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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytol 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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2
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Markel K, Novak V, Bowen BP, Tian Y, Chen YC, Sirirungruang S, Zhou A, Louie KB, Northen TR, Eudes A, Scheller HV, Shih PM. Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls. Plant Physiol 2024; 195:698-712. [PMID: 38236304 DOI: 10.1093/plphys/kiae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024]
Abstract
Many insects have evolved the ability to manipulate plant growth to generate extraordinary structures called galls, in which insect larva can develop while being sheltered and feeding on the plant. In particular, cynipid (Hymenoptera: Cynipidae) wasps have evolved to form morphologically complex galls and generate an astonishing array of gall shapes, colors, and sizes. However, the biochemical basis underlying these remarkable cellular and developmental transformations remains poorly understood. A key determinant in plant cellular development is cell wall deposition that dictates the physical form and physiological function of newly developing cells, tissues, and organs. However, it is unclear to what degree cell walls are restructured to initiate and support the formation of new gall tissue. Here, we characterize the molecular alterations underlying gall development using a combination of metabolomic, histological, and biochemical techniques to elucidate how valley oak (Quercus lobata) leaf cells are reprogrammed to form galls. Strikingly, gall development involves an exceptionally coordinated spatial deposition of lignin and xylan to form de novo gall vasculature. Our results highlight how cynipid wasps can radically change the metabolite profile and restructure the cell wall to enable the formation of galls, providing insights into the mechanism of gall induction and the extent to which plants can be entirely reprogrammed to form unique structures and organs.
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Affiliation(s)
- Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Vlastimil Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yang Tian
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Yi-Chun Chen
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Sasilada Sirirungruang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Andy Zhou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Katherine B Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aymerick Eudes
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Henrik V Scheller
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
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3
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Honerlaw J, Ho YL, Fontin F, Murray M, Galloway A, Heise D, Connatser K, Davies L, Gosian J, Maripuri M, Russo J, Sangar R, Tanukonda V, Zielinski E, Dubreuil M, Zimolzak AJ, Panickan VA, Cheng SC, Whitbourne SB, Gagnon DR, Cai T, Liao KP, Ramoni RB, Gaziano JM, Muralidhar S, Cho K. Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users. J Am Med Inform Assoc 2024; 31:1126-1134. [PMID: 38481028 PMCID: PMC11031216 DOI: 10.1093/jamia/ocae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/21/2024] [Indexed: 04/21/2024] Open
Abstract
OBJECTIVE Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. We describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. MATERIALS AND METHODS The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. RESULTS The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. DISCUSSION The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CONCLUSION CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.
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Affiliation(s)
- Jacqueline Honerlaw
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - Yuk-Lam Ho
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - Francesca Fontin
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - Michael Murray
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - Ashley Galloway
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - David Heise
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37830, United States
| | - Keith Connatser
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37830, United States
| | - Laura Davies
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN 37830, United States
| | - Jeffrey Gosian
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - Monika Maripuri
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - John Russo
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
- Department of Computer Science, Landmark College, Putney, VT 05346, United States
| | - Rahul Sangar
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - Vidisha Tanukonda
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Atlanta Healthcare System, Decatur, GA 30033, United States
| | - Edward Zielinski
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
| | - Maureen Dubreuil
- VA Boston Healthcare System, Boston, MA 02111, United States
- Section of Rheumatology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, United States
| | - Andrew J Zimolzak
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX 77030, United States
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, United States
| | - Vidul A Panickan
- VA Boston Healthcare System, Boston, MA 02111, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
| | - Su-Chun Cheng
- VA Boston Healthcare System, Boston, MA 02111, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
| | - Stacey B Whitbourne
- VA Boston Healthcare System, Boston, MA 02111, United States
- Million Veteran Program (MVP) Coordinating Center, VA Boston, Boston, MA 02111, United States
- Division of Aging, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, United States
- Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
| | - David R Gagnon
- VA Boston Healthcare System, Boston, MA 02111, United States
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, United States
| | - Tianxi Cai
- VA Boston Healthcare System, Boston, MA 02111, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, United States
| | - Katherine P Liao
- VA Boston Healthcare System, Boston, MA 02111, United States
- Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, United States
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
| | - Rachel B Ramoni
- Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
| | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA 02111, United States
- Million Veteran Program (MVP) Coordinating Center, VA Boston, Boston, MA 02111, United States
- Division of Aging, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, United States
- Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
| | - Sumitra Muralidhar
- Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
| | - Kelly Cho
- Centralized Interactive Phenomics Resource (CIPHER), Office of Research and Development, Veterans Health Administration, Washington, DC 20002, United States
- VA Boston Healthcare System, Boston, MA 02111, United States
- Million Veteran Program (MVP) Coordinating Center, VA Boston, Boston, MA 02111, United States
- Division of Aging, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, United States
- Department of Medicine, Harvard Medical School, Boston, MA 02115, United States
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4
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Wang Y, Mao J, Brelsford CM, Ricciuto DM, Yuan F, Shi X, Rastogi D, Mayes MM, Kao SC, Warren JM, Griffiths NA, Cheng X, Weston DJ, Zhou Y, Gu L, Thornton PE. Thermal, water, and land cover factors led to contrasting urban and rural vegetation resilience to extreme hot months. PNAS Nexus 2024; 3:pgae147. [PMID: 38638834 PMCID: PMC11026108 DOI: 10.1093/pnasnexus/pgae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/20/2024]
Abstract
With continuing global warming and urbanization, it is increasingly important to understand the resilience of urban vegetation to extreme high temperatures, but few studies have examined urban vegetation at large scale or both concurrent and delayed responses. In this study, we performed an urban-rural comparison using the Enhanced Vegetation Index and months that exceed the historical 90th percentile in mean temperature (referred to as "hot months") across 85 major cities in the contiguous United States. We found that hot months initially enhanced vegetation greenness but could cause a decline afterwards, especially for persistent (≥4 months) and intense (≥+2 °C) episodes in summer. The urban responses were more positive than rural in the western United States or in winter, but more negative during spring-autumn in the eastern United States. The east-west difference can be attributed to the higher optimal growth temperatures and lower water stress levels of the western urban vegetation than the rural. The urban responses also had smaller magnitudes than the rural responses, especially in deciduous forest biomes, and least in evergreen forest biomes. Within each biome, analysis at 1 km pixel level showed that impervious fraction and vegetation cover, local urban heat island intensity, and water stress were the key drivers of urban-rural differences. These findings advance our understanding of how prolonged exposure to warm extremes, particularly within urban environments, affects vegetation greenness and vitality. Urban planners and ecosystem managers should prioritize the long and intense events and the key drivers in fostering urban vegetation resilience to heat waves.
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Affiliation(s)
- Yaoping Wang
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jiafu Mao
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Christa M Brelsford
- Geospatial Science and Human Security Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Daniel M Ricciuto
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Fengming Yuan
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Xiaoying Shi
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Deeksha Rastogi
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Melanie M Mayes
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Shih-Chieh Kao
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jeffrey M Warren
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Natalie A Griffiths
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Xinghua Cheng
- Department of Natural Resources and the Environment, University of Connecticut, Storrs, CT 06269, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Yuyu Zhou
- Department of Geography, The University of Hong Kong, Hong Kong, 999077, China
| | - Lianhong Gu
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Peter E Thornton
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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5
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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. Plants (Basel) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Espinoza-Corral R, Iwai M, Zavřel T, Lechno-Yossef S, Sutter M, Červený J, Niyogi KK, Kerfeld CA. Phycobilisome protein ApcG interacts with PSII and regulates energy transfer in Synechocystis. Plant Physiol 2024; 194:1383-1396. [PMID: 37972281 PMCID: PMC10904348 DOI: 10.1093/plphys/kiad615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Photosynthetic organisms harvest light using pigment-protein complexes. In cyanobacteria, these are water-soluble antennae known as phycobilisomes (PBSs). The light absorbed by PBS is transferred to the photosystems in the thylakoid membrane to drive photosynthesis. The energy transfer between these complexes implies that protein-protein interactions allow the association of PBS with the photosystems. However, the specific proteins involved in the interaction of PBS with the photosystems are not fully characterized. Here, we show in Synechocystis sp. PCC 6803 that the recently discovered PBS linker protein ApcG (sll1873) interacts specifically with PSII through its N-terminal region. Growth of cyanobacteria is impaired in apcG deletion strains under light-limiting conditions. Furthermore, complementation of these strains using a phospho-mimicking version of ApcG causes reduced growth under normal growth conditions. Interestingly, the interaction of ApcG with PSII is affected when a phospho-mimicking version of ApcG is used, targeting the positively charged residues interacting with the thylakoid membrane, suggesting a regulatory role mediated by phosphorylation of ApcG. Low-temperature fluorescence measurements showed decreased PSI fluorescence in apcG deletion and complementation strains. The PSI fluorescence was the lowest in the phospho-mimicking complementation strain, while the pull-down experiment showed no interaction of ApcG with PSI under any tested condition. Our results highlight the importance of ApcG for selectively directing energy harvested by the PBS and imply that the phosphorylation status of ApcG plays a role in regulating energy transfer from PSII to PSI.
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Affiliation(s)
- Roberto Espinoza-Corral
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Drásov 470, CZ-66424 Drásov, Czech Republic
| | - Sigal Lechno-Yossef
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Červený
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Drásov 470, CZ-66424 Drásov, Czech Republic
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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7
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Zepernick BN, Chase EE, Denison ER, Gilbert NE, Truchon AR, Frenken T, Cody WR, Martin RM, Chaffin JD, Bullerjahn GS, McKay RML, Wilhelm SW. Declines in ice cover are accompanied by light limitation responses and community change in freshwater diatoms. ISME J 2024; 18:wrad015. [PMID: 38366077 PMCID: PMC10939406 DOI: 10.1093/ismejo/wrad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
The rediscovery of diatom blooms embedded within and beneath the Lake Erie ice cover (2007-2012) ignited interest in psychrophilic adaptations and winter limnology. Subsequent studies determined the vital role ice plays in winter diatom ecophysiology as diatoms partition to the underside of ice, thereby fixing their location within the photic zone. Yet, climate change has led to widespread ice decline across the Great Lakes, with Lake Erie presenting a nearly "ice-free" state in several recent winters. It has been hypothesized that the resultant turbid, isothermal water column induces light limitation amongst winter diatoms and thus serves as a competitive disadvantage. To investigate this hypothesis, we conducted a physiochemical and metatranscriptomic survey that spanned spatial, temporal, and climatic gradients of the winter Lake Erie water column (2019-2020). Our results suggest that ice-free conditions decreased planktonic diatom bloom magnitude and altered diatom community composition. Diatoms increased their expression of various photosynthetic genes and iron transporters, which suggests that the diatoms are attempting to increase their quantity of photosystems and light-harvesting components (a well-defined indicator of light limitation). We identified two gene families which serve to increase diatom fitness in the turbid ice-free water column: proton-pumping rhodopsins (a potential second means of light-driven energy acquisition) and fasciclins (a means to "raft" together to increase buoyancy and co-locate to the surface to optimize light acquisition). With large-scale climatic changes already underway, our observations provide insight into how diatoms respond to the dynamic ice conditions of today and shed light on how they will fare in a climatically altered tomorrow.
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Affiliation(s)
- Brittany N Zepernick
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Emily E Chase
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Elizabeth R Denison
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Naomi E Gilbert
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
- Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Alexander R Truchon
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Thijs Frenken
- HAS University of Applied Sciences, 5223 DE ‘s-Hertogenbosch, The Netherlands
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9C 1A2, Canada
| | - William R Cody
- Aquatic Taxonomy Specialists, Malinta, OH 43535, United States
| | - Robbie M Martin
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
| | - Justin D Chaffin
- Stone Laboratory and Ohio Sea Grant, The Ohio State University, Put-In-Bay, OH 43456, United States
| | - George S Bullerjahn
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, United States
| | - R Michael L McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9C 1A2, Canada
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN 37996, United States
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Bueno de Mesquita CP, Hartman WH, Ardón M, Tringe SG. Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME Commun 2024; 4:ycae040. [PMID: 38628812 PMCID: PMC11020224 DOI: 10.1093/ismeco/ycae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these changes remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing and biogeochemical measurements, to tease apart the effects of sulfate from other seawater ions. We examined changes in microbial taxonomy and function as well as emissions of carbon dioxide, methane, and nitrous oxide in response to changes in ion concentrations. Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present, whereas sulfate alone did not alter emissions or communities. Surprisingly, addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes. Similarly, genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate. These results suggest that other ions present in seawater, not sulfate, drive ecological and biogeochemical responses to seawater intrusion and may be drivers of increased methane emissions in soils that received artificial seawater addition. A better understanding of how the different components of salt water alter microbial community composition and function is necessary to forecast the consequences of coastal wetland salinization.
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Affiliation(s)
- Clifton P Bueno de Mesquita
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Wyatt H Hartman
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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9
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Yarden O, Zhang J, Marcus D, Changwal C, Mabjeesh SJ, Lipzen A, Zhang Y, Savage E, Ng V, Grigoriev IV, Hadar Y. Altered Expression of Two Small Secreted Proteins ( ssp4 and ssp6) Affects the Degradation of a Natural Lignocellulosic Substrate by Pleurotus ostreatus. Int J Mol Sci 2023; 24:16828. [PMID: 38069150 PMCID: PMC10705924 DOI: 10.3390/ijms242316828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Pleurotus ostreatus is a white-rot fungus that can degrade lignin in a preferential manner using a variety of extracellular enzymes, including manganese and versatile peroxidases (encoded by the vp1-3 and mnp1-6 genes, respectively). This fungus also secretes a family of structurally related small secreted proteins (SSPs) encoded by the ssp1-6 genes. Using RNA sequencing (RNA-seq), we determined that ssp4 and ssp6 are the predominant members of this gene family that were expressed by P. ostreatus during the first three weeks of growth on wheat straw. Downregulation of ssp4 in a strain harboring an ssp RNAi construct (KDssp1) was then confirmed, which, along with an increase in ssp6 transcript levels, coincided with reduced lignin degradation and the downregulation of vp2 and mnp1. In contrast, we observed an increase in the expression of genes related to pectin and side-chain hemicellulose degradation, which was accompanied by an increase in extracellular pectin-degrading capacity. Genome-wide comparisons between the KDssp1 and the wild-type strains demonstrated that ssp silencing conferred accumulated changes in gene expression at the advanced cultivation stages in an adaptive rather than an inductive mode of transcriptional response. Based on co-expression networking, crucial gene modules were identified and linked to the ssp knockdown genotype at different cultivation times. Based on these data, as well as previous studies, we propose that P. ostreatus SSPs have potential roles in modulating the lignocellulolytic and pectinolytic systems, as well as a variety of fundamental biological processes related to fungal growth and development.
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Affiliation(s)
- Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
| | - Jiwei Zhang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA;
| | - Dor Marcus
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
| | - Chunoti Changwal
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
| | - Sameer J. Mabjeesh
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel;
| | - Anna Lipzen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Yu Zhang
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Emily Savage
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Vivian Ng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
| | - Igor V. Grigoriev
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (Y.Z.); (E.S.); (V.N.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (D.M.); (C.C.); (Y.H.)
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10
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Bhaskara GB, Haque T, Bonnette JE, Napier JD, Bauer D, Schmutz J, Juenger TE. Evolutionary Analyses of Gene Expression Divergence in Panicum hallii: Exploring Constitutive and Plastic Responses Using Reciprocal Transplants. Mol Biol Evol 2023; 40:msad210. [PMID: 37738160 PMCID: PMC10556983 DOI: 10.1093/molbev/msad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified FST-QST outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.
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Affiliation(s)
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Jason E Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diane Bauer
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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11
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Vittorelli N, Rodríguez de la Vega RC, Snirc A, Levert E, Gautier V, Lalanne C, De Filippo E, Gladieux P, Guillou S, Zhang Y, Tejomurthula S, Grigoriev IV, Debuchy R, Silar P, Giraud T, Hartmann FE. Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores. PLoS Genet 2023; 19:e1010347. [PMID: 36763677 PMCID: PMC9949647 DOI: 10.1371/journal.pgen.1010347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/23/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.
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Affiliation(s)
- Nina Vittorelli
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
- Département de Biologie, École Normale Supérieure, PSL Université Paris, Paris, France
| | | | - Alodie Snirc
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Emilie Levert
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Christophe Lalanne
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Elsa De Filippo
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Yu Zhang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sravanthi Tejomurthula
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Fanny E. Hartmann
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- * E-mail:
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12
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Panwar P, Allen MA, Williams TJ, Haque S, Brazendale S, Hancock AM, Paez-Espino D, Cavicchioli R. Remarkably coherent population structure for a dominant Antarctic Chlorobium species. Microbiome 2021; 9:231. [PMID: 34823595 PMCID: PMC8620254 DOI: 10.1186/s40168-021-01173-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/09/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. RESULTS A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml-1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. CONCLUSION The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. Video abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present address: Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Present address: Mammoth Biosciences, Inc., 1000 Marina Blvd. Suite 600, Brisbane, CA, USA
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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13
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Pompidor N, Charron C, Hervouet C, Bocs S, Droc G, Rivallan R, Manez A, Mitros T, Swaminathan K, Glaszmann JC, Garsmeur O, D’Hont A. Three founding ancestral genomes involved in the origin of sugarcane. Ann Bot 2021; 127:827-840. [PMID: 33637991 PMCID: PMC8103802 DOI: 10.1093/aob/mcab008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/25/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. METHODS To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. KEY RESULTS The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. CONCLUSIONS This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.
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Affiliation(s)
- Nicolas Pompidor
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Carine Charron
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Manez
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Jean-Christophe Glaszmann
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- For correspondence. E-mail
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14
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Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. New Phytol 2019; 222:511-525. [PMID: 30485448 DOI: 10.1111/nph.15613] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/29/2018] [Indexed: 06/09/2023]
Abstract
Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.
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Affiliation(s)
- Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Alessandro Desirò
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Institut national de la recherche agronomique, Laboratoire d'excellence ARBRE, Centre INRA-Grand Est, Unité mixte de recherche Inra-Université de Lorraine "Interactions Arbres/Microorganismes", 54280, Champenoux, France
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
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15
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Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G, Donnadieu C, Desdevises Y, Sanchez-Ferandin S, Moreau H, Rivals E, Grigoriev IV, Grimsley N, Eyre-Walker A, Piganeau G. Population genomics of picophytoplankton unveils novel chromosome hypervariability. Sci Adv 2017; 3:e1700239. [PMID: 28695208 PMCID: PMC5498103 DOI: 10.1126/sciadv.1700239] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/25/2017] [Indexed: 05/18/2023]
Abstract
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.
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Affiliation(s)
- Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marc Krasovec
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Maxime Hebrard
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Sheree Yau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Elodie Desgranges
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald Salin
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Cecile Donnadieu
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Ferandin
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Hervé Moreau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Eric Rivals
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Nigel Grimsley
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Gwenael Piganeau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
- Corresponding author.
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