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Dries E, Meyers Y, Liesner D, Gonzaga FM, Becker JFM, Zakka EE, Beeckman T, Coelho SM, De Clerck O, Bogaert KA. Cell wall-mediated maternal control of apical-basal patterning of the kelp Undaria pinnatifida. THE NEW PHYTOLOGIST 2024; 243:1887-1898. [PMID: 38984686 DOI: 10.1111/nph.19953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024]
Abstract
The role of maternal tissue in embryogenesis remains enigmatic in many complex organisms. Here, we investigate the contribution of maternal tissue to apical-basal patterning in the kelp embryo. Focussing on Undaria pinnatifida, we studied the effects of detachment from the maternal tissue using microsurgery, staining of cell wall modifications, morphometric measurements, flow cytometry, genotyping and a modified kelp fertilisation protocol synchronising kelp embryogenesis. Detached embryos are rounder and often show aberrant morphologies. When a part of the oogonial cell wall remains attached to the zygote, the apical-basal patterning is rescued. Furthermore, the absence of contact with maternal tissue increases parthenogenesis, highlighting the critical role of maternal signals in the initial stages of development. These results show a key role for the connection to the maternal oogonial cell wall in apical-basal patterning in kelps. This observation is reminiscent of another brown alga, Fucus, where the cell wall directs the cell fate. Our findings suggest a conserved mechanism across phylogenetically distant oogamous lineages, where localised secretion of sulphated F2 fucans mediates the establishment of the apical-basal polarity. In this model, the maternal oogonial cell wall mediates basal cell fate determination by providing an extrinsic patterning cue to the future kelp embryo.
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Affiliation(s)
- Eloise Dries
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
- Laboratory of Cell and Developmental Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Yannick Meyers
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Daniel Liesner
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Floriele M Gonzaga
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Jakob F M Becker
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Eliane E Zakka
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Tom Beeckman
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
| | - Kenny A Bogaert
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281 S8, Ghent, B-9000, Belgium
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, Tübingen, 72076, Germany
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2
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Hoshino M, Cossard G, Haas FB, Kane EI, Kogame K, Jomori T, Wakimoto T, Glemin S, Coelho SM. Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality. Nat Ecol Evol 2024:10.1038/s41559-024-02490-w. [PMID: 39152327 DOI: 10.1038/s41559-024-02490-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/18/2024] [Indexed: 08/19/2024]
Abstract
Sexual reproduction is widespread, but asexual lineages have repeatedly arisen from sexual ancestors across a wide range of eukaryotic taxa. The molecular changes underpinning the switch to asexuality remain elusive, particularly in organisms with haploid sexual systems. Here we explore independent events of loss of sex in the brown alga Scytosiphon, examine the proximate and evolutionary mechanisms involved, and test the importance of sexual conflict on gene expression changes following loss of sex. We find that asexual females ('Amazons') lose ability to produce sex pheromone and, consequently, are incapable of attracting males, whereas they gain rapid parthenogenic development from large, unfertilized eggs. These phenotypic changes are accompanied by convergent changes in gene expression. Decay of female functions, rather than relaxation of sexual antagonism, may be a dominant force at play during the emergence of asexuality in haploid sexual systems. Moreover, we show that haploid purifying selection plays a key role in limiting the accumulation of deleterious alleles in Amazons, and we identify an autosomal locus associated with the Amazon phenotype. The sex chromosome, together with this autosomal locus, may underlie the switch to obligate asexuality in the Amazon populations.
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Affiliation(s)
- Masakazu Hoshino
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Research Center for Inland Seas, Kobe University, Rokkodai 1-1, Nadaku, Kobe, Japan
| | - Guillaume Cossard
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Emma I Kane
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Kazuhiro Kogame
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | | | - Sylvain Glemin
- Laboratoire ECOBIO (Ecosystèmes, biodiversité, évolution), UMR 6553, CNRS, Université de Rennes, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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3
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Patwary ZP, Zhao M, Paul NA, Cummins SF. Identification of reproductive sex-biased gene expression in Asparagopsis taxiformis (lineage 6) gametophytes. JOURNAL OF PHYCOLOGY 2024; 60:327-342. [PMID: 38156746 DOI: 10.1111/jpy.13419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 01/03/2024]
Abstract
The sub-tropical red seaweed Asparagopsis taxiformis is of significant interest due to its ability to store halogenated compounds, including bromoform, which can mitigate methane production in ruminants. Significant scale-up of aquaculture production of this seaweed is required; however, relatively little is known about the molecular mechanisms that control fundamental physiological processes, including the regulatory factors that determine sexual dimorphism in gametophytes. In this study, we used comparative RNA-sequencing analysis between different morphological parts of mature male and female A. taxiformis (lineage 6) gametophytes that resulted in greater number of sex-biased gene expression in tips (containing the reproductive structures for both sexes), compared with the somatic main axis and rhizomes. Further comparative RNA-seq against immature tips was used to identify 62 reproductive sex-biased genes (59 male-biased, 3 female-biased). Of the reproductive male-biased genes, 46% had an unknown function, while others were predicted to be regulatory factors and enzymes involved in signaling. We found that bromoform content obtained from female samples (8.5 ± 1.0 mg·g-1 dry weight) was ~10% higher on average than that of male samples (6.5 ± 1.0 mg·g-1 dry weight), although no significant difference was observed (p > 0.05). There was also no significant difference in the marine bromoform biosynthesis locus gene expression. In summary, our comparative RNA-sequencing analysis provides a first insight into the potential molecular factors relevant to gametogenesis and sexual differentiation in A. taxiformis, with potential benefits for identification of sex-specific markers.
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Affiliation(s)
- Zubaida Parveen Patwary
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
- Department of Aquaculture, Faculty of Fisheries, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - Min Zhao
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Nicholas A Paul
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Scott F Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
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4
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Krueger-Hadfield SA, Oetterer AP, Lees LE, Hoffman JM, Sotka EE, Murren CJ. Phenology and thallus size in a non-native population of Gracilaria vermiculophylla. JOURNAL OF PHYCOLOGY 2023; 59:926-938. [PMID: 37729054 DOI: 10.1111/jpy.13371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/13/2023] [Accepted: 07/03/2023] [Indexed: 09/22/2023]
Abstract
Phenology, or seasonal variation in life cycle events, is poorly described for many macroalgal species. We describe the phenology of a non-native population of Gracilaria vermiculophylla whose thalli are free-living or anchored by decorating polychaetes to tube caps. At a site in South Carolina, USA, we sampled 100 thalli approximately every month from January 2014 to January 2015. We assessed the reproductive state and measured thallus size based on wet weight, thallus length, and thallus surface area from herbarium mounts. Because life cycle stage cannot be assigned using morphology, we implemented a PCR assay to determine the life cycle stage-tetrasporophyte, female gametophyte, or male gametophyte-of each thallus. Tetrasporophytes dominated throughout the year, making up 81%-100% of thalli sampled per month. Reproductive tetrasporophytes varied between 0% and 65% of monthly samples and were most common in warm summer months (July through September) when thalli also tended to be larger. The vast majority of the reproductive thalli were worm-anchored and not fixed to hard substratum via a holdfast. Thus, free-living thalli can be reproductive and potentially seed new non-native populations. Given G. vermiculophylla reproduction seems tied closely to temperature, our work suggests phenology may change with climate-related changes in seawater temperatures. We also highlight the importance of understanding the natural history of macroalgae to better understand the consequence of range expansions on population dynamics.
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Affiliation(s)
| | - Alexis P Oetterer
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lauren E Lees
- Department of Biology, College of Charleston, Charleston, South Carolina, USA
| | - Jessica M Hoffman
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Erik E Sotka
- Department of Biology, College of Charleston, Charleston, South Carolina, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, Charleston, South Carolina, USA
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5
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Diesel J, Molano G, Montecinos GJ, DeWeese K, Calhoun S, Kuo A, Lipzen A, Salamov A, Grigoriev IV, Reed DC, Miller RJ, Nuzhdin SV, Alberto F. A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera). BMC Genomics 2023; 24:543. [PMID: 37704968 PMCID: PMC10498591 DOI: 10.1186/s12864-023-09658-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp's economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.
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Affiliation(s)
- Jose Diesel
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Gary Molano
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Gabriel J Montecinos
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kelly DeWeese
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sara Calhoun
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Daniel C Reed
- Marine Science Institute, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Robert J Miller
- Marine Science Institute, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Sergey V Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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6
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Cossard GG, Godfroy O, Nehr Z, Cruaud C, Cock JM, Lipinska AP, Coelho SM. Selection drives convergent gene expression changes during transitions to co-sexuality in haploid sexual systems. Nat Ecol Evol 2022; 6:579-589. [PMID: 35314785 PMCID: PMC9085613 DOI: 10.1038/s41559-022-01692-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022]
Abstract
Co-sexuality has evolved repeatedly from unisexual (dioicous) ancestors across a wide range of taxa. However, the molecular changes underpinning this important transition remain unknown, particularly in organisms with haploid sexual systems such as bryophytes, red algae and brown algae. Here we explore four independent events of emergence of co-sexuality from unisexual ancestors in brown algal clades to examine the nature, evolution and degree of convergence of gene expression changes that accompany the breakdown of dioicy. The amounts of male versus female phenotypic differences in dioicous species were not correlated with the extent of sex-biased gene expression, in stark contrast to what is observed in animals. Although sex-biased genes exhibited a high turnover rate during brown alga diversification, some of their predicted functions were conserved across species. Transitions to co-sexuality consistently involved adaptive gene expression shifts and rapid sequence evolution, particularly for male-biased genes. Gene expression in co-sexual species was more similar to that in females rather than males of related dioicous species, suggesting that co-sexuality may have arisen from ancestral females. Finally, extensive convergent gene expression changes, driven by selection, were associated with the transition to co-sexuality. Together, our observations provide insights on how co-sexual systems arise from ancestral, haploid UV sexual systems.
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Affiliation(s)
- Guillaume G Cossard
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
- Max Plank Institute for Biology Tübingen, Tübingen, Germany
| | - Olivier Godfroy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Zofia Nehr
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
- Max Plank Institute for Biology Tübingen, Tübingen, Germany
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France.
- Max Plank Institute for Biology Tübingen, Tübingen, Germany.
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7
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Müller DG, Gaschet E, Godfroy O, Gueno J, Cossard G, Kunert M, Peters AF, Westermeier R, Boland W, Cock JM, Lipinska AP, Coelho SM. A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in a UV sexual system. THE NEW PHYTOLOGIST 2021; 232:252-263. [PMID: 34166525 DOI: 10.1111/nph.17582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
In UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the brown alga Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and suggested that the female developmental programme may occur by 'default'. Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental programme is however incomplete, because gametes of this feminized male are unable to produce the sperm-attracting pheromone lamoxirene. We identify the transcriptomic patterns underlying the male and female specific developmental programmes, and show that the phenotypic feminization is associated with both feminization and de-masculinization of gene expression patterns. Importantly, the feminization phenotype was associated with dramatic downregulation of two V-specific genes including a candidate male-determining gene. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system, and contribute to disentangling the role of sex-linked and autosomal gene expression in the initiation of sex-specific developmental programmes. Overall, the data presented here imply that the U-specific region is not required to initiate the female developmental programme, but is critical to produce fully functional eggs, arguing against the idea that female is the 'default' sex in this species.
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Affiliation(s)
- Dieter G Müller
- Fachbereich Biologie der Universität Konstanz, Konstanz, 78457, Germany
| | - Enora Gaschet
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Olivier Godfroy
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Josselin Gueno
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Guillaume Cossard
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Maritta Kunert
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | | | - Renato Westermeier
- Instituto de Acuicultura, Universidad Austral de Chile, Casilla 1327, Puerto Montt, Chile
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - J Mark Cock
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
| | - Agnieszka P Lipinska
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
- Max Plank Institute for Developmental Biology, Tübingen, Germany
| | - Susana M Coelho
- UPMC Univ Paris 06, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, CS 90074, F-29688, France
- Max Plank Institute for Developmental Biology, Tübingen, Germany
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8
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Zhang J, Li Y, Luo S, Cao M, Zhang L, Li X. Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica. BMC PLANT BIOLOGY 2021; 21:335. [PMID: 34261451 PMCID: PMC8278619 DOI: 10.1186/s12870-021-03117-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND In brown algae, dioicy is the prevalent sexual system, and phenotypic differences between male and female gametophytes have been found in many dioicous species. Saccharina japonica show remarkable sexual dimorphism in gametophytes before gametogenesis. A higher level of phenotypic differentiation was also found in female and male gametes after gametogenesis. However, the patterns of differential gene expression throughout gametophyte development and how these changes might relate to sex-specific fitness at the gamete stage in S. japonica are not well known. RESULTS In this study, differences in gene expression between male and female gametophytes in different developmental stages were investigated using comparative transcriptome analysis. Among the 20,151 genes expressed in the haploid gametophyte generation, 37.53% were sex-biased. The abundance of sex-biased genes in mature gametophytes was much higher than that in immature gametophytes, and more male-biased than female-biased genes were observed in the mature stage. The predicted functions of most sex-biased genes were closely related to the sex-specific characteristics of gametes, including cell wall biosynthesis, sperm motility, and sperm and egg recognition. In addition, 51 genes were specifically expressed in males in both stages, showing great potential as candidate male sex-determining region (SDR) genes. CONCLUSIONS This study describes a thorough investigation into differential gene expression between male and female gametophytes in the dioicous kelp S. japonica. A large number of sex-biased genes in mature gametophytes may be associated with the divergence of phenotypic traits and physiological functions between female gametes (eggs) and male gametes (sperm) during sexual differentiation. These genes may mainly come from new sex-biased genes that have recently evolved in the S. japonica lineage. The duplication of sex-biased genes was detected, which may increase the number of sex-biased genes after gametogenesis in S. japonica to some extent. The excess of male-biased genes over female-biased genes in the mature stage may reflect the different levels of sexual selection across sexes. This study deepens our understanding of the regulation of sex development and differentiation in the dioicous kelp S. japonica.
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Affiliation(s)
- Jiaxun Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yan Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Shiju Luo
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Linan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
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9
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Krueger-Hadfield SA, Guillemin ML, Destombe C, Valero M, Stoeckel S. Exploring the Genetic Consequences of Clonality in Haplodiplontic Taxa. J Hered 2021; 112:92-107. [PMID: 33511982 DOI: 10.1093/jhered/esaa063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 11/15/2022] Open
Abstract
Partially clonality is an incredibly common reproductive mode found across all the major eukaryotic lineages. Yet, population genetic theory is based on exclusive sexuality or exclusive asexuality, and partial clonality is often ignored. This is particularly true in haplodiplontic eukaryotes, including algae, ferns, mosses, and fungi, where somatic development occurs in both the haploid and diploid stages. Haplodiplontic life cycles are predicted to be correlated with asexuality, but tests of this prediction are rare. Moreover, there are unique consequences of having long-lived haploid and diploid stages in the same life cycle. For example, clonal processes uncouple the life cycle such that the repetition of the diploid stage via clonality leads to the loss of the haploid stage. Here, we surveyed the literature to find studies that had genotyped both haploid and diploid stages and recalculated population genetic summary metrics for seven red algae, one green alga, three brown algae, and three mosses. We compared these data to recent simulations that explicitly addressed the population genetic consequences of partial clonality in haplodiplontic life cycles. Not only was partial clonality found to act as a homogenizing force, but the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetic indices. We found remarkably similar patterns across commonly used population genetic metrics between our empirical and recent theoretical expectations. To facilitate future studies, we provide some recommendations for sampling and analyzing population genetic parameters for haplodiplontic taxa.
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Affiliation(s)
| | - Marie-Laure Guillemin
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla, Valdivia, Chile
| | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Station Biologique de Roscoff, Roscoff, France
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
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10
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Krueger-Hadfield SA, Flanagan BA, Godfroy O, Hill-Spanik KM, Nice CC, Murren CJ, Strand AE, Sotka EE. Using RAD-seq to develop sex-linked markers in a haplodiplontic alga. JOURNAL OF PHYCOLOGY 2021; 57:279-294. [PMID: 33098662 DOI: 10.1111/jpy.13088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
For many taxa, including isomorphic haplodiplontic macroalgae, determining sex and ploidy is challenging, thereby limiting the scope of some population demographic and genetic studies. Here, we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to identify sex-linked molecular markers in the widespread red alga Agarophyton vermiculophyllum. In the ddRAD-seq library, we included 10 female gametophytes, 10 male gametophytes, and 16 tetrasporophytes from one native and one non-native site (N = 40 gametophytes and N = 32 tetrasporophytes total). We identified seven putatively female-linked and 19 putatively male-linked sequences. Four female- and eight male-linked markers amplified in all three life cycle stages. Using one female- and one male-linked marker that were sex-specific, we developed a duplex PCR and tested the efficacy of this assay on a subset of thalli sampled at two sites in the non-native range. We confirmed ploidy based on the visual observation of reproductive structures and previous microsatellite genotyping at 10 polymorphic loci. For 32 vegetative thalli, we were able to assign sex and confirm ploidy in these previously genotyped thalli. These markers will be integral to ongoing studies of A. vermiculophyllum invasion. We discuss the utility of RAD-seq over other approaches previously used, such as RAPDs (random amplified polymorphic DNA), for future work designing sex-linked markers in other haplodiplontic macroalgae for which genomes are lacking.
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Affiliation(s)
- Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, Alabama, 35294, USA
| | - Ben A Flanagan
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Olivier Godfroy
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Kristina M Hill-Spanik
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
| | - Chris C Nice
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, Texas, 78666, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Allan E Strand
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
| | - Erik E Sotka
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
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11
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Guzinski J, Ruggeri P, Ballenghien M, Mauger S, Jacquemin B, Jollivet C, Coudret J, Jaugeon L, Destombe C, Valero M. Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient. Genes (Basel) 2020; 11:E1503. [PMID: 33322137 PMCID: PMC7763533 DOI: 10.3390/genes11121503] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species' distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.
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Affiliation(s)
- Jaromir Guzinski
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone KT15 3NB, Surrey, UK
| | - Paolo Ruggeri
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Xelect ltd, Horizon House, Abbey Walk, St Andrews KY16 9LB, Scotland, UK
| | - Marion Ballenghien
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- UMR 7144, Adaptation et Diversité en Milieu Marin, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France
| | - Stephane Mauger
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Bertrand Jacquemin
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- CEVA, 83 Presqu’île de Pen Lan, 22610 Pleubian, France
| | - Chloe Jollivet
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
- Ecole polytechnique de Lausanne (EPFL), SV-IBI UPOATES, Route cantonale, CH-1015 Lausanne, Switzerland
| | - Jerome Coudret
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Lucie Jaugeon
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Christophe Destombe
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
| | - Myriam Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688 Roscoff CEDEX, France; (J.G.); (P.R.); (M.B.); (S.M.); (B.J.); (C.J.); (J.C.); (L.J.); (C.D.)
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12
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Abstract
Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga Ectocarpus has led to it emerging as a general model system for this group, but additional models, such as Fucus or Dictyota dichotoma, remain of interest for specific biological questions. In addition, Saccharina japonica has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.
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Affiliation(s)
- Susana M Coelho
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
- Current affiliation: Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - J Mark Cock
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
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13
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Coelho SM, Peters AF, Müller D, Cock JM. Ectocarpus: an evo-devo model for the brown algae. EvoDevo 2020; 11:19. [PMID: 32874530 PMCID: PMC7457493 DOI: 10.1186/s13227-020-00164-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Ectocarpus is a genus of filamentous, marine brown algae. Brown algae belong to the stramenopiles, a large supergroup of organisms that are only distantly related to animals, land plants and fungi. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity. For many years, little information was available concerning the molecular mechanisms underlying multicellular development in the brown algae, but this situation has changed with the emergence of Ectocarpus as a model brown alga. Here we summarise some of the main questions that are being addressed and areas of study using Ectocarpus as a model organism and discuss how the genomic information, genetic tools and molecular approaches available for this organism are being employed to explore developmental questions in an evolutionary context.
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Affiliation(s)
- Susana M. Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | | | - Dieter Müller
- Fachbereich Biologie der Universitat Konstanz, 78457 Konstanz, Germany
| | - J. Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
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14
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Augyte S, Wikfors GH, Pitchford S, Marty-Rivera M, Umanzor S, Lindell S, Bailey D, Yarish C. The application of flow cytometry for kelp meiospore isolation. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Mignerot L, Avia K, Luthringer R, Lipinska AP, Peters AF, Cock JM, Coelho SM. A key role for sex chromosomes in the regulation of parthenogenesis in the brown alga Ectocarpus. PLoS Genet 2019; 15:e1008211. [PMID: 31194744 PMCID: PMC6592573 DOI: 10.1371/journal.pgen.1008211] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/25/2019] [Accepted: 05/24/2019] [Indexed: 02/06/2023] Open
Abstract
Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of these shifts remain largely elusive. Here, we used classic quantitative trait analysis, combined with genomic and transcriptomic information to dissect the genetic basis of asexual, parthenogenetic reproduction in the brown alga Ectocarpus. We found that parthenogenesis is controlled by the sex locus, together with two additional autosomal loci, highlighting the key role of the sex chromosome as a major regulator of asexual reproduction. We identify several negative effects of parthenogenesis on male fitness, and different fitness effects of parthenogenetic capacity depending on the life cycle generation. Although allele frequencies in natural populations are currently unknown, we discuss the possibility that parthenogenesis may be under both sex-specific selection and generation/ploidally-antagonistic selection, and/or that the action of fluctuating selection on this trait may contribute to the maintenance of polymorphisms in populations. Importantly, our data provide the first empirical illustration, to our knowledge, of a trade-off between the haploid and diploid stages of the life cycle, where distinct parthenogenesis alleles have opposing effects on sexual and asexual reproduction and may help maintain genetic variation. These types of fitness trade-offs have profound evolutionary implications in natural populations and may structure life history evolution in organisms with haploid-diploid life cycles.
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Affiliation(s)
- Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Remy Luthringer
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | | | - J. Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
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16
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Hoshino M, Okino T, Kogame K. Parthenogenetic female populations in the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Ectocarpales): decay of a sexual trait and acquisition of asexual traits. JOURNAL OF PHYCOLOGY 2019; 55:204-213. [PMID: 30411801 DOI: 10.1111/jpy.12812] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
In isogamous brown algae, the sexuality of populations needs to be tested by laboratory crossing experiments, as the sexes of gametophytes are morphologically indistinguishable. In some cases, gamete fusion is not observed and the precise reproductive mode of the populations is unknown. In the isogamous brown alga Scytosiphon lomentaria in Japan, both asexual (gamete fusion is unobservable) and sexual populations (gamete fusion is observable) have been reported. In order to elucidate the reproductive mode of asexual populations in this species, we used PCR-based sex markers to investigate the sex ratio of three asexual and two sexual field populations. The markers indicated that the asexual populations consisted only of female individuals, whereas sexual populations are composed of both males and females. In culture, female gametes of most strains from asexual populations were able to fuse with male gametes; however, they had little to no detectable sexual pheromones, significantly larger cell sizes, and more rapid parthenogenetic development compared to female/male gametes from sexual populations. Investigations of sporophytic stages in the field indicated that alternation of gametophytic and parthenosporophytic stages occur in an asexual population. These results indicate that the S. lomentaria asexual populations are female populations that lack sexual reproduction and reproduce parthenogenetically. It is likely that females in the asexual populations have reduced a sexual trait (pheromone production) and have acquired asexual traits (larger gamete sizes and rapid parthenogenetic development).
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Affiliation(s)
- Masakazu Hoshino
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tatsufumi Okino
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuhiro Kogame
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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17
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Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C. Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics 2019; 20:56. [PMID: 30654742 PMCID: PMC6337836 DOI: 10.1186/s12864-019-5431-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 01/03/2019] [Indexed: 01/02/2023] Open
Abstract
Background Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes. Results Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus sp. strains and sub-cellular fractions using a shotgun approach. First, we directly generated peptide sequence tags (PSTs) from the proteomics data. Second, we mapped PSTs onto the translated genomic sequence. Closely located hits (i.e., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism. Third, we evaluated each cluster and compared it to gene predictions from existing conventional genome annotation approaches. Finally, we integrated cluster locations into GFF files to use a genome viewer. We identified two potential novel genes, a ribosomal protein L22 and an aryl sulfotransferase and corrected the gene structure of a dihydrolipoamide acetyltransferase. We experimentally validated the results by RT-PCR and using transcriptomics data. Conclusions Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu. Data are available via ProteomeXchange under identifier PXD010618. Electronic supplementary material The online version of this article (10.1186/s12864-019-5431-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laetitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Ludovic Delage
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Alain Viari
- INRIA Grenoble-Rhône-Alpes, F-38330, Montbonnot-Saint-Martin, France
| | - Yves Vandenbrouck
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000, Grenoble, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Andrés Ritter
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France.,Present address: Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Dominique Marie
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | | | - Philippe Potin
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France. .,Protim, Univ Rennes, F-35042, Rennes cedex, France.
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18
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Avia K, Lipinska AP, Mignerot L, Montecinos AE, Jamy M, Ahmed S, Valero M, Peters AF, Cock JM, Roze D, Coelho SM. Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes (Basel) 2018; 9:E286. [PMID: 29882839 PMCID: PMC6027523 DOI: 10.3390/genes9060286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes.
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Affiliation(s)
- Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Alejandro E Montecinos
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Mahwash Jamy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Sophia Ahmed
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
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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 IN PLANT SCIENCE 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] [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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Lipinska AP, Toda NRT, Heesch S, Peters AF, Cock JM, Coelho SM. Multiple gene movements into and out of haploid sex chromosomes. Genome Biol 2017; 18:104. [PMID: 28595587 PMCID: PMC5463336 DOI: 10.1186/s13059-017-1201-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/27/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out for haploid phase UV sex chromosomes. Here, we explore sex-specific sequences of seven brown algal species to understand the dynamics of the sex-determining region (SDR) gene content across 100 million years of evolution. RESULTS A core set of sex-linked genes is conserved across all the species investigated, but we also identify modifications of both the U and the V SDRs that occurred in a lineage-specific fashion. These modifications involve gene loss, gene gain and relocation of genes from the SDR to autosomes. Evolutionary analyses suggest that the SDR genes are evolving rapidly and that this is due to relaxed purifying selection. Expression analysis indicates that genes that were acquired from the autosomes have been retained in the SDR because they confer a sex-specific role in reproduction. By examining retroposed genes in Saccharina japonica, we demonstrate that UV sex chromosomes have generated a disproportionate number of functional orphan retrogenes compared with autosomes. Movement of genes out of the UV sex chromosome could be a means to compensate for gene loss from the non-recombining region, as has been suggested for Y-derived retrogenes in XY sexual systems. CONCLUSION This study provides the first analysis of gene traffic in a haploid UV system and identifies several features of general relevance to the evolution of sex chromosomes.
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Affiliation(s)
- Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Nicholas R T Toda
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Svenja Heesch
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
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Avia K, Coelho SM, Montecinos GJ, Cormier A, Lerck F, Mauger S, Faugeron S, Valero M, Cock JM, Boudry P. High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus. Sci Rep 2017; 7:43241. [PMID: 28256542 PMCID: PMC5335252 DOI: 10.1038/srep43241] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/20/2017] [Indexed: 02/06/2023] Open
Abstract
Deciphering the genetic architecture of adaptation of brown algae to environmental stresses such as temperature and salinity is of evolutionary as well as of practical interest. The filamentous brown alga Ectocarpus sp. is a model for the brown algae and its genome has been sequenced. As sessile organisms, brown algae need to be capable of resisting the various abiotic stressors that act in the intertidal zone (e.g. osmotic pressure, temperature, salinity, UV radiation) and previous studies have shown that an important proportion of the expressed genes is regulated in response to hyposaline, hypersaline or oxidative stress conditions. Using the double digest RAD sequencing method, we constructed a dense genetic map with 3,588 SNP markers and identified 39 QTLs for growth-related traits and their plasticity under different temperature and salinity conditions (tolerance to high temperature and low salinity). GO enrichment tests within QTL intervals highlighted membrane transport processes such as ion transporters. Our study represents a significant step towards deciphering the genetic basis of adaptation of Ectocarpus sp. to stress conditions and provides a substantial resource to the increasing list of tools generated for the species.
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Affiliation(s)
- Komlan Avia
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Susana M. Coelho
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Gabriel J. Montecinos
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- Centro de Conservación Marina and CeBiB, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Alexandre Cormier
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Fiona Lerck
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Stéphane Mauger
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Sylvain Faugeron
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
- Centro de Conservación Marina and CeBiB, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Myriam Valero
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - J. Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688 Roscoff, France
| | - Pierre Boudry
- Ifremer, Laboratoire des Sciences de l’Environnement Marin (UMR 6539 LEMAR, UBO, CNRS, IRD, Ifremer), Centre Bretagne – ZI de la Pointe du Diable, CS 10070, 29280 Plouzané, France
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