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De Saeger J, Coulembier Vandelannoote E, Lee H, Park J, Blomme J. Genome editing in macroalgae: advances and challenges. Front Genome Ed 2024; 6:1380682. [PMID: 38516199 PMCID: PMC10955705 DOI: 10.3389/fgeed.2024.1380682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
This minireview examines the current state and challenges of genome editing in macroalgae. Despite the ecological and economic significance of this group of organisms, genome editing has seen limited applications. While CRISPR functionality has been established in two brown (Ectocarpus species 7 and Saccharina japonica) and one green seaweed (Ulva prolifera), these studies are limited to proof-of-concept demonstrations. All studies also (co)-targeted ADENINE PHOSPHORIBOSYL TRANSFERASE to enrich for mutants, due to the relatively low editing efficiencies. To advance the field, there should be a focus on advancing auxiliary technologies, particularly stable transformation, so that novel editing reagents can be screened for their efficiency. More work is also needed on understanding DNA repair in these organisms, as this is tightly linked with the editing outcomes. Developing efficient genome editing tools for macroalgae will unlock the ability to characterize their genes, which is largely uncharted terrain. Moreover, given their economic importance, genome editing will also impact breeding campaigns to develop strains that have better yields, produce more commercially valuable compounds, and show improved resilience to the impacts of global change.
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Affiliation(s)
- Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Emma Coulembier Vandelannoote
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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2
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Borg M, Krueger-Hadfield SA, Destombe C, Collén J, Lipinska A, Coelho SM. Red macroalgae in the genomic era. THE NEW PHYTOLOGIST 2023; 240:471-488. [PMID: 37649301 DOI: 10.1111/nph.19211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023]
Abstract
Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years.
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Affiliation(s)
- Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Stacy A Krueger-Hadfield
- Department of Biology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Virginia Institute of Marine Science Eastern Shore Laboratory, Wachapreague, VA, 23480, USA
| | - Christophe Destombe
- International Research Laboratory 3614 (IRL3614) - Evolutionary Biology and Ecology of Algae, Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Roscoff, 29680, France
| | - Jonas Collén
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff, Sorbonne Université, Roscoff, 29680, France
| | - Agnieszka Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tübingen, Germany
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3
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Lian Q, Maestroni L, Gaudin M, Llorente B, Mercier R. Meiotic recombination is confirmed to be unusually high in the fission yeast Schizosaccharomyces pombe. iScience 2023; 26:107614. [PMID: 37664590 PMCID: PMC10474467 DOI: 10.1016/j.isci.2023.107614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/20/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
In most eukaryotes, meiotic crossovers (COs) are limited to 1-3 per chromosome, and are prevented from occurring close to one another by CO interference. The fission yeast Schizosaccharomyces pombe, an exception to these general rules, was reported to have the highest CO number per chromosome and no or weak interference. However, global CO frequency was indirectly estimated, calling for confirmation. Here, we used an innovative strategy to determine COs genome-wide in S. pombe. We confirmed weak CO interference, acting at physical distances compatible with the patterning of recombination precursors. We revealed a slight co-variation in CO number between chromosomes, suggesting that a limiting pro-CO factor varies between meiocytes. CO number per chromosome varies proportionally with chromosome size, with the three chromosomes having, on average, 15.9, 12.5, and 7.0 COs, respectively. This reinforces S. pombe's status as the eukaryote with the highest CO number per chromosome described to date.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Maxime Gaudin
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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4
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Blomme J, Wichard T, Jacobs TB, De Clerck O. Ulva: An emerging green seaweed model for systems biology. JOURNAL OF PHYCOLOGY 2023. [PMID: 37256696 DOI: 10.1111/jpy.13341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
Green seaweeds exhibit a wide range of morphologies and occupy various ecological niches, spanning from freshwater to marine and terrestrial habitats. These organisms, which predominantly belong to the class Ulvophyceae, showcase a remarkable instance of parallel evolution toward complex multicellularity and macroscopic thalli in the Viridiplantae lineage. Within the green seaweeds, several Ulva species ("sea lettuce") are model organisms for studying carbon assimilation, interactions with bacteria, life cycle progression, and morphogenesis. Ulva species are also notorious for their fast growth and capacity to dominate nutrient-rich, anthropogenically disturbed coastal ecosystems during "green tide" blooms. From an economic perspective, Ulva has garnered increasing attention as a promising feedstock for the production of food, feed, and biobased products, also as a means of removing excess nutrients from the environment. We propose that Ulva is poised to further develop as a model in green seaweed research. In this perspective, we focus explicitly on Ulva mutabilis/compressa as a model species and highlight the molecular data and tools that are currently available or in development. We discuss several areas that will benefit from future research or where exciting new developments have been reported in other Ulva species.
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Affiliation(s)
- Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
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5
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Godfroy O, Zheng M, Yao H, Henschen A, Peters AF, Scornet D, Colin S, Ronchi P, Hipp K, Nagasato C, Motomura T, Cock JM, Coelho SM. The baseless mutant links protein phosphatase 2A with basal cell identity in the brown alga Ectocarpus. Development 2023; 150:dev201283. [PMID: 36786333 PMCID: PMC10112911 DOI: 10.1242/dev.201283] [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: 09/15/2022] [Accepted: 01/16/2023] [Indexed: 02/15/2023]
Abstract
The first mitotic division of the initial cell is a key event in all multicellular organisms and is associated with the establishment of major developmental axes and cell fates. The brown alga Ectocarpus has a haploid-diploid life cycle that involves the development of two multicellular generations: the sporophyte and the gametophyte. Each generation deploys a distinct developmental programme autonomously from an initial cell, the first cell division of which sets up the future body pattern. Here, we show that mutations in the BASELESS (BAS) gene result in multiple cellular defects during the first cell division and subsequent failure to produce basal structures during both generations. BAS encodes a type B″ regulatory subunit of protein phosphatase 2A (PP2A), and transcriptomic analysis identified potential effector genes that may be involved in determining basal cell fate. The bas mutant phenotype is very similar to that observed in distag (dis) mutants, which lack a functional Tubulin-binding co-factor Cd1 (TBCCd1) protein, indicating that TBCCd1 and PP2A are two essential components of the cellular machinery that regulates the first cell division and mediates basal cell fate determination.
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Affiliation(s)
- Olivier Godfroy
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Min Zheng
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Haiqin Yao
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Agnes Henschen
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Delphine Scornet
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Sebastien Colin
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Katharina Hipp
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - J. Mark Cock
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M. Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Cock JM. The model system Ectocarpus: Integrating functional genomics into brown algal research. JOURNAL OF PHYCOLOGY 2023; 59:4-8. [PMID: 36477437 DOI: 10.1111/jpy.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Affiliation(s)
- J Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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7
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Embracing algal models. Semin Cell Dev Biol 2023; 134:1-3. [PMID: 35779978 DOI: 10.1016/j.semcdb.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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ddRAD Sequencing-Based Scanning of Genetic Variants in Sargassum fusiforme. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10070958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Sargassum fusiforme is a commercially important brown seaweed that has experienced significant population reduction both from heavy exploitation and degradation of the environment. Cultivated breed strains are also in a state of population mixing. These population stressors make it necessary to investigate the population genetics to discover best practices to conserve and breed this seaweed. In this study, the genetic diversity and population structure of S. fusiforme were investigated by the genome-wide SNP data acquired from double digest restriction site-associated DNA sequencing (ddRAD-seq). We found a low genetic diversity and a slight population differentiation within and between wild and cultivated populations, and the effective population size of S. fusiforme had experienced a continuous decline. Tajima’s D analysis showed the population contraction in wild populations may be related to copper pollution which showed a consistent trend with the increase of the sea surface temperature. The potential selection signatures may change the timing or level of gene expression, and further experiments are needed to investigate the effect of the mutation on relevant pathways. These results suggest an urgent need to manage and conserve S. fusiforme resources and biodiversity considering the accelerating change of the environment.
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Badis Y, Scornet D, Harada M, Caillard C, Godfroy O, Raphalen M, Gachon CMM, Coelho SM, Motomura T, Nagasato C, Cock JM. Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus. THE NEW PHYTOLOGIST 2021; 231:2077-2091. [PMID: 34076889 DOI: 10.1111/nph.17525] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Brown algae are an important group of multicellular eukaryotes, phylogenetically distinct from both the animal and land plant lineages. Ectocarpus has emerged as a model organism to study diverse aspects of brown algal biology, but this system currently lacks an effective reverse genetics methodology to analyse the functions of selected target genes. Here, we report that mutations at specific target sites are generated following the introduction of CRISPR-Cas9 ribonucleoproteins into Ectocarpus cells, using either biolistics or microinjection as the delivery method. Individuals with mutations affecting the ADENINE PHOSPHORIBOSYL TRANSFERASE (APT) gene were isolated following treatment with 2-fluoroadenine, and this selection system was used to isolate individuals in which mutations had been introduced simultaneously at APT and at a second gene. This double mutation approach could potentially be used to isolate mutants affecting any Ectocarpus gene, providing an effective reverse genetics tool for this model organism. The availability of this tool will significantly enhance the utility of Ectocarpus as a model organism for this ecologically and economically important group of marine organisms. Moreover, the methodology described here should be readily transferable to other brown algal species.
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Affiliation(s)
- Yacine Badis
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll,, PA37 1QA, UK
| | - Delphine Scornet
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Minori Harada
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Céline Caillard
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Olivier Godfroy
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Morgane Raphalen
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Claire M M Gachon
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll,, PA37 1QA, UK
- UMR 7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CP 54, 57 rue Cuvier, Paris, 75005, France
| | - Susana M Coelho
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - J Mark Cock
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
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Shan T, Pang S, Wang X, Li J, Li Q, Su L, Li X. A method to establish an "immortalized F 2 " sporophyte population in the economic brown alga Undaria pinnatifida (Laminariales: Alariaceae). JOURNAL OF PHYCOLOGY 2020; 56:1748-1753. [PMID: 32888200 DOI: 10.1111/jpy.13066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/20/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Studies of quantitative trait loci based on genetic linkage maps require the establishment of a mapping population. Permanent mapping populations are more ideal than temporary ones because they can be used repeatedly. However, there has been no reported permanent sporophyte population of economically important kelp species. Based on the characteristics of the kelp life cycle, we proposed a method to establish, and then constructed experimentally, an "immortalized F2 " (IF2 ) population of Undaria pinnatifida. Doubled-haploid "female" and "male" sporophytes were obtained through the parthenogenesis of a female gametophyte clone and the selfing of a "monoicous" gametophyte clone (originally male), respectively, and they were used as the parents. The F1 hybrid line was generated by crossing the female and male gametophytes derived from the respective female and male parents. Full-sibling F2 gametophyte clones, consisting of 260 females and 260 males, were established from an F1 hybrid sporophyte. Thirty-five females and 35 males were randomly selected and paired to give rise to an IF2 population containing 35 crossing lines. A parentage analysis using 10 microsatellite markers confirmed the accuracy of the IF2 population and indicated the feasibility of this method. This proposed method may be adapted for use in other kelp species, and thus, it will be useful for genetic studies of kelp.
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Affiliation(s)
- Tifeng Shan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd, Qingdao, 266071, China
| | - Shaojun Pang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd, Qingdao, 266071, China
| | - Xuemei Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd, Qingdao, 266071, China
| | - Jing Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd, Qingdao, 266071, China
| | - Qianxi Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd, Qingdao, 266071, China
| | - Li Su
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd, Qingdao, 266071, China
| | - Xiaodong Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Rd., Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 7 Nanhai Rd, Qingdao, 266071, China
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11
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Coelho SM, Peters AF, Müller D, Cock JM. Ectocarpus: an evo-devo model for the brown algae. EvoDevo 2020; 11:19. [PMID: 32874530 PMCID: PMC7457493 DOI: 10.1186/s13227-020-00164-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Ectocarpus is a genus of filamentous, marine brown algae. Brown algae belong to the stramenopiles, a large supergroup of organisms that are only distantly related to animals, land plants and fungi. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity. For many years, little information was available concerning the molecular mechanisms underlying multicellular development in the brown algae, but this situation has changed with the emergence of Ectocarpus as a model brown alga. Here we summarise some of the main questions that are being addressed and areas of study using Ectocarpus as a model organism and discuss how the genomic information, genetic tools and molecular approaches available for this organism are being employed to explore developmental questions in an evolutionary context.
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Affiliation(s)
- Susana M. Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | | | - Dieter Müller
- Fachbereich Biologie der Universitat Konstanz, 78457 Konstanz, Germany
| | - J. Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
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12
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Dittami SM, Corre E, Brillet-Guéguen L, Lipinska AP, Pontoizeau N, Aite M, Avia K, Caron C, Cho CH, Collén J, Cormier A, Delage L, Doubleau S, Frioux C, Gobet A, González-Navarrete I, Groisillier A, Hervé C, Jollivet D, KleinJan H, Leblanc C, Liu X, Marie D, Markov GV, Minoche AE, Monsoor M, Pericard P, Perrineau MM, Peters AF, Siegel A, Siméon A, Trottier C, Yoon HS, Himmelbauer H, Boyen C, Tonon T. The genome of Ectocarpus subulatus - A highly stress-tolerant brown alga. Mar Genomics 2020; 52:100740. [PMID: 31937506 DOI: 10.1016/j.margen.2020.100740] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/01/2020] [Indexed: 11/20/2022]
Abstract
Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.
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Affiliation(s)
- Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France.
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Loraine Brillet-Guéguen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Noé Pontoizeau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Meziane Aite
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Komlan Avia
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Université de Strasbourg, INRA, SVQV UMR-A 1131, F-68000 Colmar, France
| | - Christophe Caron
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Alexandre Cormier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Sylvie Doubleau
- IRD, UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France
| | | | - Angélique Gobet
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Irene González-Navarrete
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Agnès Groisillier
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Cécile Hervé
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Hetty KleinJan
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Xi Liu
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Dominique Marie
- Sorbonne Université, CNRS, Adaptation and Diversity in the Marine Environment (ADME), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - André E Minoche
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Misharl Monsoor
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Pierre Pericard
- CNRS, Sorbonne Université, FR2424, ABiMS platform, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Marie-Mathilde Perrineau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Scottish Association for Marine Science, Scottish Marine Institute, Oban PA37 1QA, United Kingdom
| | | | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France
| | - Amandine Siméon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Camille Trottier
- Univ Rennes, Inria, CNRS, IRISA, 35000 Rennes, France; Laboratory of Digital Sciences of Nantes (LS2N) - University of Nantes, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Heinz Himmelbauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, 1190 Vienna, Austria
| | - Catherine Boyen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Thierry Tonon
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France; Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
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Farré EM. The brown clock: circadian rhythms in stramenopiles. PHYSIOLOGIA PLANTARUM 2020; 169:430-441. [PMID: 32274814 DOI: 10.1111/ppl.13104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Circadian clocks allow organisms to anticipate environmental changes associated with the diurnal light/dark cycle. Circadian oscillators have been described in plants and green algae, cyanobacteria, animals and fungi, however, little is known about the circadian clocks of photosynthetic eukaryotes outside the green lineage. Stramenopiles are a diverse group of secondary endosymbionts whose plastid originated from a red alga. Photosynthetic stramenopiles, which include diatoms and brown algae, play key roles in biogeochemical cycles and are important components of marine ecosystems. Genome annotation efforts indicated the presence of a novel type of oscillator in these organisms and the first circadian clock component in a stramenopile has been recently discovered. This review summarizes the phenotypic characterization of circadian rhythms in stramenopiles and current efforts to determine the mechanisms of this 'brown clock'. The elucidation of this brown clock will enable a deeper understanding of the role of self-sustained oscillations in the adaptation to life in marine environments.
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Affiliation(s)
- Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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14
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instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder. Genome Biol 2020; 21:148. [PMID: 32552806 PMCID: PMC7386250 DOI: 10.1186/s13059-020-02041-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/11/2020] [Indexed: 02/06/2023] Open
Abstract
Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large genomes. instaGRAAL features a number of improvements over GRAAL, including a modular correction approach that optionally integrates independent data. We validate the program using data for two brown algae, and human, to generate near-complete assemblies with minimal human intervention.
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15
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Parallelisable non-invasive biomass, fitness and growth measurement of macroalgae and other protists with nephelometry. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Siméon A, Kridi S, Kloareg B, Hervé C. Presence of Exogenous Sulfate Is Mandatory for Tip Growth in the Brown Alga Ectocarpus subulatus. FRONTIERS IN PLANT SCIENCE 2020; 11:1277. [PMID: 33013948 PMCID: PMC7461865 DOI: 10.3389/fpls.2020.01277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/05/2020] [Indexed: 05/08/2023]
Abstract
Brown algae (Phaeophyceae) are multicellular photoautrophic organisms and the largest biomass producers in coastal regions. A variety of observations indicate that their extracellular matrix (ECM) is involved with screening of salts, development, cell fate selection, and defense responses. It is likely that these functionalities are related to its constitutive structures. The major components of the ECM of brown algae are β-glucans, alginates, and fucose-containing sulfated polysaccharides. The genus Ectocarpus comprises a wide range of species that have adapted to different environments, including isolates of Ectocarpus subulatus, a species highly resistant to low salinity. Previous studies on a freshwater strain of E. subulatus indicated that the sulfate remodeling of fucans is related to the external salt concentration. Here we show that the sulfate content of the surrounding medium is a key parameter influencing both the patterning of the alga and the occurrence of the BAM4 sulfated fucan epitope in walls of apical cells. These results indicate that sulfate uptake and incorporation in the sulfated fucans from apical cells is an essential parameter to sustain tip growth, and we discuss its influence on the architectural plasticity of Ectocarpus.
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17
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Rojo C, Puche E, Rodrigo MA. The antagonistic effect of UV radiation on warming or nitrate enrichment depends on ecotypes of freshwater macroalgae (Charophytes). JOURNAL OF PHYCOLOGY 2019; 55:714-729. [PMID: 30900746 DOI: 10.1111/jpy.12859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Increases in ultraviolet radiation (UVR), a negative global change factor, affect aquatic primary producers. This effect is expected to be modulated by other global change factors, and to be different for populations adapted to different environments. A common garden experimental approach using freshwater green macroalgae, the cosmopolitan charophyte species Chara hispida and C. vulgaris, allowed us to test whether the beneficial increases in water temperature (T) and nitrate concentration (N) mitigate negative UVR effects. Also, whether these interactions would be not only species-specific but also according to the origin of the population; therefore, two populations of each species were used: one from a coastal wetland and the other from a mountain lake. Two factorial-design experiments were performed: (i) the presence and absence of UVR × lower and higher T × four populations, and (ii) the presence and absence of UVR × lower and higher N × four populations. Response variables were: growth, morphometry, UVR-protective compounds, photosynthetic pigments, and stoichiometric composition. There were consistent response patterns in the key variables that represent different organization levels. Our main results showed that both warming and, to a lesser extent, the increase in nutrients ameliorated the negative effects of UVR on the molecular processes involved in acclimation to UVR, and that such a mitigating effect depended on the different phenotypic plasticity of each species and each ecotype. The coastal populations, being from a more variable environment, were more resilient than the mountain populations, mainly because of changes in growth and morphology.
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Affiliation(s)
- Carmen Rojo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of València, c/Catedrático José Beltrán 2, Paterna, E-46980, Spain
| | - Eric Puche
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of València, c/Catedrático José Beltrán 2, Paterna, E-46980, Spain
| | - María A Rodrigo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of València, c/Catedrático José Beltrán 2, Paterna, E-46980, Spain
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18
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Mignerot L, Avia K, Luthringer R, Lipinska AP, Peters AF, Cock JM, Coelho SM. A key role for sex chromosomes in the regulation of parthenogenesis in the brown alga Ectocarpus. PLoS Genet 2019; 15:e1008211. [PMID: 31194744 PMCID: PMC6592573 DOI: 10.1371/journal.pgen.1008211] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/25/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of these shifts remain largely elusive. Here, we used classic quantitative trait analysis, combined with genomic and transcriptomic information to dissect the genetic basis of asexual, parthenogenetic reproduction in the brown alga Ectocarpus. We found that parthenogenesis is controlled by the sex locus, together with two additional autosomal loci, highlighting the key role of the sex chromosome as a major regulator of asexual reproduction. We identify several negative effects of parthenogenesis on male fitness, and different fitness effects of parthenogenetic capacity depending on the life cycle generation. Although allele frequencies in natural populations are currently unknown, we discuss the possibility that parthenogenesis may be under both sex-specific selection and generation/ploidally-antagonistic selection, and/or that the action of fluctuating selection on this trait may contribute to the maintenance of polymorphisms in populations. Importantly, our data provide the first empirical illustration, to our knowledge, of a trade-off between the haploid and diploid stages of the life cycle, where distinct parthenogenesis alleles have opposing effects on sexual and asexual reproduction and may help maintain genetic variation. These types of fitness trade-offs have profound evolutionary implications in natural populations and may structure life history evolution in organisms with haploid-diploid life cycles.
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Affiliation(s)
- Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Remy Luthringer
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | | | - J. Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
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19
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Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C. Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics 2019; 20:56. [PMID: 30654742 PMCID: PMC6337836 DOI: 10.1186/s12864-019-5431-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 01/03/2019] [Indexed: 01/02/2023] Open
Abstract
Background Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes. Results Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus sp. strains and sub-cellular fractions using a shotgun approach. First, we directly generated peptide sequence tags (PSTs) from the proteomics data. Second, we mapped PSTs onto the translated genomic sequence. Closely located hits (i.e., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism. Third, we evaluated each cluster and compared it to gene predictions from existing conventional genome annotation approaches. Finally, we integrated cluster locations into GFF files to use a genome viewer. We identified two potential novel genes, a ribosomal protein L22 and an aryl sulfotransferase and corrected the gene structure of a dihydrolipoamide acetyltransferase. We experimentally validated the results by RT-PCR and using transcriptomics data. Conclusions Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu. Data are available via ProteomeXchange under identifier PXD010618. Electronic supplementary material The online version of this article (10.1186/s12864-019-5431-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laetitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Ludovic Delage
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Alain Viari
- INRIA Grenoble-Rhône-Alpes, F-38330, Montbonnot-Saint-Martin, France
| | - Yves Vandenbrouck
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000, Grenoble, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Andrés Ritter
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France.,Present address: Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Dominique Marie
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | | | - Philippe Potin
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France. .,Protim, Univ Rennes, F-35042, Rennes cedex, France.
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20
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Lo E, Bonizzoni M, Hemming-Schroeder E, Ford A, Janies DA, James AA, Afrane Y, Etemesi H, Zhou G, Githeko A, Yan G. Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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21
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Kumar V, Paillard S, Fopa-Fomeju B, Falentin C, Deniot G, Baron C, Vallée P, Manzanares-Dauleux MJ, Delourme R. Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1627-1643. [PMID: 29728747 DOI: 10.1007/s00122-018-3103-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/20/2018] [Indexed: 05/02/2023]
Abstract
A repertoire of the genomic regions involved in quantitative resistance to Leptosphaeria maculans in winter oilseed rape was established from combined linkage-based QTL and genome-wide association (GWA) mapping. Linkage-based mapping of quantitative trait loci (QTL) and genome-wide association studies are complementary approaches for deciphering the genomic architecture of complex agronomical traits. In oilseed rape, quantitative resistance to blackleg disease, caused by L. maculans, is highly polygenic and is greatly influenced by the environment. In this study, we took advantage of multi-year data available on three segregating populations derived from the resistant cv Darmor and multi-year data available on oilseed rape panels to obtain a wide overview of the genomic regions involved in quantitative resistance to this pathogen in oilseed rape. Sixteen QTL regions were common to at least two biparental populations, of which nine were the same as previously detected regions in a multi-parental design derived from different resistant parents. Eight regions were significantly associated with quantitative resistance, of which five on A06, A08, A09, C01 and C04 were located within QTL support intervals. Homoeologous Brassica napus genes were found in eight homoeologous QTL regions, which corresponded to 657 pairs of homoeologous genes. Potential candidate genes underlying this quantitative resistance were identified. Genomic predictions and breeding are also discussed, taking into account the highly polygenic nature of this resistance.
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Affiliation(s)
- Vinod Kumar
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Sophie Paillard
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | | | - Cyril Falentin
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Cécile Baron
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Patrick Vallée
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | | | - Régine Delourme
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France.
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22
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Avia K, Lipinska AP, Mignerot L, Montecinos AE, Jamy M, Ahmed S, Valero M, Peters AF, Cock JM, Roze D, Coelho SM. Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes (Basel) 2018; 9:E286. [PMID: 29882839 PMCID: PMC6027523 DOI: 10.3390/genes9060286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes.
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Affiliation(s)
- Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Alejandro E Montecinos
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Mahwash Jamy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Sophia Ahmed
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
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23
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Camus C, Faugeron S, Buschmann AH. Assessment of genetic and phenotypic diversity of the giant kelp, Macrocystis pyrifera, to support breeding programs. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Godfroy O, Uji T, Nagasato C, Lipinska AP, Scornet D, Peters AF, Avia K, Colin S, Mignerot L, Motomura T, Cock JM, Coelho SM. DISTAG/TBCCd1 Is Required for Basal Cell Fate Determination in Ectocarpus. THE PLANT CELL 2017; 29:3102-3122. [PMID: 29208703 PMCID: PMC5757272 DOI: 10.1105/tpc.17.00440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/14/2017] [Accepted: 12/04/2017] [Indexed: 05/09/2023]
Abstract
Brown algae are one of the most developmentally complex groups within the eukaryotes. As in many land plants and animals, their main body axis is established early in development, when the initial cell gives rise to two daughter cells that have apical and basal identities, equivalent to shoot and root identities in land plants, respectively. We show here that mutations in the Ectocarpus DISTAG (DIS) gene lead to loss of basal structures during both the gametophyte and the sporophyte generations. Several abnormalities were observed in the germinating initial cell in dis mutants, including increased cell size, disorganization of the Golgi apparatus, disruption of the microtubule network, and aberrant positioning of the nucleus. DIS encodes a TBCCd1 protein, which has a role in internal cell organization in animals, Chlamydomonas reinhardtii, and trypanosomes. Our study highlights the key role of subcellular events within the germinating initial cell in the determination of apical/basal cell identities in a brown alga and emphasizes the remarkable functional conservation of TBCCd1 in regulating internal cell organization across extremely distant eukaryotic groups.
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Affiliation(s)
- Olivier Godfroy
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Toshiki Uji
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Chikako Nagasato
- Muroran Marine Station, Hokkaido University, Hokkaido 060-0808, Japan
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Delphine Scornet
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | | | - Komlan Avia
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, 29688 Roscoff, France
| | - Sebastien Colin
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Laure Mignerot
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Taizo Motomura
- Muroran Marine Station, Hokkaido University, Hokkaido 060-0808, Japan
| | - J Mark Cock
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
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