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De Clerck O, LoDuca ST. Algal evolution: A touch of brown in a Paleozoic sea of greens and reds. Curr Biol 2024; 34:R150-R152. [PMID: 38412826 DOI: 10.1016/j.cub.2024.01.028] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Previous molecular clock studies indicated a Mesozoic origin for the brown algae (Phaeophyceae). New research based on phylogenetic evidence challenges this notion and provides novel insights into the origin and diversification of brown algae, which includes multiple transitions within the group from isogamy to oogamy (and back again!).
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Affiliation(s)
- Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent 9000, Belgium.
| | - Steven T LoDuca
- Department of Geography and Geology, Eastern Michigan University, Ypsilanti, MI 48197, USA.
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2
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van der Loos LM, D'hondt S, Engelen AH, Pavia H, Toth GB, Willems A, Weinberger F, De Clerck O, Steinhagen S. Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient. Mol Ecol 2023; 32:6260-6277. [PMID: 35395701 DOI: 10.1111/mec.16462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 12/01/2021] [Revised: 02/21/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.
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Affiliation(s)
- Luna M van der Loos
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sofie D'hondt
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Aschwin H Engelen
- Marine Microbial Ecology & Biotechnology, CCMAR, University of Algarve, Faro, Portugal
| | - Henrik Pavia
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Gunilla B Toth
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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3
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van der Loos LM, De Coninck L, Zell R, Lequime S, Willems A, De Clerck O, Matthijnssens J. Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva. Microbiol Spectr 2023; 11:e0025523. [PMID: 37724866 PMCID: PMC10581178 DOI: 10.1128/spectrum.00255-23] [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: 01/16/2023] [Accepted: 07/19/2023] [Indexed: 09/21/2023] Open
Abstract
Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.
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Affiliation(s)
- Luna M. van der Loos
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Lander De Coninck
- Laboratory of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 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: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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5
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Vieira C, Kim MS, N’Yeurt ADR, Payri C, D’Hondt S, De Clerck O, Zubia M. Marine Flora of French Polynesia: An Updated List Using DNA Barcoding and Traditional Approaches. Biology (Basel) 2023; 12:1124. [PMID: 37627008 PMCID: PMC10452401 DOI: 10.3390/biology12081124] [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: 06/26/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023]
Abstract
Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region's biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications provided the first checklists of French Polynesian marine algae, including the Chlorophyta, Rhodophyta, Ochrophyta, and Cyanobacteria, established mostly on traditional morphology-based taxonomy. We initiated a project to systematically DNA barcode the marine flora of French Polynesia. Based on a large collection of ~2452 specimens, made between 2014 and 2023, across the five French Polynesian archipelagos, we re-assessed the marine floral species diversity (Alismatales, Cyanobacteria, Rhodophyta, Ochrophyta, Chlorophyta) using DNA barcoding in concert with morphology-based classification. We provide here a major revision of French Polynesian marine flora, with an updated listing of 702 species including 119 Chlorophyta, 169 Cyanobacteria, 92 Ochrophyta, 320 Rhodophyta, and 2 seagrass species-nearly a two-fold increase from previous estimates. This study significantly improves our knowledge of French Polynesian marine diversity and provides a valuable DNA barcode reference library for identification purposes and future taxonomic and conservation studies. A significant part of the diversity uncovered from French Polynesia corresponds to unidentified lineages, which will require careful future taxonomic investigation.
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Affiliation(s)
- Christophe Vieira
- Department of Biology and Research Institute for Basic Sciences, Jeju National University, Jeju 63243, Republic of Korea;
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, 9000 Ghent, Belgium
| | - Myung Sook Kim
- Department of Biology and Research Institute for Basic Sciences, Jeju National University, Jeju 63243, Republic of Korea;
| | - Antoine De Ramon N’Yeurt
- Pacific Center for Environment an Sustainable Development, The University of the South Pacific, Private Mail Bag, Suva P.O. Box 1168, Fiji;
| | - Claude Payri
- Institut de Recherche pour le Développement, Nouméa 98848, New Caledonia
| | - Sofie D’Hondt
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, 9000 Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group, Center for Molecular Phylogenetics and Evolution, Ghent University, 9000 Ghent, Belgium
| | - Mayalen Zubia
- UMR Ecosystèmes Insulaires Océaniens, University of French Polynesia, BP6570, Faa’a 98702, Tahiti, French Polynesia
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6
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Mancuso FP, Morrissey KL, De Clerck O, Airoldi L. Warming and nutrient enrichment can trigger seaweed loss by dysregulation of the microbiome structure and predicted function. Sci Total Environ 2023; 879:162919. [PMID: 36958561 DOI: 10.1016/j.scitotenv.2023.162919] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 05/17/2023]
Abstract
Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communities. We experimentally tested in the field orthogonal stress combinations from simulated air warming and nutrient enrichment on the intertidal foundation seaweed Cystoseira compressa, and its associated bacterial communities. A total of 523 Amplicon Sequence Variance (ASVs) formed the bacterial community on C. compressa, with 222 ASVs assigned to 69 taxa at the genus level. Most bacteria taxa experienced changes in abundance as a result of additive (65 %) and antagonistic (30 %) interactions between the two stressors, with synergies (5 %) occurring less frequently. The analysis of the predicted bacterial functional profile identified 160 metabolic pathways, and showed that these were mostly affected by additive interactions (74 %) between air warming and nutrient enrichment, while antagonisms (20 %) and synergisms (6 %) were less frequent. Overall, the two stressors combined increased functions associated with seaweed disease or degradation of major cell-wall polymers and other algicidal processes, and decreased functions associated with Quorum Quenching and photosynthetic response. We conclude that warming and nutrient enrichment can dysregulate the microbiome of seaweeds, providing a plausible mechanism for their ongoing loss, and encourage more research into the effects of human impacts on crucial but yet largely unstudied host-microbiome relationships in different aquatic and terrestrial species.
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Affiliation(s)
- Francesco Paolo Mancuso
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, viale delle Scienze Ed. 16, 90128 Palermo, Italy; Department of Biological, Geological, and Environmental Sciences, University of Bologna, Ravenna, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
| | - Kathryn Lee Morrissey
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Laura Airoldi
- NBFC, National Biodiversity Future Center, Palermo 90133, Italy; Chioggia Hydrobiological Station "Umberto D'Ancona", Department of Biology, UO CoNISMa, University of Padova, Chioggia, Italy.
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7
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Delva S, De Baets B, Baetens JM, De Clerck O, Stock W. No bacterial-mediated alleviation of thermal stress in a brown seaweed suggests the absence of ecological bacterial rescue effects. Sci Total Environ 2023; 876:162532. [PMID: 36870499 DOI: 10.1016/j.scitotenv.2023.162532] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
While microbiome alterations are increasingly proposed as a rapid mechanism to buffer organisms under changing environmental conditions, studies of these processes in the marine realm are lagging far behind their terrestrial counterparts. Here, we used a controlled laboratory experiment to examine whether the thermal tolerance of the brown seaweed Dictyota dichotoma, a common species in European coastal ecosystems, could be enhanced by the repeated addition of bacteria from its natural environment. Juvenile algae from three genotypes were subjected for two weeks to a temperature gradient, spanning almost the entire thermal range that can be tolerated by the species (11-30 °C). At the start of the experiment and again in the middle of the experiment, the algae were inoculated with bacteria from their natural environment or left untouched as a control. Relative growth rate was measured over the two-week period, and we assessed bacterial community composition prior to and at the end of the experiment. Since the growth of D. dichotoma over the full thermal gradient was not affected by supplementing bacteria, our results indicate no scope for bacterial-mediated stress alleviation. The minimal changes in the bacterial communities linked to bacterial addition, particularly at temperatures above the thermal optimum (22-23 °C), suggest the existence of a barrier to bacterial recruitment. These findings indicate that ecological bacterial rescue is unlikely to play a role in mitigating the effects of ocean warming on this brown seaweed.
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Affiliation(s)
- Soria Delva
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium; Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Bernard De Baets
- Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Jan M Baetens
- Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium.
| | - Willem Stock
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium.
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8
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Blomme J, Wichard T, Jacobs TB, De Clerck O. Ulva: An emerging green seaweed model for systems biology. J Phycol 2023. [PMID: 37256696 DOI: 10.1111/jpy.13341] [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: 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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9
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Bafort Q, Prost L, Aydogdu E, Van de Vloet A, Casteleyn G, Van de Peer Y, De Clerck O. Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas. Methods Mol Biol 2023; 2545:351-372. [PMID: 36720822 DOI: 10.1007/978-1-0716-2561-3_18] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this chapter, we present the use of Chlamydomonas reinhardtii in experiments designed to study the evolutionary impacts of whole genome duplication. We shortly introduce the algal species and depict why it is an excellent model for experimental evolution. Subsequently, we discuss the most relevant steps and methods in the design of a ploidy-related Chlamydomonas experiment. These steps include strain selection, ploidy determination, different methods of making diplo- and polyploid Chlamydomonas cells, replication, culturing conditions, preservation, and the ways to quantify phenotypic and genotypic change.
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Affiliation(s)
- Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Lucas Prost
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,Department of Biology, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Eylem Aydogdu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Antoine Van de Vloet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Griet Casteleyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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10
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Bafort Q, Wu T, Natran A, De Clerck O, Van de Peer Y. The immediate effects of polyploidization of Spirodela polyrhiza change in a strain-specific way along environmental gradients. Evol Lett 2023; 7:37-47. [PMID: 37065435 PMCID: PMC10091501 DOI: 10.1093/evlett/qrac003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
The immediate effects of plant polyploidization are well characterized and it is generally accepted that these morphological, physiological, developmental, and phenological changes contribute to polyploid establishment. Studies on the environmental dependence of the immediate effects of whole-genome duplication (WGD) are, however, scarce but suggest that these immediate effects are altered by stressful conditions. As polyploid establishment seems to be associated with environmental disturbance, the relationship between ploidy-induced phenotypical changes and environmental conditions is highly relevant. Here, we use a common garden experiment on the greater duckweed Spirodela polyrhiza to test whether the immediate effects of WGD can facilitate the establishment of tetraploid duckweed along gradients of two environmental stressors. Because successful polyploid establishment often depends on recurrent polyploidization events, we include four genetically diverse strains and assess whether these immediate effects are strain-specific. We find evidence that WGD can indeed confer a fitness advantage under stressful conditions and that the environment affects ploidy-induced changes in fitness and trait reaction norms in a strain-specific way.
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Affiliation(s)
- Quinten Bafort
- Department of Biology, Ghent University , Ghent , Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | - Tian Wu
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing , China
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria , South Africa
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11
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Bogaert KA, Zakka EE, Coelho SM, De Clerck O. Polarization of brown algal zygotes. Semin Cell Dev Biol 2023; 134:90-102. [PMID: 35317961 DOI: 10.1016/j.semcdb.2022.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/29/2022]
Abstract
Brown algae are a group of multicellular, heterokont algae that have convergently evolved developmental complexity that rivals that of embryophytes, animals or fungi. Early in development, brown algal zygotes establish a basal and an apical pole, which will become respectively the basal system (holdfast) and the apical system (thallus) of the adult alga. Brown algae are interesting models for understanding the establishment of cell polarity in a broad evolutionary context, because they exhibit a large diversity of life cycles, reproductive strategies and, importantly, their zygotes are produced in large quantities free of parental tissue, with symmetry breaking and asymmetric division taking place in a highly synchronous manner. This review describes the current knowledge about the establishment of the apical-basal axis in the model brown seaweeds Ectocarpus, Dictyota, Fucus and Saccharina, highlighting the advantages and specific interests of each system. Ectocarpus is a genetic model system that allows access to the molecular basis of early development and life-cycle control over apical-basal polarity. The oogamous brown alga Fucus, together with emerging comparative models Dictyota and Saccharina, emphasize the diversity of strategies of symmetry breaking in determining a cell polarity vector in brown algae. A comparison with symmetry-breaking mechanisms in land plants, animals and fungi, reveals that the one-step zygote polarisation of Fucus compares well to Saccharomyces budding and Arabidopsis stomata development, while the two-phased symmetry breaking in the Dictyota zygote compares to Schizosaccharomyces fission, the Caenorhabditis anterior-posterior zygote polarisation and Arabidopsis prolate pollen polarisation. The apical-basal patterning in Saccharina zygotes on the other hand, may be seen as analogous to that of land plants. Overall, brown algae have the potential to bring exciting new information on how a single cell gives rise to an entire complex body plan.
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Affiliation(s)
- Kenny A Bogaert
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium.
| | - Eliane E Zakka
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium
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12
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Boo GH, Leliaert F, Le Gall L, Coppejans E, De Clerck O, Van Nguyen T, Payri CE, Miller KA, Yoon HS. Ancient Tethyan Vicariance and Long-Distance Dispersal Drive Global Diversification and Cryptic Speciation in the Red Seaweed Pterocladiella. Front Plant Sci 2022; 13:849476. [PMID: 35720545 PMCID: PMC9201827 DOI: 10.3389/fpls.2022.849476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
We investigated the globally distributed red algal genus Pterocladiella, comprising 24 described species, many of which are economically important sources of agar and agarose. We used DNA-based species delimitation approaches, phylogenetic, and historical biogeographical analyses to uncover cryptic diversity and infer the drivers of biogeographic patterns. We delimited 43 species in Pterocladiella, of which 19 are undescribed. Our multigene time-calibrated phylogeny and ancestral area reconstruction indicated that Pterocladiella most likely originated during the Early Cretaceous in the Tethys Sea. Ancient Tethyan vicariance and long-distance dispersal have shaped current distribution patterns. The ancestor of Eastern Pacific species likely arose before the formation of the formidable Eastern Pacific Barrier-a first confirmation using molecular data in red algae. Divergences of Northeast and Southeast Pacific species have been driven by the Central American Seaway barrier, which, paradoxically, served as a dispersal pathway for Atlantic species. Both long- and short-distance dispersal scenarios are supported by genetic relationships within cosmopolitan species based on haplotype analysis. Asymmetrical distributions and the predominance of peripatry and sympatry between sister species suggest the importance of budding speciation in Pterocladiella. Our study highlights the underestimation of global diversity in these crucial components of coastal ecosystems and provides evidence for the complex evolution of current species distributions.
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Affiliation(s)
- Ga Hun Boo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- University Herbarium, University of California, Berkeley, CA, United States
| | - Frederik Leliaert
- Meise Botanic Garden, Meise, Belgium
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Line Le Gall
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Eric Coppejans
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Tu Van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Claude E. Payri
- UMR Entropie (IRD, Ifremer, Univ Nouvelle-Calédonie, Univ La Réunion, CNRS), Nouméa, New Caledonia
| | - Kathy Ann Miller
- University Herbarium, University of California, Berkeley, CA, United States
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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13
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Rodríguez-Prieto C, De Clerck O, Guiry MD, Lin SM. Revisiting the systematics of the genera Grateloupia, Phyllymenia, and Prionitis (Halymeniaceae, Rhodophyta) with a description of a new species-Prionitis taiwani-borealis. J Phycol 2022; 58:234-250. [PMID: 34850392 DOI: 10.1111/jpy.13226] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The taxonomy of the genera Grateloupia, Phyllymenia, and Prionitis has been revised several times but remains controversial. The anatomy of female reproductive structures in combination with phylogenetic reconstructions is mostly used to define the genera. However, the architecture and behavior of the auxiliary cell ampullae before and after diploidization are not well documented for most species. To fill this knowledge gap, we examined the female reproductive structures of a new species (Prionitis taiwani-borealis sp. nov.) from Taiwan and compared our observations to the species currently placed in the Phyllymenia/Prionitis complex. The female reproductive structures of the Phyllymenia/Prionitis complex are characterized by (1) 2-celled carpogonial branches with the supporting cell being the basal cell of a third-order ampullar filament; (2) auxiliary cell ampullae composed of three orders of unbranched ampullar filaments before diploidization; (3) cells of auxiliary cell ampullar filaments forming a cellular cluster after diploidization and surrounding the developing gonimoblasts; (4) gonimoblast initials produced from the diploidized auxiliary cells before fusing with them; and (5) branched auxiliary cell ampullar and secondary medullary filaments involved in early pericarp formation. A monophyletic relationship of species possessing female structures similar to those of Pr. taiwani-borealis and related species was highly supported based on combined rbcL and LSU rDNA sequence analyses. The female reproductive structures of other species of Grateloupia sensu lato, phylogenetically closely related to the Prionitis and Phyllymenia assemblage, require reinvestigation as correct interpretations of pre- and post-fertilization events have proven to be informative for resolving the systematics of the Halymeniaceae.
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Affiliation(s)
- Conxi Rodríguez-Prieto
- Department of Environmental Sciences, Faculty of Sciences, University of Girona, M. Aurèlia Capmany 69, 17003, Girona, Spain
| | - Olivier De Clerck
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Michael D Guiry
- AlgaeBase, Ryan Institute, National University of Ireland, University Road, Galway, H91 TK33, Ireland
| | - Showe-Mei Lin
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan, R.O.C
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14
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Hou Z, Ma X, Shi X, Li X, Yang L, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomic insights into a Mesoproterozoic-Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae). Nat Commun 2022; 13:1610. [PMID: 35318329 PMCID: PMC8941102 DOI: 10.1038/s41467-022-29282-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/09/2022] [Indexed: 01/09/2023] Open
Abstract
The Ulvophyceae, a major group of green algae, is of particular evolutionary interest because of its remarkable morphological and ecological diversity. Its phylogenetic relationships and diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- and concatenation-based approaches to reconstruct the phylogeny of the Ulvophyceae and to explore the sources of conflict in previous phylogenomic studies. The Ulvophyceae is recovered as a paraphyletic group, with the Bryopsidales being a sister group to the Chlorophyceae, and the remaining taxa forming a clade (Ulvophyceae sensu stricto). Molecular clock analyses with different calibration strategies emphasize the large impact of fossil calibrations, and indicate a Meso-Neoproterozoic origin of the Ulvophyceae (sensu stricto), earlier than previous estimates. The results imply that ulvophyceans may have had a profound influence on oceanic redox structures and global biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition. “Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
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Affiliation(s)
- Zheng Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xi Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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Bogaert KA, Blomme J, Beeckman T, De Clerck O. Auxin's origin: do PILS hold the key? Trends Plant Sci 2022; 27:227-236. [PMID: 34716098 DOI: 10.1016/j.tplants.2021.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/23/2021] [Accepted: 09/28/2021] [Indexed: 05/12/2023]
Abstract
Auxin is a key regulator of many developmental processes in land plants and plays a strikingly similar role in the phylogenetically distant brown seaweeds. Emerging evidence shows that the PIN and PIN-like (PILS) auxin transporter families have preceded the evolution of the canonical auxin response pathway. A wide conservation of PILS-mediated auxin transport, together with reports of auxin function in unicellular algae, would suggest that auxin function preceded the advent of multicellularity. We find that PIN and PILS transporters form two eukaryotic subfamilies within a larger bacterial family. We argue that future functional characterisation of algal PIN and PILS transporters can shed light on a common origin of an auxin function followed by independent co-option in a multicellular context.
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Affiliation(s)
- Kenny Arthur Bogaert
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium.
| | - Jonas Blomme
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB-UGent, Technologiepark 72, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB-UGent, Technologiepark 72, B-9052 Ghent, Belgium
| | - Olivier De Clerck
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium
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16
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Liu X, Blomme J, Bogaert KA, D’hondt S, Wichard T, Deforce D, Van Nieuwerburgh F, De Clerck O. Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction. BMC Plant Biol 2022; 22:19. [PMID: 34991492 PMCID: PMC8734247 DOI: 10.1186/s12870-021-03361-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/17/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. RESULTS Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, was studied. We analyzed transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrated that 45% of the genes in the genome were differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionarily conserved transcription factor containing an RWP-RK domain suggested a key role during Ulva gametogenesis. CONCLUSIONS Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in the induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.
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Affiliation(s)
- Xiaojie Liu
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Jonas Blomme
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Kenny A. Bogaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Sofie D’hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | | | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
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17
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Morrissey KL, Iveša L, Delva S, D'Hondt S, Willems A, De Clerck O. Impacts of environmental stress on resistance and resilience of algal-associated bacterial communities. Ecol Evol 2021; 11:15004-15019. [PMID: 34765156 PMCID: PMC8571626 DOI: 10.1002/ece3.8184] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
Algal-associated bacteria are fundamental to the ecological success of marine green macroalgae such as Caulerpa. The resistance and resilience of algal-associated microbiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal morphological niches. Therefore, the level of response to various environmental perturbations may in fact be different for each niche-specific community. Factorial in situ experiments were set up to investigate the effect of nutrient enrichment and temperature stress on the bacterial communities associated with Caulerpa cylindracea. Bacteria were characterized using the 16S rRNA gene, and the community compositions were compared between different parts of the algal thallus (endo-, epi-, and rhizomicrobiome). Resistance and resilience were calculated to further understand the changes of microbial composition in response to perturbations. The results of this study provide evidence that nutrient enrichment has a significant influence on the taxonomic and functional structure of the epimicrobiota, with a low community resistance index observed for both. Temperature and nutrient stress had a significant effect on the rhizomicrobiota taxonomic composition, exhibiting the lowest overall resistance to change. The functional performance of the rhizomicrobiota had low resilience to the combination of stressors, indicating potential additive effects. Interestingly, the endomicrobiota had the highest overall resistance, yet the lowest overall resilience to environmental stress. This further contributes to our understanding of algal microbiome dynamics in response to environmental changes.
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Affiliation(s)
| | - Ljiljana Iveša
- Center for Marine ResearchRuđer Bošković InstituteRovinjCroatia
| | - Soria Delva
- Phycology Research GroupDepartment of BiologyGhent UniversityGhentBelgium
| | - Sofie D'Hondt
- Phycology Research GroupDepartment of BiologyGhent UniversityGhentBelgium
| | - Anne Willems
- Laboratory of MicrobiologyDepartment of Biochemistry and MicrobiologyGhent UniversityGhentBelgium
| | - Olivier De Clerck
- Phycology Research GroupDepartment of BiologyGhent UniversityGhentBelgium
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18
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19
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Paix B, Vieira C, Potin P, Leblanc C, De Clerck O, Briand JF, Culioli G. French Mediterranean and Atlantic populations of the brown algal genus Taonia (Dictyotales) display differences in phylogeny, surface metabolomes and epibacterial communities. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Blomme J, Liu X, Jacobs TB, De Clerck O. A molecular toolkit for the green seaweed Ulva mutabilis. Plant Physiol 2021; 186:1442-1454. [PMID: 33905515 PMCID: PMC8260120 DOI: 10.1093/plphys/kiab185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/02/2021] [Indexed: 06/02/2023]
Abstract
The green seaweed Ulva mutabilis is an ecologically important marine primary producer as well as a promising cash crop cultivated for multiple uses. Despite its importance, several molecular tools are still needed to better understand seaweed biology. Here, we report the development of a flexible and modular molecular cloning toolkit for the green seaweed U. mutabilis based on a Golden Gate cloning system. The toolkit presently contains 125 entry vectors, 26 destination vectors, and 107 functionally validated expression vectors. We demonstrate the importance of endogenous regulatory sequences for transgene expression and characterize three endogenous promoters suitable to drive transgene expression. We describe two vector architectures to express transgenes via two expression cassettes or a bicistronic approach. The majority of selected transformants (50%-80%) consistently give clear visual transgene expression. Furthermore, we made different marker lines for intracellular compartments after evaluating 13 transit peptides and 11 tagged endogenous Ulva genes. Our molecular toolkit enables the study of Ulva gain-of-function lines and paves the way for gene characterization and large-scale functional genomics studies in a green seaweed.
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Affiliation(s)
- Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent 9000, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
| | - Xiaojie Liu
- Department of Biology, Phycology Research Group, Ghent University, Ghent 9000, Belgium
| | - Thomas B Jacobs
- VIB-UGent Center for Plant Systems Biology, Ghent 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Ghent 9000, Belgium
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21
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Tran LAT, Bafort Q, Steen F, Gómez Garreta A, D'Hondt S, Miller KA, Vranken S, Žuljević A, Smith JE, De Clerck O. Dictyota cyanoloma (Dictyotales, Phaeophyceae), a Newly Introduced Brown Algal Species in California. J Phycol 2021; 57:370-378. [PMID: 33179252 DOI: 10.1111/jpy.13100] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
Here, we report for the first time the presence of Dictyota cyanoloma in southern California. Dictyota cyanoloma is conspicuous in harbors and bays by its distinctive bright blue-iridescent margins. This species was originally described from Europe, but subsequent studies have revealed that it represented an introduction from Australia. The current distribution of D. cyanoloma comprises southern Australia and the North East Atlantic, including the Mediterranean Sea and the Macaronesian islands. The presence of D. cyanoloma in southern California is supported by molecular cox1 and psbA gene sequences. A reconstruction of the invasive history based on nine polymorphic microsatellite markers reveals a close affinity of the Californian specimens with European populations. Dictyota cyanoloma in the United States appears to be (so far) restricted to the Californian coast from San Diego Bay in the south to Santa Catalina Island and Long Beach Harbor in the north. A correlative species distribution model suggests gradually declining habitat suitability north of the Southern Californian Bight and high suitability in Baja California, including the Gulf of California. Finally, its widespread abundance in bays and harbors suggests shipping is a likely transport mechanism.
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Affiliation(s)
- Lan-Anh T Tran
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Quinten Bafort
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Frederique Steen
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Amelia Gómez Garreta
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l'Alimentació, IRBio & CeDocBiV, Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028, Barcelona, Spain
| | - Sofie D'Hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Kathy Ann Miller
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
| | - Sofie Vranken
- School of Biological Sciences & UWA Oceans Institute, The University of Western Australia, Fairway 64, 6009, Crawley, Western Australia, Australia
| | - Ante Žuljević
- Laboratory of Phytobenthos, Institute of Oceanography and Fisheries, I Meštrovića 63, Split, Croatia
| | - Jennifer E Smith
- Marine Biology Research Division, Scripps Institution of Oceanography, UC San Diego, 9500 Gilman Dr #0202, La Jolla, California, 92093-0202, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
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22
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Lin SM, De Clerck O, Leliaert F, Chuang YC. Systematics and Biogeography of the Red Algal Genus Yonagunia (Halymeniaceae, Rhodophyta) from the Indo-Pacific Including the Description of Two New Species from Taiwan. J Phycol 2020; 56:1542-1556. [PMID: 32713001 DOI: 10.1111/jpy.13055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
Carpopeltis maillardii has been regarded as a widely distributed species in the Indo-Pacific region. In this study, we analyzed the genetic diversity of C. maillardii and related species collected from Taiwan and the Indian Ocean based on rbcL sequences, in order to elucidate species boundaries, diversity, and biogeographic patterns. Our analyses show that C. maillardii specimens are only distantly related to the genus Carpopeltis (type: C. phyllophora) but instead form a clade together with species of Yonagunia. We therefore propose the new combination Yonagunia maillardii comb. nov. In addition, two new species (Yonagunia palmata sp. nov. and Yonagunia taiwani-borealis sp. nov.) are described from Taiwan. The close relationship of Yonagunia to Grateloupia is corroborated by detailed observations of the female reproductive structures, which demonstrate that the development of auxiliary cell ampullae before and after diploidization is similar to that of Grateloupia sensu stricto. Namely, the ampullae are composed of only two orders of unbranched filaments in which only a few ampullar cells are incorporated into a basal fusion cell after diploidization of the auxiliary cell and the pericarp consists almost entirely of secondary medullary filaments. Of all Yonagunia species, Y. maillardii has the widest distribution in the Indo-Pacific, and can be identified in the field by its relatively thin, feathery, and highly branched morphology. Most other species, including those that occur in Taiwan, are seemingly more range-restricted. Our phylogenetic analyses resulted in a well-resolved phylogeny of Yonagunia, with an origin estimated in the Eocene-Oligocene, and diversification of species mainly in the Miocene.
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Affiliation(s)
- Showe-Mei Lin
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan, R.O.C
| | - Olivier De Clerck
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
| | - Ya-Chu Chuang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan, R.O.C
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23
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Booy O, Robertson PA, Moore N, Ward J, Roy HE, Adriaens T, Shaw R, Van Valkenburg J, Wyn G, Bertolino S, Blight O, Branquart E, Brundu G, Caffrey J, Capizzi D, Casaer J, De Clerck O, Coughlan NE, Davis E, Dick JTA, Essl F, Fried G, Genovesi P, González-Moreno P, Huysentruyt F, Jenkins SR, Kerckhof F, Lucy FE, Nentwig W, Newman J, Rabitsch W, Roy S, Starfinger U, Stebbing PD, Stuyck J, Sutton-Croft M, Tricarico E, Vanderhoeven S, Verreycken H, Mill AC. Using structured eradication feasibility assessment to prioritize the management of new and emerging invasive alien species in Europe. Glob Chang Biol 2020; 26:6235-6250. [PMID: 32851731 DOI: 10.1111/gcb.15280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
Prioritizing the management of invasive alien species (IAS) is of global importance and within Europe integral to the EU IAS regulation. To prioritize management effectively, the risks posed by IAS need to be assessed, but so too does the feasibility of their management. While the risk of IAS to the EU has been assessed, the feasibility of management has not. We assessed the feasibility of eradicating 60 new (not yet established) and 35 emerging (established with limited distribution) species that pose a threat to the EU, as identified by horizon scanning. The assessment was carried out by 34 experts in invasion management from across Europe, applying the Non-Native Risk Management scheme to defined invasion scenarios and eradication strategies for each species, assessing the feasibility of eradication using seven key risk management criteria. Management priorities were identified by combining scores for risk (derived from horizon scanning) and feasibility of eradication. The results show eradication feasibility score and risk score were not correlated, indicating that risk management criteria evaluate different information than risk assessment. In all, 17 new species were identified as particularly high priorities for eradication should they establish in the future, whereas 14 emerging species were identified as priorities for eradication now. A number of species considered highest priority for eradication were terrestrial vertebrates, a group that has been the focus of a number of eradication attempts in Europe. However, eradication priorities also included a diverse range of other taxa (plants, invertebrates and fish) suggesting there is scope to broaden the taxonomic range of attempted eradication in Europe. We demonstrate that broad scale structured assessments of management feasibility can help prioritize IAS for management. Such frameworks are needed to support evidence-based decision-making.
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Affiliation(s)
- Olaf Booy
- Animal and Plant Health Agency, Non-Native Species Secretariat, Sand Hutton, York, UK
- Modelling, Evidence and Policy Group, Newcastle University, Newcastle upon Tyne, UK
| | - Pete A Robertson
- Modelling, Evidence and Policy Group, Newcastle University, Newcastle upon Tyne, UK
| | - Niall Moore
- Animal and Plant Health Agency, Non-Native Species Secretariat, Sand Hutton, York, UK
| | - Jess Ward
- Modelling, Evidence and Policy Group, Newcastle University, Newcastle upon Tyne, UK
| | - Helen E Roy
- UK Centre for Ecology and Hydrology, Wallingford, UK
| | - Tim Adriaens
- Research Institute for Nature and Forest (INBO), Wildlife Management and Invasive Species, Brussels, Belgium
| | | | - Johan Van Valkenburg
- Netherlands Food and Consumer Product Safety Authority, National Reference Centre, Wageningen, Netherlands
| | | | - Sandro Bertolino
- Department of Agriculture, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Olivier Blight
- Institut Méditerranéen de Biodiversité et d'Ecologie, Avignon Université, UMR CNRS IRD Aix Marseille Université, Avignon, France
| | - Etienne Branquart
- Invasive Species Unit, Service Public de Wallonie, Wallonia, Belgium
| | - Giuseppe Brundu
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Joe Caffrey
- INVAS Biosecurity, Stillorgan, Co Dublin, Ireland
| | - Dario Capizzi
- Directorate for Natural Capital, Latium Region, Parks and Protected Areas, Rome, Italy
| | - Jim Casaer
- Research Institute for Nature and Forest (INBO), Wildlife Management and Invasive Species, Brussels, Belgium
| | - Olivier De Clerck
- Biology Department, Research Group Phycology, Ghent University, Ghent, Belgium
| | | | - Eithne Davis
- Department of Environmental Science, Centre for Environmental Research, Innovation and Sustainability, Institute of Technology, Ash Lane, Sligo, Ireland
| | | | - Franz Essl
- Division of Conservation Biology, Vegetation Ecology and Landscape Ecology, University Vienna, Vienna, Austria
| | - Guillaume Fried
- Entomology and Invasive Plants Unit, Plant Health Laboratory, Montferrier-sur-Lez, France
| | - Piero Genovesi
- Institute for Environmental Protection and Research (ISPRA), and Chair IUCN SSC Invasive Species Specialist Group, Rome, Italy
| | - Pablo González-Moreno
- CABI Science Centre, Egham, Surrey, UK
- Department of Forest Engineering (ERSAF), University of Córdoba, Córdoba, Spain
| | - Frank Huysentruyt
- Research Institute for Nature and Forest (INBO), Wildlife Management and Invasive Species, Brussels, Belgium
| | | | - Francis Kerckhof
- Royal Belgian Institute of Natural Sciences (RBINS), Oostende, Belgium
| | - Frances E Lucy
- Department of Environmental Science, Centre for Environmental Research, Innovation and Sustainability, Institute of Technology, Ash Lane, Sligo, Ireland
| | | | | | | | - Sugoto Roy
- International Union for the Conservation of Nature, Gland, Switzerland
| | | | | | - Jan Stuyck
- Research Institute for Nature and Forest (INBO), Wildlife Management and Invasive Species, Brussels, Belgium
| | | | | | | | - Hugo Verreycken
- Research Institute for Nature and Forest (INBO), Wildlife Management and Invasive Species, Brussels, Belgium
| | - Aileen C Mill
- Modelling, Evidence and Policy Group, Newcastle University, Newcastle upon Tyne, UK
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24
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Peña V, Vieira C, Braga JC, Aguirre J, Rösler A, Baele G, De Clerck O, Le Gall L. Radiation of the coralline red algae (Corallinophycidae, Rhodophyta) crown group as inferred from a multilocus time-calibrated phylogeny. Mol Phylogenet Evol 2020; 150:106845. [DOI: 10.1016/j.ympev.2020.106845] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 01/20/2023]
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25
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Zhang Z, Qu C, Zhang K, He Y, Zhao X, Yang L, Zheng Z, Ma X, Wang X, Wang W, Wang K, Li D, Zhang L, Zhang X, Su D, Chang X, Zhou M, Gao D, Jiang W, Leliaert F, Bhattacharya D, De Clerck O, Zhong B, Miao J. Adaptation to Extreme Antarctic Environments Revealed by the Genome of a Sea Ice Green Alga. Curr Biol 2020; 30:3330-3341.e7. [PMID: 32619486 DOI: 10.1016/j.cub.2020.06.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023]
Abstract
The unicellular green alga Chlamydomonas sp. ICE-L thrives in polar sea ice, where it tolerates extreme low temperatures, high salinity, and broad seasonal fluctuations in light conditions. Despite the high interest in biotechnological uses of this species, little is known about the adaptations that allow it to thrive in this harsh and complex environment. Here, we assembled a high-quality genome sequence of ∼542 Mb and found that retrotransposon proliferation contributed to the relatively large genome size of ICE-L when compared to other chlorophytes. Genomic features that may support the extremophilic lifestyle of this sea ice alga include massively expanded gene families involved in unsaturated fatty acid biosynthesis, DNA repair, photoprotection, ionic homeostasis, osmotic homeostasis, and reactive oxygen species detoxification. The acquisition of multiple ice binding proteins through putative horizontal gene transfer likely contributed to the origin of the psychrophilic lifestyle in ICE-L. Additional innovations include the significant upregulation under abiotic stress of several expanded ICE-L gene families, likely reflecting adaptive changes among diverse metabolic processes. Our analyses of the genome, transcriptome, and functional assays advance general understanding of the Antarctic green algae and offer potential explanations for how green plants adapt to extreme environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Changfeng Qu
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Kaijian Zhang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Yingying He
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Zhou Zheng
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xixi Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Wenyu Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Kai Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Dan Li
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Liping Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xin Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Danyan Su
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Dan Gao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Frederik Leliaert
- Biology Department, Ghent University, 9000 Ghent, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China.
| | - Jinlai Miao
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China.
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26
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Vieira C, Morrow K, D'Hondt S, Camacho O, Engelen AH, Payri CE, De Clerck O. Diversity, Ecology, Biogeography, and Evolution of the Prevalent Brown Algal Genus Lobophora in the Greater Caribbean Sea, Including the Description of Five New Species 1. J Phycol 2020; 56:592-607. [PMID: 32159226 DOI: 10.1111/jpy.12986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Distributed in tropical and warm-temperate waters worldwide, Lobophora species are found across the Greater Caribbean (i.e., Caribbean sensu stricto, Gulf of Mexico, Florida, the Bahamas, and Bermuda). We presently discuss the diversity, ecology, biogeography, and evolution of the Greater Caribbean Lobophora species based on previous studies and an extensive number of samples collected across the eastern, southern, and to a lesser extent western Caribbean. A total of 18 Lobophora species are now documented from the Greater Caribbean, of which five are newly described (L. agardhii sp. nov., L. dickiei sp. nov., L. lamourouxii sp. nov., L. richardii sp. nov., and L. setchellii sp. nov.). Within the Greater Caribbean, the eastern Caribbean and the Central Province are the most diverse ecoregion and province (16 spp.), respectively. Observed distribution patterns indicate that Lobophora species from the Greater Caribbean have climate affinities (i.e., warm-temperate vs. tropical affinities). In total, 11 Lobophora species exclusively occur in the Greater Caribbean; six are present in the western Atlantic; two in the Indo-Pacific; and one in the eastern Pacific. Biogeographic analyses support that no speciation occurred across the Isthmus of Panama, and that the Greater Caribbean acted as a recipient region for species from the Indo-Pacific and as a region of diversification as well as a donor region to the North-eastern Atlantic. The Greater Caribbean is not an evolutionary dead end for Lobophora, but instead generates and exports diversity. Present results illustrate how sampling based on DNA identification is reshaping biogeographic patterns, as we know them.
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Affiliation(s)
- Christophe Vieira
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
- Kobe University Research Center for Inland Seas, Rokkodai, Kobe, 657-8501, Japan
| | - Kathleen Morrow
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, 03824, USA
| | - Sofie D'Hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Olga Camacho
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | - Aschwin H Engelen
- CCMAR, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
- CARMABI Research Station, Piscadera Bay, Willemstad, Curaçao
| | - Claude E Payri
- UMR ENTROPIE (IRD, UR, CNRS), LabEx-CORAIL, Institut de Recherche pour le Développement, B.P. A5, Nouméa Cedex, Nouvelle-Calédonie, 98848, France
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
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Vieira C, Henriques F, D'hondt S, Neto A, Almada CH, Kaufmann M, Sansón M, Sangil C, Clerck OD. Lobophora (Dictyotales) Species Richness, Ecology and Biogeography Across the North-Eastern Atlantic Archipelagos and Description of Two New Species 1. J Phycol 2020; 56:346-357. [PMID: 31849038 DOI: 10.1111/jpy.12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
The brown alga Lobophora (Dictyotales, Phaeophyceae) is an important macroalga in the North-eastern Atlantic archipelagos (i.e., Macaronesia). Notably in the Canaries it can dominate benthic assemblages. While the genus has been the subject of several ecological studies in the Canaries, no study has yet been conducted to assess species-level diversity of Lobophora in Macaronesia. We reassessed the diversity of Lobophora in Macaronesia, reporting the presence of seven species (L. caboverdeana sp. nov., L. canariensis, L. dagamae sp. nov., L. delicata, L. dispersa, L. littlerorum, and L. schneideri). Lobophora spp. from Macaronesia are morphologically and ecologically distinguishable. In the Canaries, L. schneideri dominates the photophilic assemblages from the intertidal to 20-30 m depth. Lobophora dagamae sp. nov. grows in less illuminated shallow habitats, and replaces L. schneideri from 30 to ~80 m. Lobophora canariensis also has a wide vertical distribution, from the intertidal to deep waters, while L. delicata, L. dispersa and L. littlerorum grow in shallow waters. The dominance of species with an upright habit versus prostrate or crustose species may be mediated by the pressure of herbivores. Four species have an amphi-Atlantic distribution: L. littlerorum, L. canariensis, L. delicata, and L. schneideri. Lobophora schneideri and L. delicata are furthermore distributed in the Mediterranean Sea. By sampling a pivotal region in the Atlantic, this study significantly improves our knowledge of Lobophora biogeography in the Atlantic Ocean. Macaronesia constitutes a species-poor region for Lobophora where no diversification events occurred, and a region of overlap between the Greater Caribbean and the Indo-Pacific.
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Affiliation(s)
- Christophe Vieira
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Filipe Henriques
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Gambelas, 8005-139, Faro, Portugal
- MARE-Marine and Environmental Sciences Centre, Quinta do Lorde Marina, Sítio da Piedade, 9200-044, Caniçal, Madeira Island, Portugal
| | - Sofie D'hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Ana Neto
- GBA-cE3c, Azorean Biodiversity Group-Centre for Ecology, Evolution & Environmental Changes, Faculdade de Ciências e Tecnologia, Departamento de Biologia, Universidade dos Açores, Rua da Mãe de Deus, 9500-321, Ponta Delgada, São Miguel, Açores, Portugal
| | - Carmen H Almada
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde, Campus do Palmarejo, CP - 279, Praia, Santiago - Cabo Verde
| | - Manfred Kaufmann
- Marine Biology Station of Funchal, Faculty of Life Sciences, University of Madeira, 9000-107, Funchal, Madeira, Portugal
- Interdisciplinary Center of Marine and Environmental Research-CIMAR/CIIMAR, University of Porto, Novo Edificio do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, 4450-208, Matosinhos, Portugal
| | - Marta Sansón
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, Canary Islands, Spain
| | - Carlos Sangil
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, Canary Islands, Spain
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
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28
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Lespinats S, De Clerck O, Colange B, Gorelova V, Grando D, Maréchal E, Van Der Straeten D, Rébeillé F, Bastien O. Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase. Acta Biotheor 2020; 68:139-156. [PMID: 31312977 DOI: 10.1007/s10441-019-09352-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/10/2019] [Indexed: 11/27/2022]
Abstract
During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the evolutionary trajectories of proteins in the sequence space. Using the data-driven high-dimensional scaling method, we show that it is possible to predict and represent potential evolutionary trajectories by representing phylogenetic trees into a 3D projection of the sequence space. With the case of the aminodeoxychorismate synthase, an enzyme involved in folate synthesis, we show that this representation raises interesting questions about the complexity of the evolution of a given biological function, in particular concerning its capacity to explore the sequence space.
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Affiliation(s)
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Benoît Colange
- Univ. Grenoble Alpes, INES, 73375, Le Bourget du Lac, France
| | - Vera Gorelova
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium
- Department of Botany and Plant Biology, Laboratory of Plant Biochemistry and Physiology, University of Geneva, Quai E. Ansermet 30, 1211, Geneva, Switzerland
| | - Delphine Grando
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France
| | - Eric Maréchal
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France
| | - Dominique Van Der Straeten
- Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Fabrice Rébeillé
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France
| | - Olivier Bastien
- Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France.
- Laboratoire de Physiologie Cellulaire Végétale, Département Réponse et Dynamique Cellulaire, CEA Grenoble, UMR 5168, CNRS-CEA-INRA-Université J. Fourier, 17 rue des Martyrs, 38054, Grenoble Cedex 09, France.
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29
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Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci U S A 2020; 117:2551-2559. [PMID: 31911467 PMCID: PMC7007542 DOI: 10.1073/pnas.1910060117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | | | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Sofie D'hondt
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
- School of Biological Sciences, University of Western Australia, WA 6009, Australia
- Climate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium;
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Meise Botanic Garden, 1860 Meise, Belgium
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30
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Boo GH, Qiu YX, Kim JY, Ang PO, Bosch S, De Clerck O, He P, Higa A, Huang B, Kogame K, Liu SL, van Nguyen T, Suda S, Terada R, Miller KA, Boo SM. Contrasting patterns of genetic structure and phylogeography in the marine agarophytes Gelidiophycus divaricatus and G. freshwateri (Gelidiales, Rhodophyta) from East Asia. J Phycol 2019; 55:1319-1334. [PMID: 31390066 DOI: 10.1111/jpy.12910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.
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Affiliation(s)
- Ga Hun Boo
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jung Yeon Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Put O Ang
- Marine Science Laboratory, The Chinese University of Hong Kong, Shatin N.T, Hong Kong SAR, China
| | - Samuel Bosch
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000, Gent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000, Gent, Belgium
| | - Peimin He
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Atsushi Higa
- Okinawa Environmental Analysis Center Co. Ltd, 3-7-24 Maehara, Ginowan, Okinawa, 901-2215, Japan
| | - Bangqin Huang
- Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Fujian, China
| | - Kazuhiro Kogame
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
| | - Tu van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan, District 3, Ho Chi Minh City, Vietnam
| | - Shoichiro Suda
- Department of Chemistry, Biology & Marine Science, Faculty of Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Ryuta Terada
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto 1-21-24, Kagoshima, 890-0065, Japan
| | - Kathy Ann Miller
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
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31
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Westmeijer G, Everaert G, Pirlet H, De Clerck O, Vandegehuchte MB. Mechanistic niche modelling to identify favorable growth sites of temperate macroalgae. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101529] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Morrissey KL, Çavaş L, Willems A, De Clerck O. Disentangling the Influence of Environment, Host Specificity and Thallus Differentiation on Bacterial Communities in Siphonous Green Seaweeds. Front Microbiol 2019; 10:717. [PMID: 31024496 PMCID: PMC6460459 DOI: 10.3389/fmicb.2019.00717] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/21/2019] [Indexed: 12/14/2022] Open
Abstract
Siphonous green seaweeds, such as Caulerpa, are among the most morphologically complex algae with differentiated algal structures (morphological niches). Caulerpa is also host to a rich diversity of bacterial endo- and epibionts. The degree to which these bacterial communities are species-, or even niche-specific remains largely unknown. To address this, we investigated the diversity of bacteria associated to different morphological niches of both native and invasive species of Caulerpa from different geographic locations along the Turkish coastline of the Aegean sea. Associated bacteria were identified using the 16S rDNA marker gene for three morphological niches, such as the endobiome, epibiome, and rhizobiome. Bacterial community structure was explored and deterministic factors behind bacterial variation were investigated. Of the total variation, only 21.5% could be explained. Pronounced differences in bacterial community composition were observed and variation was partly explained by a combination of host species, biogeography and nutrient levels. The majority of the explained bacterial variation within the algal holobiont was attributed to the micro-environments established by distinct morphological niches. This study further supports the hypothesis that the bacterial assembly is largely stochastic in nature and bacterial community structure is most likely linked to functional genes rather than taxonomy.
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Affiliation(s)
| | - Levent Çavaş
- Department of Chemistry, Biochemistry Division, Faculty of Science, Dokuz Eylül University, İzmir, Turkey
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
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Bogaert KA, Blommaert L, Ljung K, Beeckman T, De Clerck O. Auxin Function in the Brown Alga Dictyota dichotoma. Plant Physiol 2019; 179:280-299. [PMID: 30420566 PMCID: PMC6324224 DOI: 10.1104/pp.18.01041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/30/2018] [Indexed: 05/14/2023]
Abstract
Auxin controls body plan patterning in land plants and has been proposed to play a similar role in the development of brown algae (Phaeophyta) despite their distant evolutionary relationship with land plants. The mechanism of auxin action in brown algae remains controversial because of contradicting conclusions derived from pharmacological studies on Fucus In this study, we used Dictyota dichotoma as a model system to show that auxin plays a role during the apical-basal patterning of the embryo of brown algae. Indole-3-acetic acid was detectable in D. dichotoma germlings and mature tissue. Although two-celled D. dichotoma zygotes normally develop a rhizoid from one pole and a thallus meristem from the other, addition of exogenous auxins to one-celled embryos affected polarization, and both poles of the spheroidal embryo developed into rhizoids instead. The effect was strongest at lower pH and when variable extrinsic informational cues were applied. 2-[4-(diethylamino)-2-hydroxybenzoyl]benzoic acid, an inhibitor of the ABC-B/multidrug resistance/P-glycoprotein subfamily of transporters in land plants, affected rhizoid formation by increasing rhizoid branching and inducing ectopic rhizoids. An in silico survey of auxin genes suggested that a diverse range of biosynthesis genes and transport genes, such as PIN-LIKES, and the ATP-binding cassette subfamily (ABC-B/multidrug resistance/P-glycoprotein) transporters from land plants have homologs in D. dichotoma and Ectocarpus siliculosus Together with reports on auxin function in basal lineages of green algae, these results suggest that auxin function predates the divergence between the green and brown lineage and the transition toward land plants.
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Affiliation(s)
- Kenny A Bogaert
- Department of Biology, Ghent University, 9000 Ghent, Belgium
| | | | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Tom Beeckman
- VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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De Clerck O, Kao SM, Bogaert KA, Blomme J, Foflonker F, Kwantes M, Vancaester E, Vanderstraeten L, Aydogdu E, Boesger J, Califano G, Charrier B, Clewes R, Del Cortona A, D’Hondt S, Fernandez-Pozo N, Gachon CM, Hanikenne M, Lattermann L, Leliaert F, Liu X, Maggs CA, Popper ZA, Raven JA, Van Bel M, Wilhelmsson PK, Bhattacharya D, Coates JC, Rensing SA, Van Der Straeten D, Vardi A, Sterck L, Vandepoele K, Van de Peer Y, Wichard T, Bothwell JH. Insights into the Evolution of Multicellularity from the Sea Lettuce Genome. Curr Biol 2018; 28:2921-2933.e5. [DOI: 10.1016/j.cub.2018.08.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/21/2018] [Accepted: 08/03/2018] [Indexed: 10/28/2022]
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35
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Paiano MO, Del Cortona A, Costa JF, Liu SL, Verbruggen H, De Clerck O, Necchi O. Complete mitochondrial genomes of six species of the freshwater red algal order Batrachospermales (Rhodophyta). Mitochondrial DNA B Resour 2018; 3:607-610. [PMID: 33474260 PMCID: PMC7799738 DOI: 10.1080/23802359.2018.1473734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/02/2018] [Indexed: 11/03/2022] Open
Abstract
Only two mitochondrial (mt) genomes had been reported in members of the red algal order Batrachospermales, which are confined to freshwater habitats. Additional mt genomes of six representative members (Batrachospermum macrosporum, Kumanoa ambigua, K. mahlacensis, Paralemanea sp., Sheathia arcuata, and Sirodotia delicatula) were sequenced aiming to gain insights on the evolution of their mt genomes from a comparative analysis with other red algal groups. Mt genomes sequenced had the following characteristics: lengths ranging between 24,864 nt and 29,785 nt, 22 to 26 protein-coding genes, G + C contents of 21.3 to 30.7%, number of tRNA of 16 to 37, non-coding DNA from 3.8% to 14.8%. Comparative analysis revealed that mt genomes in Batrachospermales are highly conserved in terms of genome size and gene content and synteny. Phylogenetic analyses based on COI nucleotide data revealed high bootstrap support only for the genera usually recovered in the phylogenetic analyses but no support for supra-generic groups. The insertion of a group II intron carrying an ORF coding for the corresponding intron maturase interrupting the COI gene was observed in Paralamenea sp. and accounted for its larger genome in comparison to the other Batrachospermales mt genomes.
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Affiliation(s)
- Monica O. Paiano
- Zoology and Botany Department, São Paulo State University, São José do Rio Preto, Brazil
| | | | - Joana F. Costa
- School of Biosciences, University of Melbourne, Melbourne, Australia
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, Australia
| | | | - Orlando Necchi
- Zoology and Botany Department, São Paulo State University, São José do Rio Preto, Brazil
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36
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Paiano MO, Del Cortona A, Costa JF, Liu SL, Verbruggen H, De Clerck O, Necchi O. Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta). J Phycol 2018; 54:25-33. [PMID: 29077982 DOI: 10.1111/jpy.12602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
Little is known about genome organization in members of the order Batrachospermales, and the infra-ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra-ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene-dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein-coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling.
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Affiliation(s)
- Monica Orlandi Paiano
- Zoology and Botany Department, São Paulo State University, São José do Rio Preto, 15054-000, Brazil
| | - Andrea Del Cortona
- Phycology Research Group, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Joana F Costa
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Olivier De Clerck
- Phycology Research Group, Ghent University, Krijgslaan 281-S8, 9000, Ghent, Belgium
| | - Orlando Necchi
- Zoology and Botany Department, São Paulo State University, São José do Rio Preto, 15054-000, Brazil
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37
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Charrier B, Abreu MH, Araujo R, Bruhn A, Coates JC, De Clerck O, Katsaros C, Robaina RR, Wichard T. Furthering knowledge of seaweed growth and development to facilitate sustainable aquaculture. New Phytol 2017; 216:967-975. [PMID: 28800196 DOI: 10.1111/nph.14728] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Macroalgae (seaweeds) are the subject of increasing interest for their potential as a source of valuable, sustainable biomass in the food, feed, chemical and pharmaceutical industries. Compared with microalgae, the pace of knowledge acquisition in seaweeds is slower despite the availability of whole-genome sequences and model organisms for the major seaweed groups. This is partly a consequence of specific hurdles related to the large size of these organisms and their slow growth. As a result, this basic scientific field is falling behind, despite the societal and economic importance of these organisms. Here, we argue that sustainable management of seaweed aquaculture requires fundamental understanding of the underlying biological mechanisms controlling macroalgal life cycles - from the production of germ cells to the growth and fertility of the adult organisms - using diverse approaches requiring a broad range of technological tools. This Viewpoint highlights several examples of basic research on macroalgal developmental biology that could enable the step-changes which are required to adequately meet the demands of the aquaculture sector.
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Affiliation(s)
- Bénédicte Charrier
- Morphogenesis of Macroalgae, UMR8227, CNRS-UPMC, Station Biologique, Roscoff, 29680, France
| | - Maria Helena Abreu
- Travessa Alexandre da Conceição, ALGAplus Lda, Ílhavo, 3830-196, Portugal
| | - Rita Araujo
- Water and Marine Resources Unit, Joint Research Centre - Directorate for Sustainable Resources, European Commission, via E. Fermi, Ispra (VA), 2749-21027, Italy
| | - Annette Bruhn
- Department of BioScience, Aarhus University, Vejlsøvej 25, Silkeborg, 8600, Denmark
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Olivier De Clerck
- Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, 9000, Belgium
| | - Christos Katsaros
- Department of Biology, Morphogenesis of Macroalgae, National and Kapodistrian University of Athens, Athens, 157 84, Greece
| | - Rafael R Robaina
- Facultad de Ciencias del Mar, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, 35017, Spain
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, Jena, 07743, Germany
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38
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Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes. Curr Biol 2017; 27:3771-3782.e6. [PMID: 29199074 DOI: 10.1016/j.cub.2017.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/28/2022]
Abstract
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Kenny A Bogaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine, Québec City, QC G1V 0A6, Canada
| | - Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, New Kirk Building, Kelburn Parade, P.O. Box 600, Wellington 6012, New Zealand
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Juan M Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35484-0345, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Professors Walk, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium.
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Bosch S, Tyberghein L, Deneudt K, Hernandez F, De Clerck O. In search of relevant predictors for marine species distribution modelling using the MarineSPEED benchmark dataset. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12668] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Samuel Bosch
- Flanders Marine Institute (VLIZ); Ostend Belgium
- Research Group Phycology; Biology Department; Ghent University; Ghent Belgium
| | | | | | | | - Olivier De Clerck
- Research Group Phycology; Biology Department; Ghent University; Ghent Belgium
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40
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Brodie J, Ball SG, Bouget FY, Chan CX, De Clerck O, Cock JM, Gachon C, Grossman AR, Mock T, Raven JA, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D. Biotic interactions as drivers of algal origin and evolution. New Phytol 2017; 216:670-681. [PMID: 28857164 DOI: 10.1111/nph.14760] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 05/07/2023]
Abstract
Contents 670 I. 671 II. 671 III. 676 IV. 678 678 References 678 SUMMARY: Biotic interactions underlie life's diversity and are the lynchpin to understanding its complexity and resilience within an ecological niche. Algal biologists have embraced this paradigm, and studies building on the explosive growth in omics and cell biology methods have facilitated the in-depth analysis of nonmodel organisms and communities from a variety of ecosystems. In turn, these advances have enabled a major revision of our understanding of the origin and evolution of photosynthesis in eukaryotes, bacterial-algal interactions, control of massive algal blooms in the ocean, and the maintenance and degradation of coral reefs. Here, we review some of the most exciting developments in the field of algal biotic interactions and identify challenges for scientists in the coming years. We foresee the development of an algal knowledgebase that integrates ecosystem-wide omics data and the development of molecular tools/resources to perform functional analyses of individuals in isolation and in populations. These assets will allow us to move beyond mechanistic studies of a single species towards understanding the interactions amongst algae and other organisms in both the laboratory and the field.
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Affiliation(s)
- Juliet Brodie
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Steven G Ball
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille CNRS, F 59000, Lille, France
| | - François-Yves Bouget
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, University Pierre et Marie Curie, University of Paris VI, CNRS, F-66650, Banyuls-sur-Mer, France
| | - Cheong Xin Chan
- Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Olivier De Clerck
- Phycology Research Group, Ghent University, Krijgslaan 281, S8, 9000, Gent, Belgium
| | - 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, Roscoff, F-29688, France
| | | | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Mahasweta Saha
- Helmholtz Center for Ocean Research, Kiel, 24105, Germany
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
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Bogaert KA, Beeckman T, De Clerck O. Egg activation-triggered shape change in the Dictyota dichotoma (Phaeophyceae) zygote is actin-myosin and secretion dependent. Ann Bot 2017; 120:529-538. [PMID: 28961769 PMCID: PMC5737549 DOI: 10.1093/aob/mcx085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Background and Aims Cellular morphogenesis in land plants and brown algae is typically a slow process involving growth established by an interplay of turgor pressure and cell wall rigidity. However, a recent study showed that zygotes of the brown alga Dictyota dichotoma undergo a rapid shape change from a sphere to an elongated spheroid in about 90 s, establishing the first body axis. Methods Using a combination of pharmacology, staining techniques, membrane depolarization and microscopy techniques (brightfield, transmission electron microscopy and confocal laser scanning microscopy), egg activation and the shape change of the egg cell of D. dichotoma was studied. Key Results It was established that elongation of the zygote does not involve growth, i.e. a positive change in size. The elongation is dependent on F-actin and myosin but independent of microtubules. Secretion was also found to be necessary for elongation after addition of brefeldin A. Moreover, a temporal correlation between extracellular matrix secretion and elongation was observed. Ionomycin and high potassium seawater are capable of triggering the onset of elongation, suggesting a role for membrane depolarization and calcium influx in the signalling mechanism. The elongated cells are shorter in the presence of ionomycin, suggesting a role for calcium in elongation. Conclusions A model is proposed in which the fast elongation of the fertilized egg in Dictyota is accomplished by a force generated by F-actin and myosin, regulated by cytoplasmic calcium concentrations and by secretion during elongation lowering the antagonistic force. The finding of early extracellular matrix secretion, membrane depolarization and ionophore-triggered egg activation suggest significant differences in the mechanism of egg activation signalling between D. dichotoma and the oogamous brown algal model system Fucus .
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Affiliation(s)
- Kenny A Bogaert
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium
| | - Tom Beeckman
- VIB-UGent Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Olivier De Clerck
- Department of Biology, Ghent University, Krijgslaan 281 S8, B-9000 Ghent, Belgium
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Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. The Algal Revolution. Trends Plant Sci 2017; 22:726-738. [PMID: 28610890 DOI: 10.1016/j.tplants.2017.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 01/19/2017] [Revised: 05/04/2017] [Accepted: 05/16/2017] [Indexed: 05/28/2023]
Abstract
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.
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Affiliation(s)
- Juliet Brodie
- Natural History Museum, Department of Life Sciences, London SW7 5BD, UK
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Olivier De Clerck
- Research Group Phycology, Ghent University, Krijgslaan 281, S8, 9000 Ghent, Belgium
| | - 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, Roscoff F-29688, France
| | - 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, Roscoff F-29688, France
| | - Claire Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, UK
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John A Raven
- Permanent address: Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, UK; School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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De Smet Y, De Clerck O, Uemachi T, Granados Mendoza C, Wanke S, Goetghebeur P, Samain MS. Multilocus coalescent species delimitation to evaluate traditionally defined morphotypes in Hydrangea sect. Asperae (Hydrangeaceae). Mol Phylogenet Evol 2017; 114:415-425. [PMID: 28606445 DOI: 10.1016/j.ympev.2017.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 11/29/2022]
Abstract
The number of species recognized in section Asperae of the flowering plant genus Hydrangea differs widely between subsequent revisions. This variation is largely centered around the H. aspera species complex, with numbers of recognized species varying from one to nearly a dozen. Despite indications of molecular variation in this complex, no sequence-based species delimitation methods have been employed to evaluate the primarily morphology-based species boundaries. In the present study, a multi-locus coalescent-based approach to species delimitation is employed in order to identify separate evolutionary lines within H. sect. Asperae, using four chloroplast and four nuclear molecular markers. Eight lineages were recovered within the focal group, of which five correspond with named morphotypes. The other three lineages illustrate types of conflict between molecular species delimitation and traditional morphology-based taxonomy. One molecular lineage comprises two named morphotypes, which possibly diverged recently enough to not have developed sufficient molecular divergence. A second conflict is found in H. strigosa. This morphotype is recovered as a separate lineage when occurring in geographic isolation, but when occurring in sympatry with two other morphotypes (H. aspera and H. robusta), the coalescent species delimitation lumps these taxa into a single putative species.
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Affiliation(s)
- Yannick De Smet
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000 Gent, Belgium
| | - Tatsuya Uemachi
- School of Environmental Science, The University of Shiga Prefecture, Hikone 522-8533, Japan
| | - Carolina Granados Mendoza
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium; Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Distrito Federal, Mexico; CONACyT División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica AC, Camino a la Presa de San José 2055, Lomas 4a. sección, C.P. 78216 San Luis Potosí, San Luis Potosí, Mexico
| | - Stefan Wanke
- Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Paul Goetghebeur
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Marie-Stéphanie Samain
- Ghent University, Department of Biology, Research Group Spermatophytes, K.L. Ledeganckstraat 35, 9000 Gent, Belgium; Instituto de Ecología, A.C., Centro Regional del Bajío, Avenida Lázaro Cárdenas 253, 61600 Pátzcuaro, Michoacán, Mexico(1)
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Vieira C, Camacho O, Sun Z, Fredericq S, Leliaert F, Payri C, De Clerck O. Historical biogeography of the highly diverse brown seaweed Lobophora (Dictyotales, Phaeophyceae). Mol Phylogenet Evol 2017; 110:81-92. [PMID: 28279809 DOI: 10.1016/j.ympev.2017.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/22/2017] [Accepted: 03/04/2017] [Indexed: 11/23/2022]
Abstract
The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98-121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (-75 to -60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events.
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Affiliation(s)
- Christophe Vieira
- ENTROPIE (IRD, UR, CNRS), LabEx-CORAIL, Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France; Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Gent B-9000, Belgium; Sorbonne Universités, UPMC Univ Paris 06, IFD, Paris F75252, France.
| | - Olga Camacho
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504-3602, USA
| | - Zhongmin Sun
- Institute of Oceanology, Chinese Academy of Sciences, Department of Marine Organism Taxonomy and Phylogeny, China
| | - Suzanne Fredericq
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504-3602, USA
| | - Frederik Leliaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Gent B-9000, Belgium; Botanic Garden Meise, 1860 Meise, Belgium
| | - Claude Payri
- ENTROPIE (IRD, UR, CNRS), LabEx-CORAIL, Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Gent B-9000, Belgium
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Bogaert KA, Beeckman T, De Clerck O. Corrigendum: Two-step cell polarization in algal zygotes. Nat Plants 2017; 3:17022. [PMID: 28191882 DOI: 10.1038/nplants.2017.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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Affiliation(s)
- Frederik Leliaert
- Botanic Garden Meise, Nieuwelaan 38, 1860, Meise, Belgium
- Phycology Research Group, Biology Department, Ghent University, 9000, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group, Biology Department, Ghent University, 9000, Ghent, Belgium
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Abstract
In most complex eukaryotes, development starts with the establishment of cell polarity determining the first axis of the body plan. This polarity axis is established by the asymmetrical distribution of intrinsic factors1-3, which breaks the symmetry in a single step. Zygotes of the brown alga Fucus, which unlike land plant and animal zygotes4,5 do not possess a maternally predetermined polarity axis, serve as models to study polarity establishment6,7. Here, we studied this process in Dictyota, and concluded that sense and direction of the cell polarization vector are established in two mechanistically and temporally distinct phases that are under control of different life cycle stages. On egg activation, the zygote elongates rapidly according to a maternally predetermined direction expressing the first phase of cell polarization. Which of the two poles of the resulting prolate spheroidal zygote will acquire the basal cell fate is subsequently environmentally determined. The second phase is accompanied by and dependent on zygotic transcription instead of relying uniquely on maternal factors8. Cell polarization, whereby determination of direction and sense of the polarization vector are temporally and mechanistically uncoupled, is unique and represents a favourable system to gain insight into the processes underlying cell polarity establishment in general.
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Affiliation(s)
- Kenny A Bogaert
- Department of Biology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium
| | - Tom Beeckman
- VIB-UGent Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Olivier De Clerck
- Department of Biology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium
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Mancuso FP, D'Hondt S, Willems A, Airoldi L, De Clerck O. Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin. Front Microbiol 2016; 7:476. [PMID: 27092130 PMCID: PMC4824759 DOI: 10.3389/fmicb.2016.00476] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/22/2016] [Indexed: 02/01/2023] Open
Abstract
Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti—Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria, and Cyanobacteria especially of the Rhodobacteriaceae, Flavobacteriaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobacteriaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegeria, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of the microbial communities in contributing to the extensive ongoing declines of populations of Cystoseira spp. in the Mediterranean Sea.
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Affiliation(s)
- Francesco P Mancuso
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Centro Interdipartimentale di Ricerca per le Scienze Ambientali, UO CoNISMa, University of BolognaRavenna, Italy; Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent UniversityGhent, Belgium
| | - Sofie D'Hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University Ghent, Belgium
| | - Anne Willems
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Laura Airoldi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Centro Interdipartimentale di Ricerca per le Scienze Ambientali, UO CoNISMa, University of Bologna Ravenna, Italy
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University Ghent, Belgium
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Vieira C, Engelen AH, Guentas L, Aires T, Houlbreque F, Gaubert J, Serrão EA, De Clerck O, Payri CE. Species Specificity of Bacteria Associated to the Brown Seaweeds Lobophora (Dictyotales, Phaeophyceae) and Their Potential for Induction of Rapid Coral Bleaching in Acropora muricata. Front Microbiol 2016; 7:316. [PMID: 27047453 PMCID: PMC4800410 DOI: 10.3389/fmicb.2016.00316] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/29/2016] [Indexed: 11/13/2022] Open
Abstract
While reef degradation is occurring worldwide, it is not uncommon to see phase shifts from coral to macroalgal dominated reefs. Numerous studies have addressed the mechanisms by which macroalgae may outcompete corals and a few recent studies highlighted the putative role of bacteria at the interface between macroalgae and corals. Some studies suggest that macroalgae may act as vectors and/or foster proliferation of microorganisms pathogenic for corals. Using a combination of high throughput sequencing, bacterial culturing, and in situ bioassays we question if the adversity of macroalgal-associated bacteria to corals is mediated by specific bacterial taxa. Using Illumina sequencing, we characterized and compared the bacterial community from two Lobophora (Dictyotales, Phaeophyceae) species. The two species presented distinctive bacterial communities. Both species shared approximately half of their OTUs, mainly the most abundant bacteria. Species-specific OTUs belong to Planctomycetes, Proteobacteria, and Bacteroidetes. In total, 16 culturable bacterial strain were isolated and identified from the Lobophora surface, consisting of 10 genera (from nine families, four classes, and three phyla), some of which are not known as, but are related to pathogens involved in coral diseases, and others are naturally associated to corals. When patches of marine agar with 24 h cultures of each of these bacteria were placed in direct contact with the branches of the scleractinian coral Acropora muricata, they caused severe bleaching after 24 h exposure. Results suggest that regardless of taxonomic affinities, increase in density of these bacteria can be adverse to corals. Nevertheless, the microbial community associated to macroalgal surface may not represent a threat to corals, because the specific bacterial screening and control exerted by the alga preventing specific bacterial proliferation.
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Affiliation(s)
- Christophe Vieira
- IFD, Sorbonne Universités, UPMC Univ Paris 06Paris, France; UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le DéveloppementNouméa, New Caledonia; Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent UniversityGhent, Belgium
| | | | - Linda Guentas
- Laboratoire MAPIEM EA 4323, Université de ToulonLa Garde, France; Laboratoire LIVE, Université de Nouvelle-CalédonieNouméa, New Caledonia
| | - Tânia Aires
- Centre of Marine Sciences, University of the Algarve Portugal
| | - Fanny Houlbreque
- UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le Développement Nouméa, New Caledonia
| | - Julie Gaubert
- UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le Développement Nouméa, New Caledonia
| | - Ester A Serrão
- Centre of Marine Sciences, University of the Algarve Portugal
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University Ghent, Belgium
| | - Claude E Payri
- UMR ENTROPIE (UR, IRD, Centre National de la Recherche Scientifique), Institut de Recherche pour le Développement Nouméa, New Caledonia
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Lipinska AP, Van Damme EJM, De Clerck O. Molecular evolution of candidate male reproductive genes in the brown algal model Ectocarpus. BMC Evol Biol 2016; 16:5. [PMID: 26728038 PMCID: PMC4700764 DOI: 10.1186/s12862-015-0577-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/21/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Evolutionary studies of genes that mediate recognition between sperm and egg contribute to our understanding of reproductive isolation and speciation. Surface receptors involved in fertilization are targets of sexual selection, reinforcement, and other evolutionary forces including positive selection. This observation was made across different lineages of the eukaryotic tree from land plants to mammals, and is particularly evident in free-spawning animals. Here we use the brown algal model species Ectocarpus (Phaeophyceae) to investigate the evolution of candidate gamete recognition proteins in a distant major phylogenetic group of eukaryotes. RESULTS Male gamete specific genes were identified by comparing transcriptome data covering different stages of the Ectocarpus life cycle and screened for characteristics expected from gamete recognition receptors. Selected genes were sequenced in a representative number of strains from distant geographical locations and varying stages of reproductive isolation, to search for signatures of adaptive evolution. One of the genes (Esi0130_0068) showed evidence of selective pressure. Interestingly, that gene displayed domain similarities to the receptor for egg jelly (REJ) protein involved in sperm-egg recognition in sea urchins. CONCLUSIONS We have identified a male gamete specific gene with similarity to known gamete recognition receptors and signatures of adaptation. Altogether, this gene could contribute to gamete interaction during reproduction as well as reproductive isolation in Ectocarpus and is therefore a good candidate for further functional evaluation.
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Affiliation(s)
- Agnieszka P Lipinska
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000, Ghent, Belgium.
| | - Els J M Van Damme
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000, Ghent, Belgium.
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