins made by multiple gene gains and duplications as well as domain rearrangements. We showed that some Chlorophytes have only three (AtVPS13M, S, Y) whereas some Charophytes have up to six VPS13 paralogs (AtVPS13M1, M2, S, Y, X, B). We also highlighted specific structural features of VPS13M and X paralogs. This study reveals the complex evolution of VPS13 family and opens important perspectives for their functional characterization in photosynthetic organisms.
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Affiliation(s)
- Sébastien Leterme
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Olivier Bastien
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | | | - Alberto Amato
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
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33
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Gololobova MA, Belyakova GA. Position of Algae on the Tree of Life. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 507:312-326. [PMID: 36781528 DOI: 10.1134/s0012496622060035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 02/15/2023]
Abstract
Issues related to evolution of algal chloroplasts are considered. The position of algae on the Tree of Life is discussed. Algae are now included in five of the monophyletic eukaryotic supergroups: Archaeplastida (Glaucocystophyta, Rhodophyta, Prasinodermophyta, Chlorophyta, and Charophyta), TSAR (Ochrophyta; Dinophyta; Chlorarachniophyta; and photosynthetic species of the genera Chromera, Vetrella, and Paulinella), Haptista (Prymnesiophyta and Rappemonads), Cryptista (Cryptophyta), and Discoba (Euglenophyta). The algal divisions and the respective supergroups are characterized in brief.
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Affiliation(s)
- M A Gololobova
- Biological Faculty, Moscow State University, Moscow, Russia.
| | - G A Belyakova
- Biological Faculty, Moscow State University, Moscow, Russia
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34
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Davies KM, Landi M, van Klink JW, Schwinn KE, Brummell DA, Albert NW, Chagné D, Jibran R, Kulshrestha S, Zhou Y, Bowman JL. Evolution and function of red pigmentation in land plants. ANNALS OF BOTANY 2022; 130:613-636. [PMID: 36070407 PMCID: PMC9670752 DOI: 10.1093/aob/mcac109] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/05/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Land plants commonly produce red pigmentation as a response to environmental stressors, both abiotic and biotic. The type of pigment produced varies among different land plant lineages. In the majority of species they are flavonoids, a large branch of the phenylpropanoid pathway. Flavonoids that can confer red colours include 3-hydroxyanthocyanins, 3-deoxyanthocyanins, sphagnorubins and auronidins, which are the predominant red pigments in flowering plants, ferns, mosses and liverworts, respectively. However, some flowering plants have lost the capacity for anthocyanin biosynthesis and produce nitrogen-containing betalain pigments instead. Some terrestrial algal species also produce red pigmentation as an abiotic stress response, and these include both carotenoid and phenolic pigments. SCOPE In this review, we examine: which environmental triggers induce red pigmentation in non-reproductive tissues; theories on the functions of stress-induced pigmentation; the evolution of the biosynthetic pathways; and structure-function aspects of different pigment types. We also compare data on stress-induced pigmentation in land plants with those for terrestrial algae, and discuss possible explanations for the lack of red pigmentation in the hornwort lineage of land plants. CONCLUSIONS The evidence suggests that pigment biosynthetic pathways have evolved numerous times in land plants to provide compounds that have red colour to screen damaging photosynthetically active radiation but that also have secondary functions that provide specific benefits to the particular land plant lineage.
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Affiliation(s)
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Italy
| | - John W van Klink
- The New Zealand Institute for Plant and Food Research Limited, Department of Chemistry, Otago University, Dunedin, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Samarth Kulshrestha
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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35
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Schreiber M, Rensing SA, Gould SB. The greening ashore. TRENDS IN PLANT SCIENCE 2022; 27:847-857. [PMID: 35739050 DOI: 10.1016/j.tplants.2022.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/30/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.
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Affiliation(s)
- Mona Schreiber
- Plant Cell Biology, University of Marburg, 35043 Marburg, Germany.
| | - Stefan A Rensing
- Plant Cell Biology, University of Marburg, 35043 Marburg, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany.
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University (HHU) Düsseldorf, 40225 Düsseldorf, Germany.
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36
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Puginier C, Keller J, Delaux PM. Plant-microbe interactions that have impacted plant terrestrializations. PLANT PHYSIOLOGY 2022; 190:72-84. [PMID: 35642902 PMCID: PMC9434271 DOI: 10.1093/plphys/kiac258] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/09/2022] [Indexed: 05/30/2023]
Abstract
Plants display a tremendous diversity of developmental and physiological features, resulting from gains and losses of functional innovations across the plant phylogeny. Among those, the most impactful have been undoubtedly the ones that allowed plant terrestrializations, the transitions from an aquatic to a terrestrial environment. Although the embryophyte terrestrialization has been particularly scrutinized, others occurred across the plant phylogeny with the involvement of mutualistic symbioses as a common theme. Here, we review the current pieces of evidence supporting that the repeated colonization of land by plants has been facilitated by interactions with mutualistic symbionts. In that context, we detail two of these mutualistic symbioses: the arbuscular mycorrhizal symbiosis in embryophytes and the lichen symbiosis in chlorophyte algae. We suggest that associations with bacteria should be revisited in that context, and we propose that overlooked symbioses might have facilitated the emergence of other land plant clades.
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Affiliation(s)
- Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
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Barcytė D, Zátopková M, Němcová Y, Richtář M, Yurchenko T, Jaške K, Fawley KP, Škaloud P, Ševčíková T, Fawley MW, Eliáš M. Redefining Chlorobotryaceae as one of the principal and most diverse lineages of eustigmatophyte algae. Mol Phylogenet Evol 2022; 177:107607. [PMID: 35963589 DOI: 10.1016/j.ympev.2022.107607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/11/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
Abstract
Eustigmatophyceae is one of the ∼17 classes of the vast algal phylum Ochrophyta. Over the last decade, the eustigmatophytes emerged as an expansive group that has grown from the initially recognized handful of species to well over 200 genetically distinct entities (potential species). Yet the majority of eustigs, remain represented by unidentified strains, or even only metabarcode sequences obtained from environmental samples. Moreover, the formal classification of the group has not yet been harmonized with the recently uncovered diversity and phylogenetic relationships within the class. Here we make a major step towards resolving this issue by addressing the diversity, phylogeny and classification of one of the most prominent eustigmatophyte clades previously informally called the "Eustigmataceae group". We obtained 18S rDNA and rbcL gene sequences from four new strains from the "Eustigmataceae group", and from several additional eustig strains, and performed the most comprehensive phylogenetic analyses of Eustigmatophyceae to date. Our results of these analyses confirm the monophyly of the "Eustigmataceae group" and define its major subclades. We also sequenced plastid genomes of five "Eustigmataceae group" strains to not only improve our understanding of the plastid gene content evolution in eustigs, but also to obtain a robustly resolved eustigmatophyte phylogeny. With this new genomic data, we have solidified the view of the "Eustigmataceae group" as a well-defined family level clade. Crucially, we also have firmly established the genus Chlorobotrys as a member of the "Eustigmataceae group". This new molecular evidence, together with a critical analysis of the literature going back to the 19th century, provided the basis to radically redefine the historical concept of the family Chlorobotryaceae as the formal taxonomic rubric corresponding to the "Eustigmataceae group". With this change, the family names Eustigmataceae and Characiopsidaceae are reduced to synonymy with the Chlorobotryaceae, with the latter having taxonomic priority. We additionally studied in detail the morphology and ultrastructure of two Chlorobotryaceae members, which we describe as Neustupella aerophytica gen. et sp. nov. and Lietzensia polymorpha gen. et sp. nov. Finally, our analyses of partial genomic data from several Chlorobotryaceae representatives identified genes for hallmark flagellar proteins in all of these strains. The presence of the flagellar proteins strongly suggests that zoosporogenesis is a common trait of the family and also occurs in the members never observed to produce flagellated stages. Altogether, our work paints a rich picture of one of the most diverse principal lineages of eustigmatophyte algae.
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Affiliation(s)
- Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
| | - Martina Zátopková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Yvonne Němcová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00 Prague, Czech Republic
| | - Michal Richtář
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Tatiana Yurchenko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Karin Jaške
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Karen P Fawley
- Division of Science and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00 Prague, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Marvin W Fawley
- Division of Science and Mathematics, University of the Ozarks, Clarksville, AR 72830, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.
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Xu Y, Wang H, Sahu SK, Li L, Liang H, Günther G, Wong GKS, Melkonian B, Melkonian M, Liu H, Wang S. Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment. THE NEW PHYTOLOGIST 2022; 235:1409-1425. [PMID: 35560066 DOI: 10.1111/nph.18220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.
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Affiliation(s)
- Yan Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Hongping Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gerd Günther
- Private Laboratory, Knittkuhler Str. 61, Düsseldorf, 40629, Germany
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Barbara Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Michael Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Huan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
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Bachy C, Wittmers F, Muschiol J, Hamilton M, Henrissat B, Worden AZ. The Land-Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:585-616. [PMID: 35259927 DOI: 10.1146/annurev-arplant-071921-100530] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems-the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.
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Affiliation(s)
- Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jan Muschiol
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Maria Hamilton
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille Université (AMU), Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Biological Laboratories, Woods Hole, Massachusetts, USA
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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40
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Bachy C, Sudek L, Choi CJ, Eckmann CA, Nöthig EM, Metfies K, Worden AZ. Phytoplankton Surveys in the Arctic Fram Strait Demonstrate the Tiny Eukaryotic Alga Micromonas and Other Picoprasinophytes Contribute to Deep Sea Export. Microorganisms 2022; 10:961. [PMID: 35630405 PMCID: PMC9144618 DOI: 10.3390/microorganisms10050961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/20/2022] [Accepted: 04/24/2022] [Indexed: 12/10/2022] Open
Abstract
Critical questions exist regarding the abundance and, especially, the export of picophytoplankton (≤2 µm diameter) in the Arctic. These organisms can dominate chlorophyll concentrations in Arctic regions, which are subject to rapid change. The picoeukaryotic prasinophyte Micromonas grows in polar environments and appears to constitute a large, but variable, proportion of the phytoplankton in these waters. Here, we analyze 81 samples from the upper 100 m of the water column from the Fram Strait collected over multiple years (2009−2015). We also analyze sediment trap samples to examine picophytoplankton contributions to export, using both 18S rRNA gene qPCR and V1-V2 16S rRNA Illumina amplicon sequencing to assess the Micromonas abundance within the broader diversity of photosynthetic eukaryotes based on the phylogenetic placement of plastid-derived 16S amplicons. The material sequenced from the sediment traps in July and September 2010 showed that 11.2 ± 12.4% of plastid-derived amplicons are from picoplanktonic prasinophyte algae and other green lineage (Viridiplantae) members. In the traps, Micromonas dominated (83.6 ± 21.3%) in terms of the overall relative abundance of Viridiplantae amplicons, specifically the species Micromonas polaris. Temporal variations in Micromonas abundances quantified by qPCR were also observed, with higher abundances in the late-July traps and deeper traps. In the photic zone samples, four prasinophyte classes were detected in the amplicon data, with Micromonas again being the dominant prasinophyte, based on the relative abundance (89.4 ± 8.0%), but with two species (M. polaris and M. commoda-like) present. The quantitative PCR assessments showed that the photic zone samples with higher Micromonas abundances (>1000 gene copies per mL) had significantly lower standing stocks of phosphate and nitrate, and a shallower average depth (20 m) than those with fewer Micromonas. This study shows that despite their size, prasinophyte picophytoplankton are exported to the deep sea, and that Micromonas is particularly important within this size fraction in Arctic marine ecosystems.
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Affiliation(s)
- Charles Bachy
- Monterey Bay Aquarium Research Institute, Moss Landing, Monterey, CA 95039, USA; (C.B.); (L.S.); (C.J.C.); (C.A.E.)
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, Monterey, CA 95039, USA; (C.B.); (L.S.); (C.J.C.); (C.A.E.)
| | - Change Jae Choi
- Monterey Bay Aquarium Research Institute, Moss Landing, Monterey, CA 95039, USA; (C.B.); (L.S.); (C.J.C.); (C.A.E.)
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - Charlotte A. Eckmann
- Monterey Bay Aquarium Research Institute, Moss Landing, Monterey, CA 95039, USA; (C.B.); (L.S.); (C.J.C.); (C.A.E.)
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - Eva-Maria Nöthig
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; (E.-M.N.); (K.M.)
| | - Katja Metfies
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; (E.-M.N.); (K.M.)
| | - Alexandra Z. Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, Monterey, CA 95039, USA; (C.B.); (L.S.); (C.J.C.); (C.A.E.)
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
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41
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Dewees SI, Vargová R, Hardin KR, Turn RE, Devi S, Linnert J, Wolfrum U, Caspary T, Eliáš M, Kahn RA. Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E. Mol Biol Cell 2022; 33:ar33. [PMID: 35196065 PMCID: PMC9250359 DOI: 10.1091/mbc.e21-10-0509-t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/11/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
The ARF family of regulatory GTPases is ancient, with 16 members predicted to have been present in the last eukaryotic common ancestor. Our phylogenetic profiling of paralogues in diverse species identified four family members whose presence correlates with that of a cilium/flagellum: ARL3, ARL6, ARL13, and ARL16. No prior evidence links ARL16 to cilia or other cell functions, despite its presence throughout eukaryotes. Deletion of ARL16 in mouse embryonic fibroblasts (MEFs) results in decreased ciliogenesis yet increased ciliary length. We also found Arl16 knockout (KO) in MEFs to alter ciliary protein content, including loss of ARL13B, ARL3, INPP5E, and the IFT-A core component IFT140. Instead, both INPP5E and IFT140 accumulate at the Golgi in Arl16 KO lines, while other intraflagellar transport (IFT) proteins do not, suggesting a specific defect in traffic from Golgi to cilia. We propose that ARL16 regulates a Golgi-cilia traffic pathway and is required specifically in the export of IFT140 and INPP5E from the Golgi.
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Affiliation(s)
- Skylar I. Dewees
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
| | - Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, CZ-710 00, Ostrava, Czech Republic
| | - Katherine R. Hardin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
| | - Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30307
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305-5124
| | - Saroja Devi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Joshua Linnert
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, CZ-710 00, Ostrava, Czech Republic
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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42
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Liu Y, Wang S, Li L, Yang T, Dong S, Wei T, Wu S, Liu Y, Gong Y, Feng X, Ma J, Chang G, Huang J, Yang Y, Wang H, Liu M, Xu Y, Liang H, Yu J, Cai Y, Zhang Z, Fan Y, Mu W, Sahu SK, Liu S, Lang X, Yang L, Li N, Habib S, Yang Y, Lindstrom AJ, Liang P, Goffinet B, Zaman S, Wegrzyn JL, Li D, Liu J, Cui J, Sonnenschein EC, Wang X, Ruan J, Xue JY, Shao ZQ, Song C, Fan G, Li Z, Zhang L, Liu J, Liu ZJ, Jiao Y, Wang XQ, Wu H, Wang E, Lisby M, Yang H, Wang J, Liu X, Xu X, Li N, Soltis PS, Van de Peer Y, Soltis DE, Gong X, Liu H, Zhang S. The Cycas genome and the early evolution of seed plants. NATURE PLANTS 2022; 8:389-401. [PMID: 35437001 PMCID: PMC9023351 DOI: 10.1038/s41477-022-01129-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/10/2022] [Indexed: 05/05/2023]
Abstract
Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ting Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shengdan Wu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jianchao Ma
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Guanxiao Chang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Yong Yang
- College of Biology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hongli Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Liang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jin Yu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuqing Cai
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaowu Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yannan Fan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Weixue Mu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shuchun Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoan Lang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- Nanning Botanical Garden, Nanning, China
| | - Leilei Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Na Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Sadaf Habib
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yongqiong Yang
- Sichuan Cycas panzhihuaensis National Nature Reserve, Panzhihua, China
| | | | - Pei Liang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Dexiang Li
- Nanning Botanical Garden, Nanning, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Xiaobo Wang
- Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jue Ruan
- Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chi Song
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guangyi Fan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB UGent Center for Plant Systems Biology, Gent, Belgium
| | - Liangsheng Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Jianquan Liu
- The College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhong-Jian Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Nan Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB UGent Center for Plant Systems Biology, Gent, Belgium.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China.
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43
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Kwantes M, Wichard T. The APAF1_C/WD40 repeat domain-encoding gene from the sea lettuce Ulva mutabilis sheds light on the evolution of NB-ARC domain-containing proteins in green plants. PLANTA 2022; 255:76. [PMID: 35235070 PMCID: PMC8891106 DOI: 10.1007/s00425-022-03851-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/07/2022] [Indexed: 06/02/2023]
Abstract
We advance Ulva's genetic tractability and highlight its value as a model organism by characterizing its APAF1_C/WD40 domain-encoding gene, which belongs to a family that bears homology to R genes. The multicellular chlorophyte alga Ulva mutabilis (Ulvophyceae, Ulvales) is native to coastal ecosystems worldwide and attracts both high socio-economic and scientific interest. To further understand the genetic mechanisms that guide its biology, we present a protocol, based on adapter ligation-mediated PCR, for retrieving flanking sequences in U. mutabilis vector-insertion mutants. In the created insertional library, we identified a null mutant with an insertion in an apoptotic protease activating factor 1 helical domain (APAF1_C)/WD40 repeat domain-encoding gene. Protein domain architecture analysis combined with phylogenetic analysis revealed that this gene is a member of a subfamily that arose early in the evolution of green plants (Viridiplantae) through the acquisition of a gene that also encoded N-terminal nucleotide-binding adaptor shared by APAF-1, certain R-gene products and CED-4 (NB-ARC) and winged helix-like (WH-like) DNA-binding domains. Although phenotypic analysis revealed no mutant phenotype, gene expression levels in control plants correlated to the presence of bacterial symbionts, which U. mutabilis requires for proper morphogenesis. In addition, our analysis led to the discovery of a putative Ulva nucleotide-binding site and leucine-rich repeat (NBS-LRR) Resistance protein (R-protein), and we discuss how the emergence of these R proteins in green plants may be linked to the evolution of the APAF1_C/WD40 protein subfamily.
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Affiliation(s)
- Michiel Kwantes
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany.
- Jena School for Microbial Communication, 07743, Jena, Germany.
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44
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Repetti SI, Iha C, Uthanumallian K, Jackson CJ, Chen Y, Chan CX, Verbruggen H. Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. THE NEW PHYTOLOGIST 2022; 233:2144-2154. [PMID: 34923642 DOI: 10.1111/nph.17926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the core Chlorophyta and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most prasinophytes and the remainder of the core Chlorophyta. Our results suggest positive selection for genome streamlining in the Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their last common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. Results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising before diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.
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Affiliation(s)
- Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | | | | | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
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45
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Radin I, Haswell ES. Looking at mechanobiology through an evolutionary lens. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102112. [PMID: 34628340 DOI: 10.1016/j.pbi.2021.102112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Mechanical forces were arguably among the first stimuli to be perceived by cells, and they continue to shape the evolution of all organisms. Great strides have been made in recent years in the field of plant cell and molecular mechanobiology, in part owing to focused efforts on key model systems. Here, we propose to enrich such work through evolutionary mechanobiology, or 'evo-mechano', and describe three major themes that could drive research in this area. We use plastid evo-mechano as a case study, describing how plastids from different lineages perceive their mechanical environments, how their mechanical properties vary across lineages, and their distinct roles in graviperception. Finally, we argue that future research into the biomechanical properties and mechanobiological signaling mechanisms that have been elaborated by green species over the past 1.5 billion years will help us understand both the universal and the unique adaptations of plants to their physical environment.
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Affiliation(s)
- Ivan Radin
- Department of Biology, MSC 1137-154-314, Washington University, 1 Brookings Drive, St. Louis, MO, 63130-489, United States; NSF Center for Engineering Mechanobiology, United States
| | - Elizabeth S Haswell
- Department of Biology, MSC 1137-154-314, Washington University, 1 Brookings Drive, St. Louis, MO, 63130-489, United States; NSF Center for Engineering Mechanobiology, United States.
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46
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Chen XL, Sun MC, Chong SL, Si JP, Wu LS. Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant-Endophyte Interactions. FRONTIERS IN PLANT SCIENCE 2022; 12:700200. [PMID: 35154169 PMCID: PMC8828500 DOI: 10.3389/fpls.2021.700200] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 12/22/2021] [Indexed: 05/10/2023]
Abstract
In natural systems, plant-symbiont-pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant-microbe interactions, especially plant-endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant-endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant-microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.
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Affiliation(s)
| | | | | | | | - Ling-shang Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
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47
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Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:808156. [PMID: 35498716 PMCID: PMC9038950 DOI: 10.3389/fpls.2022.808156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 05/03/2023]
Abstract
The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.
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Affiliation(s)
- Ting Yang
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sunil Kumar Sahu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- *Correspondence: Sunil Kumar Sahu,
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yang Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Weixue Mu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Xin Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Huan Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Bojian Zhong,
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48
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Fang Y, Jiang J, Hou X, Guo J, Li X, Zhao D, Xie X. Plant protein-coding gene families: Their origin and evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:995746. [PMID: 36160967 PMCID: PMC9490259 DOI: 10.3389/fpls.2022.995746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/15/2022] [Indexed: 05/13/2023]
Abstract
Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Degang Zhao
- Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Ministry of Education, College of Life Sciences, Institute of Agricultural Bioengineering, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- *Correspondence: Degang Zhao,
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- Xin Xie,
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49
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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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50
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Xu JJ, Zhang XF, Jiang Y, Fan H, Li JX, Li CY, Zhao Q, Yang L, Hu YH, Martin C, Chen XY. A unique flavoenzyme operates in ubiquinone biosynthesis in photosynthesis-related eukaryotes. SCIENCE ADVANCES 2021; 7:eabl3594. [PMID: 34878842 PMCID: PMC8654299 DOI: 10.1126/sciadv.abl3594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Coenzyme Q (CoQ) is an electron transporter in the mitochondrial respiratory chain, yet the biosynthetic pathway in eukaryotes remains only partially resolved. C6-hydroxylation completes the benzoquinone ring full substitution, a hallmark of CoQ. Here, we show that plants use a unique flavin-dependent monooxygenase (CoqF), instead of di-iron enzyme (Coq7) operating in animals and fungi, as a C6-hydroxylase. CoqF evolved early in eukaryotes and became widely distributed in photosynthetic and related organisms ranging from plants, algae, apicomplexans, and euglenids. Independent alternative gene losses in different groups and lateral gene transfer have ramified CoqF across the eukaryotic tree with predominance in green lineages. The exclusive presence of CoqF in Streptophyta hints at an association of the flavoenzyme with photoautotrophy in terrestrial environments. CoqF provides a phylogenetic marker distinguishing eukaryotes and represents a previously unknown target for drug design against parasitic protists.
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Affiliation(s)
- Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Xiao-Fan Zhang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Yan Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- School of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hang Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Jian-Xu Li
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chen-Yi Li
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yong-Hong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Cathie Martin
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiao-Ya Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
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