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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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2
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Liu YJ, Zhang TY, Wang QQ, Draisma SGA, Hu ZM. Comparative structure and evolution of the organellar genomes of Padina usoehtunii (Dictyotales) with the brown algal crown radiation clade. BMC Genomics 2024; 25:747. [PMID: 39080531 PMCID: PMC11290263 DOI: 10.1186/s12864-024-10616-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Organellar genomes have become increasingly essential for studying genetic diversity, phylogenetics, and evolutionary histories of seaweeds. The order Dictyotales (Dictyotophycidae), a highly diverse lineage within the Phaeophyceae, is long-term characterized by a scarcity of organellar genome datasets compared to orders of the brown algal crown radiation (Fucophycidae). RESULTS We sequenced the organellar genomes of Padina usoehtunii, a representative of the order Dictyotales, to investigate the structural and evolutionary differences by comparing to five other major brown algal orders. Our results confirmed previously reported findings that the rate of structural rearrangements in chloroplast genomes is higher than that in mitochondria, whereas mitochondrial sequences exhibited a higher substitution rate compared to chloroplasts. Such evolutionary patterns contrast with land plants and green algae. The expansion and contraction of the inverted repeat (IR) region in the chloroplast correlated with the changes in the number of boundary genes. Specifically, the size of the IR region influenced the position of the boundary gene rpl21, with complete rpl21 genes found within the IR region in Dictyotales, Sphacelariales and Ectocarpales, while the rpl21 genes in Desmarestiales, Fucales, and Laminariales span both the IR and short single copy (SSC) regions. The absence of the rbcR gene in the Dictyotales may indicate an endosymbiotic transfer from the chloroplast to the nuclear genome. Inversion of the SSC region occurred at least twice in brown algae. Once in a lineage only represented by the Ectocarpales in the present study and once in a lineage only represented by the Fucales. Photosystem genes in the chloroplasts experienced the strongest signature of purifying selection, while ribosomal protein genes in both chloroplasts and mitochondria underwent a potential weak purifying selection. CONCLUSIONS Variations in chloroplast genome structure among different brown algal orders are evolutionarily linked to their phylogenetic positions in the Phaeophyceae tree. Chloroplast genomes harbor more structural rearrangements than the mitochondria, despite mitochondrial genes exhibiting faster mutation rates. The position and the change in the number of boundary genes likely shaped the IR regions in the chloroplast, and the produced structural variability is important mechanistically to create gene diversity in brown algal chloroplast.
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Affiliation(s)
- Yi-Jia Liu
- Ocean School, Yantai University, Yantai, 264005, China
| | | | - Qi-Qi Wang
- Ocean School, Yantai University, Yantai, 264005, China
| | - Stefano G A Draisma
- Excellence Center for Biodiversity of Peninsular Thailand, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
| | - Zi-Min Hu
- Ocean School, Yantai University, Yantai, 264005, China.
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Vieira C, Kim MS, Zubia M. French Polynesian Scytosiphonaceae (Ectocarpales, Phaeophyceae): A combined molecular and morphological approach to their diversity and systematics. JOURNAL OF PHYCOLOGY 2024; 60:447-464. [PMID: 38310617 DOI: 10.1111/jpy.13432] [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: 07/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 02/06/2024]
Abstract
This study revisited the taxonomy and diversity of brown macroalgae within the Scytosiphonaceae family in French Polynesia, which had previously been recognized as encompassing only six species. Using the chloroplast and mitochondrial genes rbcL, psbA, and cox3 as molecular markers in conjunction with morpho-anatomical observations, we unveiled the presence of 11 species spanning six genera: Chnoospora minima, Colpomenia claytoniae, Co. sinuosa [groups IIIa and IIIb], Hydroclathrus rapanuii, H. tenuis, H. tilesii, Manzaea minuta, Pseudochnoospora implexa, Rosenvingea australis, and the newly described species R. polynesiensis sp. nov. and R. tahitiensis sp. nov. This encompasses the recognition of two previously unreported genera in this region: Manzaea and Pseudochnoospora. Sequences were successfully acquired for four taxa that had been documented previously, while the absence of sequences for H. clathratus and H. tumulis in French Polynesia raises queries about their presence in this region. With these additions, the total species count now stands at 13 (including H. clathratus and H. tumulis), one being an endemic species. The molecular-assisted alpha taxonomic approach used here allowed for a critical revision of the Scytosiphonaceae species checklist for French Polynesia. The diversity revealed in this region accounts for a substantial 20% of the family's global diversity. Additionally, our study presents an updated species-level phylogeny for the Scytosiphonaceae.
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Affiliation(s)
- Christophe Vieira
- Research Institute for Basic Sciences, Jeju National University, Jeju, Korea
| | - Myung Sook Kim
- Research Institute for Basic Sciences, Jeju National University, Jeju, Korea
| | - Mayalen Zubia
- UMR EIO (UPF-IRD-ILM-IFREMER) Université de la Polynésie française, Tahiti, French Polynesia
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Gonzalez‐Aragon D, Rivadeneira MM, Lara C, Torres FI, Vásquez JA, Broitman BR. A species distribution model of the giant kelp Macrocystis pyrifera: Worldwide changes and a focus on the Southeast Pacific. Ecol Evol 2024; 14:e10901. [PMID: 38435006 PMCID: PMC10905252 DOI: 10.1002/ece3.10901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/29/2023] [Accepted: 12/14/2023] [Indexed: 03/05/2024] Open
Abstract
Worldwide climate-driven shifts in the distribution of species is of special concern when it involves habitat-forming species. In the coastal environment, large Laminarian algae-kelps-form key coastal ecosystems that support complex and diverse food webs. Among kelps, Macrocystis pyrifera is the most widely distributed habitat-forming species and provides essential ecosystem services. This study aimed to establish the main drivers of future distributional changes on a global scale and use them to predict future habitat suitability. Using species distribution models (SDM), we examined the changes in global distribution of M. pyrifera under different emission scenarios with a focus on the Southeast Pacific shores. To constrain the drivers of our simulations to the most important factors controlling kelp forest distribution across spatial scales, we explored a suite of environmental variables and validated the predictions derived from the SDMs. Minimum sea surface temperature was the single most important variable explaining the global distribution of suitable habitat for M. pyrifera. Under different climate change scenarios, we always observed a decrease of suitable habitat at low latitudes, while an increase was detected in other regions, mostly at high latitudes. Along the Southeast Pacific, we observed an upper range contraction of -17.08° S of latitude for 2090-2100 under the RCP8.5 scenario, implying a loss of habitat suitability throughout the coast of Peru and poleward to -27.83° S in Chile. Along the area of Northern Chile where a complete habitat loss is predicted by our model, natural stands are under heavy exploitation. The loss of habitat suitability will take place worldwide: Significant impacts on marine biodiversity and ecosystem functioning are likely. Furthermore, changes in habitat suitability are a harbinger of massive impacts in the socio-ecological systems of the Southeast Pacific.
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Affiliation(s)
- Daniel Gonzalez‐Aragon
- Doctorado en Ciencias, mención en Biodiversidad y Biorecursos, Facultad de CienciasUniversidad Católica de la Santísima ConcepciónConcepcionChile
- Instituto Milenio en Socio‐Ecología Costera (SECOS)SantiagoChile
- Núcleo Milenio UPWELL
| | - Marcelo M. Rivadeneira
- Centro de Estudios Avanzados en Zonas ÁridasCoquimboChile
- Departamento de Biología Marina, Facultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
| | - Carlos Lara
- Departamento de Ecología, Facultad de CienciasUniversidad Católica de la Santísima ConcepciónConcepcionChile
- Centro de Investigación en Recursos Naturales y SustentabilidadUniversidad Bernardo O'HigginsSantiagoChile
| | - Felipe I. Torres
- Doctorado en Ciencias, mención en Biodiversidad y Biorecursos, Facultad de CienciasUniversidad Católica de la Santísima ConcepciónConcepcionChile
- Instituto Milenio en Socio‐Ecología Costera (SECOS)SantiagoChile
- Data Observatory Foundation, ANID Technology Center No. DO210001SantiagoChile
| | - Julio A. Vásquez
- Instituto Milenio en Socio‐Ecología Costera (SECOS)SantiagoChile
- Departamento de Biología Marina, Facultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
- Centro de Investigación y Desarrollo Tecnológico en Algas y Otros Recursos Biológicos (CIDTA)CoquimboChile
| | - Bernardo R. Broitman
- Instituto Milenio en Socio‐Ecología Costera (SECOS)SantiagoChile
- Núcleo Milenio UPWELL
- Facultad de Artes LiberalesUniversidad Adolfo IbañezViña Del MarChile
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Kim ST, Conklin SD, Redan BW, Ho KK. Determination of the Nutrient and Toxic Element Content of Wild-Collected and Cultivated Seaweeds from Hawai'i. ACS FOOD SCIENCE & TECHNOLOGY 2024; 4:595-605. [PMID: 38528908 PMCID: PMC10961648 DOI: 10.1021/acsfoodscitech.3c00476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
For centuries, Hawaiians have gathered seaweed for food, medicine, and ceremonial purposes. Seaweed contains nutrients, but some varieties can accumulate toxic elements. We measured target macrominerals (Na, Mg, P, K, Ca), microminerals (B, V, Mn, Co, Cu, Zn, Mo), and nonessential/toxic elements (As, Sr, Cd, Sn, Hg, Pb, and U) in a sample of wild-collected and cultivated seaweeds from Hawai'i. The samples consisted of brown (Sargassum aquifolium, Sargassum echinocarpum), red (Gracilaria parvispora, Halymenia formosa, Halymenia hawaiiana), and green (Ulva ohnoi) seaweed. Elemental composition was determined by inductively coupled plasma (ICP)-atomic emission spectroscopy and ICP-mass spectrometry (MS). Speciation of As was conducted by using liquid chromatography-ICP-MS. S. echinocarpum per 80 g serving was high in Ca (~37% daily value [DV]), U. ohnoi was high in Mg (~40%DV), H. formosa was high in Fe (~40%DV), and G. parvispora was high in Mn (~128%DV). In this study, the highest amounts of toxic elements were observed in S. aquifolium and S. echinocarpum (27.6 mg inorganic As/kg fdw), G. parvispora (43.3 mg Pb/kg fdw) and H. formosa (46.6 mg Pb/kg fdw). These results indicate that although seaweeds from Hawai'i contain a variety of nutrients, some species can accumulate high amounts of toxic elements.
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Affiliation(s)
- Samuel T. Kim
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, 96822, United States
| | - Sean D. Conklin
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740, United States
| | - Benjamin W. Redan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Safety, Bedford Park, IL, 60501, United States
| | - Kacie K.H.Y. Ho
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, 96822, United States
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Choi SW, Graf L, Choi JW, Jo J, Boo GH, Kawai H, Choi CG, Xiao S, Knoll AH, Andersen RA, Yoon HS. Ordovician origin and subsequent diversification of the brown algae. Curr Biol 2024; 34:740-754.e4. [PMID: 38262417 DOI: 10.1016/j.cub.2023.12.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024]
Abstract
Brown algae are the only group of heterokont protists exhibiting complex multicellularity. Since their origin, brown algae have adapted to various marine habitats, evolving diverse thallus morphologies and gamete types. However, the evolutionary processes behind these transitions remain unclear due to a lack of a robust phylogenetic framework and problems with time estimation. To address these issues, we employed plastid genome data from 138 species, including heterokont algae, red algae, and other red-derived algae. Based on a robust phylogeny and new interpretations of algal fossils, we estimated the geological times for brown algal origin and diversification. The results reveal that brown algae first evolved true multicellularity, with plasmodesmata and reproductive cell differentiation, during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna (the Great Ordovician Biodiversification Event) and a proliferation of multicellular green algae. Despite its early Paleozoic origin, the diversification of major orders within this brown algal clade accelerated only during the Mesozoic Era, coincident with both Pangea rifting and the diversification of other heterokont algae (e.g., diatoms), coccolithophores, and dinoflagellates, with their red algal-derived plastids. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous Period. These are concordant with a positive character correlation between parthenogenesis and isogamy. Our new brown algal timeline, combined with a knowledge of past environmental conditions, shed new light on brown algal diversification and the intertwined evolution of multicellularity and sexual reproduction.
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Affiliation(s)
- Seok-Wan Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea; Institut de Biologie de l'École Normale Supérieure, Université Paris Sciences et Lettres, Paris 75005, France
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jihoon Jo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea; Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Ga Hun Boo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai, Nadaku, Kobe 657-8501, Japan
| | - Chang Geun Choi
- Department of Ecological Engineering, College of Environmental and Marine Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, WA 98250, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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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] [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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8
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Takeuchi Y, Sato S, Nagasato C, Motomura T, Okuda S, Kasahara M, Takahashi F, Yoshikawa S. Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri. Sci Rep 2024; 14:3387. [PMID: 38336896 PMCID: PMC10858212 DOI: 10.1038/s41598-024-53729-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024] Open
Abstract
Spermatogenesis is one of the most dramatic changes in cell differentiation. Remarkable chromatin condensation of the nucleus is observed in animal, plant, and algal sperm. Sperm nuclear basic proteins (SNBPs), such as protamine and sperm-specific histone, are involved in chromatin condensation of the sperm nucleus. Among brown algae, sperm of the oogamous Fucales algae have a condensed nucleus. However, the existence of sperm-specific SNBPs in Fucales algae was unclear. Here, we identified linker histone (histone H1) proteins in the sperm and analyzed changes in their gene expression pattern during spermatogenesis in Sargassum horneri. A search of transcriptomic data for histone H1 genes in showed six histone H1 genes, which we named ShH1.1a, ShH1b, ShH1.2, ShH1.3, ShH1.4, and ShH1.5. Analysis of SNBPs using SDS-PAGE and LC-MS/MS showed that sperm nuclei contain histone ShH1.2, ShH1.3, and ShH1.4 in addition to core histones. Both ShH1.2 and ShH1.3 genes were expressed in the vegetative thallus and the male and female receptacles (the organs producing antheridium or oogonium). Meanwhile, the ShH1.4 gene was expressed in the male receptacle but not in the vegetative thallus and female receptacles. From these results, ShH1.4 may be a sperm-specific histone H1 of S. horneri.
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Affiliation(s)
- Yu Takeuchi
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuencho, Obama, Fukui, 917-0003, Japan
| | - Shinya Sato
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuencho, Obama, Fukui, 917-0003, Japan
| | - Chikako Nagasato
- Field Science Center for Northern Biosphere, Muroran Marine Station, Hokkaido University, Muroran, 051-0013, Japan
| | - Taizo Motomura
- Field Science Center for Northern Biosphere, Muroran Marine Station, Hokkaido University, Muroran, 051-0013, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Science, Niigata University, 1-757 Asahimachi, Chuoku, Niigata, Niigata, 951-8501, Japan
| | - Masahiro Kasahara
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Fumio Takahashi
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
- Faculty of Pharmaceutical Sciences, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Shinya Yoshikawa
- Faculty of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuencho, Obama, Fukui, 917-0003, Japan.
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Kosek K, Kukliński P. Impact of kelp forest on seawater chemistry - A review. MARINE POLLUTION BULLETIN 2023; 196:115655. [PMID: 37839130 DOI: 10.1016/j.marpolbul.2023.115655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Kelp forests, globally distributed in cool temperate and polar waters, are renowned for their pivotal role in supporting species diversity and fostering macroalgae productivity. These high-canopy algal ecosystems dynamically influence their surroundings, particularly by altering the physicochemical properties of seawater. This review article aims to underscore the significance of kelp forests in modifying water masses. By serving as effective carbon sinks through the absorption of bicarbonate (HCO3-) and carbon dioxide (CO2) for photosynthesis, kelp forests mitigate nearby acidity levels while enhancing dissolved oxygen concentrations, essential for sustaining diverse marine communities. Additionally, kelp beds have exhibited the need to use inorganic ions (NO3-, NO2-, PO43-) from seawater in order to grow, albeit with associated increases in NH4+ concentrations. Specific examples and findings from relevant studies will be presented to illustrate the profound impact of kelp forests on seawater chemistry, emphasizing their vital role in marine ecosystems.
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Affiliation(s)
- Klaudia Kosek
- Marine Ecology Department, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland.
| | - Piotr Kukliński
- Marine Ecology Department, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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Miwa Y, Awanthi MGG, Soga K, Tanaka A, Ito M, Numata Y, Sato Y, Konishi T. The Cell Wall Characterization of Brown Alga Cladosiphon okamuranus during Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:3274. [PMID: 37765437 PMCID: PMC10536011 DOI: 10.3390/plants12183274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
The present study provides new insights into the growth of the brown algal cell wall by showing that cell wall polysaccharides play an important role in the process of growth, considering the physicochemical characteristic of young and old Cladosiphon okamuranus. To determine its structural variation in detail, the cell wall was sequentially fractionated into five fractions: hot water (HW), ammonium oxalate, hemicellulose-I (HC-I), HC-II, and cellulose, and analyzed physicochemically. Results showed that almost 80% of the total recovery cell wall from both young and old thalli was HW, and HC-I contained mainly fucoidan composed of Fucose, Glucuronic acid, and sulfate in molar ratios of 1.0:0.3:0.6~0.7 and 1.0:0.3:0.2~0.3, respectively. Fucoidan in HW was a highly sulfated matrix polysaccharide abundance in young thalli, while fucoidan in HC-I was rich in old thalli and functions as hemicellulose in land plants, crosslinking with cellulose and strengthening the cell wall. We found that HW and HC-I were particularly involved in the growth and strength of old thalli appeared to be due to the deposition of HC-I and the reduction in water content during the growth process.
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Affiliation(s)
- Yuka Miwa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Senbaru, Nishihara-cho 903-0213, Okinawa, Japan
| | | | - Kouichi Soga
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Sugimoto, Sumiyoshi-ku 558-8585, Osaka, Japan
| | - Atsuko Tanaka
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara-cho 903-0213, Okinawa, Japan
| | - Michihiro Ito
- Center of Molecular Biosciences, Tropical Biosphere Research Center, University of the Ryukyus, Senbaru, Nishihara-cho 903-0213, Okinawa, Japan
| | - Yuichiro Numata
- Bio-Resources Business Development Division, Riken Food Co., Ltd., Miyauchi, Tagajo-shi 985-0844, Miyagi, Japan
| | - Yoichi Sato
- Bio-Resources Business Development Division, Riken Food Co., Ltd., Miyauchi, Tagajo-shi 985-0844, Miyagi, Japan
| | - Teruko Konishi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Senbaru, Nishihara-cho 903-0213, Okinawa, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima-shi 890-0065, Kagoshima, Japan
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11
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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 2023; 12:1124. [PMID: 37627008 PMCID: PMC10452401 DOI: 10.3390/biology12081124] [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: 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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12
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Gao B, Xu M, Shan D, Zhang C, Yang Y, Dong Z, Zhang H, Han B, Huang L, Zhang C. The genomes of Vischeria oleaginous microalgae shed light on the molecular basis of hyper-accumulation of lipids. BMC Biol 2023; 21:133. [PMID: 37280620 DOI: 10.1186/s12915-023-01618-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND With the urgent need to reduce carbon emissions, and the dwindling reserves of easily exploitable fossil fuel, microalgae-based biofuels that can be used for transport systems and CO2 abatement have attracted great attention worldwide in recent years. One useful characteristic of microalgae is their ability to accumulate high levels of lipid content, in particular under conditions of nitrogen deprivation, with numerous species identified so far. However, a trade-off between levels of lipid accumulation and biomass productivity hinders the commercial applicability of lipids from microalgae. Here, we sequenced the genomes of Vischeria sp. CAUP H4302 and Vischeria stellata SAG 33.83, which can accumulate high content of lipids rich in nutraceutical fatty acids and with excellent biomass yield in nitrogen-limiting culture. RESULTS A whole-genome duplication (WGD) event was revealed in V. sp. CAUP H4302, which is a rare event in unicellular microalgae. Comparative genomic analyses showed that a battery of genes encoding pivotal enzymes involved in fatty acids and triacylglycerol biosynthesis, storage polysaccharide hydrolysis, and nitrogen and amino acid-related metabolisms are expanded in the genus Vischeria or only in V. sp. CAUP H4302. The most highlighted is the expansion of cyanate lyase genes in the genus Vischeria, which may enhance their detoxification ability against the toxic cyanate by decomposing cyanate to NH3 and CO2, especially under nitrogen-limiting conditions, resulting in better growth performance and sustained accumulation of biomass under the aforementioned stress conditions. CONCLUSIONS This study presents a WGD event in microalgae, providing new insights into the genetic and regulatory mechanism underpinning hyper-accumulation of lipids and offering potentially valuable targets for future improvements in oleaginous microalgae by metabolic engineering.
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Affiliation(s)
- Baoyan Gao
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China
| | - Meng Xu
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yulan Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Hu Zhang
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China
| | - Boping Han
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China.
| | - Luodong Huang
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China.
| | - Chengwu Zhang
- Department of Ecology & Research Center for Hydrobiology, Jinan University, Guangzhou, 510632, China.
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13
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King NG, Moore PJ, Thorpe JM, Smale DA. Consistency and Variation in the Kelp Microbiota: Patterns of Bacterial Community Structure Across Spatial Scales. MICROBIAL ECOLOGY 2023; 85:1265-1275. [PMID: 35589992 DOI: 10.1007/s00248-022-02038-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/09/2022] [Indexed: 05/10/2023]
Abstract
Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK.
| | - Pippa J Moore
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jamie M Thorpe
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK
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14
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Hatchett WJ, Jueterbock AO, Kopp M, Coyer JA, Coelho SM, Hoarau G, Lipinska AP. Evolutionary dynamics of sex-biased gene expression in a young XY system: insights from the brown alga genus Fucus. THE NEW PHYTOLOGIST 2023; 238:422-437. [PMID: 36597732 DOI: 10.1111/nph.18710] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Sex-biased gene expression is considered to be an underlying cause of sexually dimorphic traits. Although the nature and degree of sex-biased expression have been well documented in several animal and plant systems, far less is known about the evolution of sex-biased genes in more distant eukaryotic groups. Here, we investigate sex-biased gene expression in two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. We find that in contrast to evolutionary distant plant and animal lineages, male-biased genes do not experience high turnover rates, but instead reveal remarkable conservation of bias and expression levels between the two species, suggesting their importance in sexual differentiation. Genes with consistent male bias were enriched in functions related to gamete production, along with sperm competition and include three flagellar proteins under positive selection. We present one of the first reports, outside of the animal kingdom, showing that male-biased genes display accelerated rates of coding sequence evolution compared with female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels, resulting in unique properties of differentially expressed transcripts during reproductive development in Fucus algae.
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Affiliation(s)
- William J Hatchett
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | | | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - James A Coyer
- Shoals Marine Laboratory, University of New Hampshire, Durham, NH, 03824, USA
| | - Susana M Coelho
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - Agnieszka P Lipinska
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
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15
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Rendina F, Falace A, Alongi G, Buia MC, Neiva J, Appolloni L, Marletta G, Russo GF. The Lush Fucales Underwater Forests off the Cilento Coast: An Overlooked Mediterranean Biodiversity Hotspot. PLANTS (BASEL, SWITZERLAND) 2023; 12:1497. [PMID: 37050123 PMCID: PMC10096796 DOI: 10.3390/plants12071497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Fucales (Phaeophyceae) are ecosystem engineers and forest-forming macroalgae whose populations are declining dramatically. In the Mediterranean Sea, Cystoseira sensu lato (s.l.)-encompassing the genera Cystoseira sensu stricto, Ericaria, and Gongolaria-is the most diverse group, and many species have been shown to be locally extinct in many areas, resulting in a shift toward structurally less complex habitats with the consequent loss of ecosystem functions and services. In this study, we report on the extensive occurrence of healthy and dense marine forests formed by Fucales in the Santa Maria di Castellabate Marine Protected Area in Cilento, Italy (Tyrrhenian Sea, Mediterranean). On a total area of 129.45 ha, 10 Cystoseira s.l. taxa were detected using a combined morphological and molecular approach, with an average cover of more than 70%. One of these taxa has been sequenced for the first time. These findings underline the high ecological value of this area as a hotspot of benthic biodiversity and highlight the importance of marine protected area management and regional monitoring programs to ensure the conservation of these valuable yet fragile coastal ecosystems.
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Affiliation(s)
- Francesco Rendina
- Department of Science and Technology, University of Naples “Parthenope”, 80143 Naples, Italy
| | - Annalisa Falace
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
- CoNISMa National Inter University Consortium for Marine Sciences, 00196 Roma, Italy
| | - Giuseppina Alongi
- CoNISMa National Inter University Consortium for Marine Sciences, 00196 Roma, Italy
- Department of Biological, Geological and Environmental Sciences, University of Catania, 95124 Catania, Italy
| | | | - João Neiva
- Centro de Ciências do Mar do Algarve (CCMAR), University of Algarve, 8005-139 Faro, Portugal
| | - Luca Appolloni
- Department of Science and Technology, University of Naples “Parthenope”, 80143 Naples, Italy
| | - Giuliana Marletta
- Department of Biological, Geological and Environmental Sciences, University of Catania, 95124 Catania, Italy
| | - Giovanni Fulvio Russo
- Department of Science and Technology, University of Naples “Parthenope”, 80143 Naples, Italy
- CoNISMa National Inter University Consortium for Marine Sciences, 00196 Roma, Italy
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16
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Awanthi MGG, Umosa M, Yuguchi Y, Oku H, Kitahara K, Ito M, Tanaka A, Konishi T. Fractionation and characterization of cell wall polysaccharides from the brown alga Cladosiphon okamuranus. Carbohydr Res 2023; 523:108722. [PMID: 36459703 DOI: 10.1016/j.carres.2022.108722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/01/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022]
Abstract
Brown algae contain a polysaccharide-rich cell wall, mainly composed of alginate and fucoidan which have been extensively studied for their individual structure and bioactivities. Particularly, the cell wall of Cladosiphon okamuranus is rich in fucoidan rather than alginate. However, little is known about its arrangement or interlinking with other polysaccharides such as cellulose in the cell wall. To determine its structure in detail, the cell wall was sequentially fractionated into five fractions: hot water (HW), ammonium oxalate, hemicellulose-I (HC-I), HC-II, and cellulose. Almost 80% of the total cell wall recovered from alcohol insoluble residue in C. okamuranus consisted of HW and HC-I, which mainly contained fucoidan composed of fucose, glucuronic acid, and sulfate in molar ratios of 1.0:0.3:0.9 and 1.0:0.2:0.3, respectively. Methylation analysis revealed that fucoidan in HW and HC-I structurally differed in terms of content of sulfate, and sugar residue which was 1,4-linked xylose and 1,4-linked fucose. Small angle X-ray scattering measurements also showed distinct conformational differences between HW and HC-I. These structural heterogeneities of fucoidan may be related to their localization, and fucoidan in HC-I may be involved in reinforcing cell wall structure by cross-linking to cellulose.
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Affiliation(s)
- Mahanama Geegana Gamage Awanthi
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan
| | - Manatsu Umosa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 903-0213, Japan
| | - Yoshiaki Yuguchi
- Faculty of Engineering, Osaka Electro-Communication University, 18-8 Hatsucho, Neyagawa-shi, Osaka, 572-8530, Japan
| | - Hirosuke Oku
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan; Center of Molecular Biosciences, Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 903-0213, Japan
| | - Kanefumi Kitahara
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan; Department of Food Science and Biotechnology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan
| | - Michihiro Ito
- Center of Molecular Biosciences, Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 903-0213, Japan
| | - Atsuko Tanaka
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 903-0213, Japan
| | - Teruko Konishi
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan; Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Okinawa, 903-0213, Japan.
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17
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Zhang S, Liang Y, Zhang J, Draisma SGA, Duan D. Organellar genome comparisons of Sargassum polycystum and S. plagiophyllum (Fucales, Phaeophyceae) with other Sargassum species. BMC Genomics 2022; 23:629. [PMID: 36050627 PMCID: PMC9438170 DOI: 10.1186/s12864-022-08862-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/31/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Sargassum polycystum C. Agardh and Sargassum plagiophyllum C. Agardh are inhabitants of tropical coastal areas, their populations are negatively influenced by global warming and marine environment changes. The mitochondrial and chloroplast genomes of these species have not been sequenced. RESULTS The mitochondrial genomes of S. polycystum and S. plagiophyllum were 34,825 bp and 34,862 bp, respectively, and their corresponding chloroplast genomes were 124,493 bp and 124,536 bp, respectively. The mitochondrial and chloroplast genomes of these species share conserved synteny, sequence regions and gene number when compared with the organellar genomes of other Sargassum species. Based on sequence analysis of 35 protein-coding genes, we deduced that S. polycystum and S. plagiophyllum were closely related with S. ilicifolium; these species diverged approximately 0.3 million years ago (Ma; 0.1-0.53 Ma) during the Pleistocene period (0.01-2.59 Ma). Rates of synonymous and non-synonymous substitutions in the mitochondrial genome of the Sargassum genus were 3 times higher than those in the chloroplast genome. In the mitochondrial genome, rpl5, rpl31 and rps11 had the highest synonymous substitution rates. In the chloroplast genome, psaE, rpl14 and rpl27 had the highest synonymous substitution rates. CONCLUSIONS Phylogenetic analysis confirms the close relationship between the two sequenced species and S. ilicifolium. Both synonymous and non-synonymous substitution rates show significant divergence between the group of mitochondrial genomes versus the group of chloroplast genomes. The deciphering of complete mitochondrial and chloroplast genomes is significant as it advances our understanding of the evolutionary and phylogenetic relationships between species of brown seaweeds.
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Affiliation(s)
- Shuangshuang Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy Sciences, Beijing, 100094, China
| | - Yanshuo Liang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- University of Chinese Academy Sciences, Beijing, 100094, China
| | - Jie Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Stefano G A Draisma
- Excellence Center for Biodiversity of Peninsular Thailand, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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18
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Martins NT, Cassano V, Gurgel CFD. Phylogeography of Colpomenia sinuosa (Ectocarpales, Phaeophyceae) along the Brazilian coast. JOURNAL OF PHYCOLOGY 2022; 58:543-554. [PMID: 35545902 DOI: 10.1111/jpy.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/19/2022] [Indexed: 06/15/2023]
Abstract
Colpomenia sinuosa is a cosmopolitan brown macroalgal species complex and hence a great candidate for evolutionary studies in the marine environment. Since 2009, three major C. sinuosa phylogenetic lineages, subdivided into eight subgroups, have been identified based on cox3 DNA sequences from worldwide collections. However, worldwide sampling remains limited and spotty. To date molecular data from Brazilian C. sinuosa populations have been limited to 10 specimens collected in a single locality. Nonetheless, C. sinuosa populations occur along the entire ~8,000 km Brazilian coast. Consequently, knowledge on population genetic diversity and spatial genetic structuring along most of the Brazilian coastline is nonexistent. To fulfill this gap in knowledge, we performed a phylogeographic analysis of C. sinuosa populations in Brazil. The highly variable cox3 marker was sequenced for 148 individuals collected in 12 localities in Brazil. Results identified two genetically distinct population groups (north vs. south) separated at 20.5° S latitude. Genetic diversity in northern populations is 14.6 and 15.5 times greater than southern populations in terms of haplotype and nucleotide diversity, respectively. Among northern populations, the Bahia state holds the largest genetic diversity. The southern populations had lower genetic diversity and no internal genetic sub-structure suggesting past bottlenecks followed by recent colonization from northern haplotypes. Our results do not indicate recent introductions of foreign haplotypes in Brazil and reinforce the crucial importance of historical and extant allopatric, parapatric, and sympatric processes driving marine macroalgal evolution in the Southwestern Atlantic Ocean.
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Affiliation(s)
- Nuno Tavares Martins
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, 05508-090, Brazil
| | - Valéria Cassano
- Departamento de Botânica, Universidade de São Paulo, Instituto de Biociências, São Paulo, São Paulo, 05508-090, Brazil
| | - Carlos Frederico Deluqui Gurgel
- NUPEM - Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, 27965-045, Brazil
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19
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Liang Y, Choi HG, Zhang S, Hu ZM, Duan D. The organellar genomes of Silvetia siliquosa (Fucales, Phaeophyceae) and comparative analyses of the brown algae. PLoS One 2022; 17:e0269631. [PMID: 35709195 PMCID: PMC9202911 DOI: 10.1371/journal.pone.0269631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/24/2022] [Indexed: 11/18/2022] Open
Abstract
The brown alga Silvetia siliquosa (Tseng et Chang) Serrão, Cho, Boo & Brawly is endemic to the Yellow-Bohai Sea and southwestern Korea. It is increasingly endangered due to habitat loss and excessive collection. Here, we sequenced the mitochondrial (mt) and chloroplast (cp) genomes of S. siliquosa. De novo assembly showed that the mt-genome was 36,036 bp in length, including 38 protein-coding genes (PCGs), 26 tRNAs, and 3 rRNAs, and the cp-genome was 124,991 bp in length, containing 139 PCGs, 28 tRNAs, and 6 rRNAs. Gene composition, gene number, and gene order of the mt-genome and cp-genome were very similar to those of other species in Fucales. Phylogenetic analysis revealed a close genetic relationship between S. siliquosa and F. vesiculosus, which diverged approximately 8 Mya (5.7-11.0 Mya), corresponding to the Late Miocene (5.3-11.6 Ma). The synonymous substitution rate of mitochondrial genes of phaeophycean species was 1.4 times higher than that of chloroplast genes, but the cp-genomes were more structurally variable than the mt-genomes, with numerous gene losses and rearrangements among the different orders in Phaeophyceae. This study reports the mt- and cp-genomes of the endangered S. siliquosa and improves our understanding of its phylogenetic position in Phaeophyceae and of organellar genomic evolution in brown algae.
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Affiliation(s)
- Yanshuo Liang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Han-Gil Choi
- Faculty of Biological Science and Institute for Environmental Science, Wonkwang University, Iksan, Korea
| | - Shuangshuang Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Min Hu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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20
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Akita S, Vieira C, Hanyuda T, Rousseau F, Cruaud C, Couloux A, Heesch S, Cock JM, Kawai H. Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences. Mol Phylogenet Evol 2022; 168:107408. [PMID: 35031471 DOI: 10.1016/j.ympev.2022.107408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/16/2021] [Accepted: 12/26/2021] [Indexed: 11/23/2022]
Abstract
In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.
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Affiliation(s)
- Shingo Akita
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan; Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, Hokkaido 041-8611, Japan
| | - Christophe Vieira
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan.
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan
| | - Florence Rousseau
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39 75005 Paris, France
| | - Corinne Cruaud
- Génoscope, Centre National de Séquençage, 2 rue G. Crémieux, Evry CP 5706, France
| | - Arnaud Couloux
- Génoscope, Centre National de Séquençage, 2 rue G. Crémieux, Evry CP 5706, France
| | - Svenja Heesch
- CNRS, Sorbonne Université, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models, Station Biologique, F 29688 Roscoff, France; Universität Rostock Institut für Biowissenschaften Angewandte Ökologie & Phykologie Albert-Einstein-Straße, 21 18059 Rostock, Germany.
| | - J Mark Cock
- CNRS, Sorbonne Université, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models, Station Biologique, F 29688 Roscoff, France
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe 657-8501, Japan
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21
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Senanayake IC, Pem D, Rathnayaka AR, Wijesinghe SN, Tibpromma S, Wanasinghe DN, Phookamsak R, Kularathnage ND, Gomdola D, Harishchandra D, Dissanayake LS, Xiang MM, Ekanayaka AH, McKenzie EHC, Hyde KD, Zhang HX, Xie N. Predicting global numbers of teleomorphic ascomycetes. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00498-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
AbstractSexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.
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22
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Fournier GP, Parsons CW, Cutts EM, Tamre E. Standard Candles for Dating Microbial Lineages. Methods Mol Biol 2022; 2569:41-74. [PMID: 36083443 DOI: 10.1007/978-1-0716-2691-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Chris W Parsons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erik Tamre
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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23
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Rashed ZE, Grasselli E, Khalifeh H, Canesi L, Demori I. Brown-Algae Polysaccharides as Active Constituents against Nonalcoholic Fatty Liver Disease. PLANTA MEDICA 2022; 88:9-19. [PMID: 33142346 DOI: 10.1055/a-1273-3159] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nonalcoholic fatty liver disease is a metabolic disorder characterized by lipid overloading in hepatocytes that can progress pathogenically and even end in hepatocellular carcinoma. Nonalcoholic fatty liver disease pharmacological treatment is still limited by unwanted side effects, whereas the use of food components with therapeutic potential is advisable. The culinary use of marine algae is traditional for some populations and reviving worldwide, with promising health outcomes due to the large number of bioactive compounds found in seaweeds. The present review focuses on brown-algae polysaccharides, particularly fucoidan, alginate, and laminarin, and summarizes the experimental evidence of their potential effects against nonalcoholic fatty liver disease onset and progression. In vitro and in vivo studies demonstrate that brown-algae polysaccharides exert beneficial actions on satiety feeling, caloric intake, fat absorption, and modulation of the gut microbiota, which could account for indirect effects on energy and lipid homeostasis, thus diminishing the fat overload in the liver. Specific effects against nonalcoholic fatty liver disease pathogenesis and worsening are also described and sustained by the antioxidant, anti-inflammatory, and antisteatotic properties of brown-algae polysaccharides. Further studies are required to clarify the mechanism of action of brown-algae polysaccharides on liver cells, to determine the composition and bioavailability of brown-algae polysaccharides present in different algal sources and to probe the clinical availability of these compounds in the form of algal foods, food supplements, and regulated therapeutics.
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Affiliation(s)
- Zeinab El Rashed
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
- Rammal Rammal Laboratory (ATAC group), Faculty of Sciences I, Lebanese University, Beirut, Lebanon
| | - Elena Grasselli
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Hala Khalifeh
- Rammal Rammal Laboratory (ATAC group), Faculty of Sciences I, Lebanese University, Beirut, Lebanon
| | - Laura Canesi
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Ilaria Demori
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
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24
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Coelho SM, Umen J. Switching it up: algal insights into sexual transitions. PLANT REPRODUCTION 2021; 34:287-296. [PMID: 34181073 PMCID: PMC8566403 DOI: 10.1007/s00497-021-00417-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
While the process of meiosis is highly conserved across eukaryotes, the sexual systems that govern life cycle phase transitions are surprisingly labile. Switches between sexual systems have profound evolutionary and ecological consequences, in particular for plants, but our understanding of the fundamental mechanisms and ultimate causes underlying these transitions is still surprisingly incomplete. We explore here the idea that brown and green algae may be interesting comparative models that can increase our understanding of relevant processes in plant reproductive biology, from evolution of gamete dimorphism, gametogenesis, sex determination and transitions in sex-determining systems.
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Affiliation(s)
- Susana M Coelho
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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25
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Assessment of Arabian Gulf Seaweeds from Kuwait as Sources of Nutritionally Important Polyunsaturated Fatty Acids (PUFAs). Foods 2021; 10:foods10102442. [PMID: 34681494 PMCID: PMC8536129 DOI: 10.3390/foods10102442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 02/03/2023] Open
Abstract
The fatty acid (FA) compositions of ten seaweeds representative of Chlorophyta, Rhodophyta, and Ochrophyta from Kuwait in the Arabian Gulf region were determined and are discussed in the context of their potential nutritional perspectives for seaweed valorization. All the seaweeds had higher saturated fatty acid (SFA) and lower monounsaturated (MUFA) and polyunsaturated fatty acid (PUFA) contents than those typical of tropical environments. Palmitic, myristic, stearic, oleic, linoleic, α-linolenic, and stearidonic acids were the major FAs detected. Arachidonic, eicosapentaenoic, and docosahexaenoic acids were detected in minor amounts. Conserved fatty acid patterns revealed phylogenetic relationships among phyla, classes, and orders matching the molecular phylogenies at higher taxonomic ranks. Hierarchical clustering analyses clearly segregated different seaweeds (except Codium papillatum and Iyengaria stellata) into distinct groups based on their FA signatures. All but one species (Chondria sp.) had health-beneficial n6/n3 PUFAs (0.33:1–2.94:1) and atherogenic (0.80–2.52) and thrombogenic indices (0.61–5.17). However, low PUFA/SFA contents in most of the species (except Ulva spp.) may limit their utilization in the formulation of PUFA-rich functional foods. Ulva spp. had substantially high PUFAs with PUFA/SFA > 0.4, n6/n3 (0.33–0.66) and atherogenic (0.80–1.15) and thrombogenic indices (0.49–0.72), providing substantial potential for their utilization in food and feed applications.
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26
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Lagourgue L, Payri CE. Diversity and taxonomic revision of tribes Rhipileae and Rhipiliopsideae (Halimedaceae, Chlorophyta) based on molecular and morphological data. JOURNAL OF PHYCOLOGY 2021; 57:1450-1471. [PMID: 34003495 DOI: 10.1111/jpy.13186] [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: 08/05/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Genera and species of the tribes Rhipileae and Rhipiliopsideae are abundant in most coral reef ecosystems worldwide. However, the group has been largely overlooked, and very little genetic data is available to accurately assess its diversity, phylogenetic relationships, and geographic distribution. Our study provided an in-depth reassessment of tribes Rhipileae and Rhipiliopsideae based on a species-rich dataset and the combination of molecular species delimitation, multilocus phylogenetic analyses (tufA, rbcL, and 18S rDNA), and morpho-anatomic observations. Our results revealed an unexpected diversity of 38 morphologically validated species hypotheses, including 20 new species, two of which are described in this paper and one resurrected species (Rhipilia diaphana). Based on our phylogenetic results we proposed to redefine the genera Rhipilia and Rhipiliopsis and described two new genera, Kraftalia gen. nov. (Rhipileae) and Rhipiliospina gen. nov. (Rhipiliopsideae). Finally, we validated Rhipiliella Kraft and included it in the tribe Rhipileae. Although Rhipilia and Rhipiliopsis have a pantropical distribution, none of the species studied here appeared cosmopolitan; instead, they have restricted distributions.
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Affiliation(s)
- Laura Lagourgue
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, Paris Cedex 05, 75252, France
- UMR ENTROPIE (IRD, UR, UNC, Ifremer, CNRS), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France
| | - Claude E Payri
- UMR ENTROPIE (IRD, UR, UNC, Ifremer, CNRS), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France
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27
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Lehtonen J, Horinouchi Y, Togashi T, Parker GA. Evolution of Anisogamy in Organisms with Parthenogenetic Gametes. Am Nat 2021; 198:360-378. [PMID: 34403316 DOI: 10.1086/715185] [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] [Indexed: 11/03/2022]
Abstract
AbstractThe two sexes are defined by the sizes of the gametes they produce, anisogamy being the state with two differing gamete sizes (hence, females and males). The origin of this divergence has received much research interest, both theoretically and empirically. The gamete dynamics (GD) theory is a widely accepted theoretical explanation for anisogamy, and green algae have been an important empirical testing ground for the theory. However, some green and brown algae produce parthenogenetic gametes (gametes that can develop without fusing with another gamete), in contrast to an assumption in GD theory that unfused gametes do not develop. Here, we construct a GD model accounting for parthenogenetic gametes. We find that under conditions of panmixia and highly efficient fertilization (i.e., conditions of classical GD models from 1972 onward), the results remain largely unaltered by parthenogametes. However, under gamete-limited conditions anisogamy evolves less easily in the new model, and a novel result emerges: whereas previous models typically predict the evolution of either anisogamy or small isogamy, the current model shows that large isogamy can evolve when parthenogenetic gametes evolve under conditions of inefficient fertilization. Our analyses uncover unexplored complications relating to sex ratios under this relatively uncharted gametic system. We discuss limitations these complications impose on our models and suggest avenues for future research. We compare model results to algae with parthenogenetic gametes in nature.
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28
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Starko S, Bringloe TT, Soto Gomez M, Darby H, Graham SW, Martone PT. Genomic Rearrangements and Sequence Evolution across Brown Algal Organelles. Genome Biol Evol 2021; 13:evab124. [PMID: 34061182 PMCID: PMC8290108 DOI: 10.1093/gbe/evab124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
Organellar genomes serve as useful models for genome evolution and contain some of the most widely used phylogenetic markers, but they are poorly characterized in many lineages. Here, we report 20 novel mitochondrial genomes and 16 novel plastid genomes from the brown algae. We focused our efforts on the orders Chordales and Laminariales but also provide the first plastid genomes (plastomes) from Desmarestiales and Sphacelariales, the first mitochondrial genome (mitome) from Ralfsiales and a nearly complete mitome from Sphacelariales. We then compared gene content, sequence evolution rates, shifts in genome structural arrangements, and intron distributions across lineages. We confirm that gene content is largely conserved in both organellar genomes across the brown algal tree of life, with few cases of gene gain or loss. We further show that substitution rates are generally lower in plastid than mitochondrial genes, but plastomes are more variable in gene arrangement, as mitomes tend to be colinear even among distantly related lineages (with exceptions). Patterns of intron distribution across organellar genomes are complex. In particular, the mitomes of several laminarialean species possess group II introns that have T7-like ORFs, found previously only in mitochondrial genomes of Pylaiella spp. (Ectocarpales). The distribution of these mitochondrial introns is inconsistent with vertical transmission and likely reflects invasion by horizontal gene transfer between lineages. In the most extreme case, the mitome of Hedophyllum nigripes is ∼40% larger than the mitomes of close relatives because of these introns. Our results provide substantial insight into organellar evolution across the brown algae.
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Affiliation(s)
- Samuel Starko
- Department of Biology, University of Victoria, Victoria, Canada
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Trevor T Bringloe
- Department of BioSciences, University of Melbourne, Melbourne, Australia
| | - Marybel Soto Gomez
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Hayley Darby
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Patrick T Martone
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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29
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Heesch S, Serrano-Serrano M, Barrera-Redondo J, Luthringer R, Peters AF, Destombe C, Cock JM, Valero M, Roze D, Salamin N, Coelho SM. Evolution of life cycles and reproductive traits: Insights from the brown algae. J Evol Biol 2021; 34:992-1009. [PMID: 34096650 DOI: 10.1101/530477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/18/2021] [Indexed: 05/28/2023]
Abstract
A vast diversity of types of life cycles exists in nature, and several theories have been advanced to explain how this diversity has evolved and how each type of life cycle is retained over evolutionary time. Here, we exploited the diversity of life cycles and reproductive traits of the brown algae (Phaeophyceae) to test several hypotheses on the evolution of life cycles. We investigated the evolutionary dynamics of four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assigned states to up to 77 representative species of the taxonomic diversity of the brown algal group, in a multi-gene phylogeny. We used maximum likelihood and Bayesian analyses of correlated evolution, while taking the phylogeny into account, to test for correlations between traits and to investigate the chronological sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth evolves when sexual reproduction is preferred over asexual reproduction, possibly because it allows the complementation of deleterious mutations. We also found that haploid sex determination is ancestral in relation to diploid sex determination. However, our results could not address whether increased zygotic and diploid growth are associated with increased sexual dimorphism. Our analyses suggest that in the brown algae, isogamous species evolved from anisogamous ancestors, contrary to the commonly reported pattern where evolution proceeds from isogamy to anisogamy.
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Affiliation(s)
- Svenja Heesch
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
- Applied Ecology & Phycology, Institute for Biosciences, University of Rostock, Rostock, Germany
| | | | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Rémy Luthringer
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
| | | | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - J Mark Cock
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Susana M Coelho
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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30
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Heesch S, Serrano-Serrano M, Barrera-Redondo J, Luthringer R, Peters AF, Destombe C, Cock JM, Valero M, Roze D, Salamin N, Coelho SM. Evolution of life cycles and reproductive traits: Insights from the brown algae. J Evol Biol 2021; 34:992-1009. [PMID: 34096650 DOI: 10.1111/jeb.13880] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023]
Abstract
A vast diversity of types of life cycles exists in nature, and several theories have been advanced to explain how this diversity has evolved and how each type of life cycle is retained over evolutionary time. Here, we exploited the diversity of life cycles and reproductive traits of the brown algae (Phaeophyceae) to test several hypotheses on the evolution of life cycles. We investigated the evolutionary dynamics of four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assigned states to up to 77 representative species of the taxonomic diversity of the brown algal group, in a multi-gene phylogeny. We used maximum likelihood and Bayesian analyses of correlated evolution, while taking the phylogeny into account, to test for correlations between traits and to investigate the chronological sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth evolves when sexual reproduction is preferred over asexual reproduction, possibly because it allows the complementation of deleterious mutations. We also found that haploid sex determination is ancestral in relation to diploid sex determination. However, our results could not address whether increased zygotic and diploid growth are associated with increased sexual dimorphism. Our analyses suggest that in the brown algae, isogamous species evolved from anisogamous ancestors, contrary to the commonly reported pattern where evolution proceeds from isogamy to anisogamy.
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Affiliation(s)
- Svenja Heesch
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
- Applied Ecology & Phycology, Institute for Biosciences, University of Rostock, Rostock, Germany
| | | | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Rémy Luthringer
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
| | | | - Christophe Destombe
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - J Mark Cock
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, UC, UACH, IRL 3614, Roscoff, France
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Susana M Coelho
- CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Univ Paris 06, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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31
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Anderson AB, Assis J, Batista MB, Serrão EA, Guabiroba HC, Delfino SDT, Pinheiro HT, Pimentel CR, Gomes LEO, Vilar CC, Bernardino AF, Horta P, Ghisolfi RD, Joyeux JC. Global warming assessment suggests the endemic Brazilian kelp beds to be an endangered ecosystem. MARINE ENVIRONMENTAL RESEARCH 2021; 168:105307. [PMID: 33984550 DOI: 10.1016/j.marenvres.2021.105307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Kelps are canopy-forming brown seaweed sustaining critical ecosystem services in coastal habitats, including shelter, nursery grounds, and providing food resources to a myriad of associated species. This study modeled the fundamental niche of Laminaria abyssalis along the Brazilian continental margin, an endemic species of the South Atlantic, to anticipate potential distributional range shifts under two contrasting scenarios of future environmental changes (RCP2.6 and RCP8.5). The model for fundamental niche predictions considering the "present scenario" has shown a wider potential area than the realized niche (i.e., the area where the species actually occurs) along the Brazilian coast. In both future scenarios, the models have shown niche erosion on the northern portion of the Brazilian coast and niche gains towards the south. In both scenarios, L. abyssalis populations tend to shift to deeper regions of the reef. The restricted range of occurrence (33,000 km2), intense anthropic activities along these beds (e.g., trawling fisheries, oil/gas mining, or removal for agricultural purposes) acting synergically with global warming, may drive this ecosystem to collapse faster than kelp species' ability to adapt. We propose to classify L. abyssalis as Endangered - (EN) under IUCN criteria, and highlight that long-term monitoring of kelp beds is an urgent need to develop effective conservation initiatives to protect such rare and invaluable ecosystem.
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Affiliation(s)
- A B Anderson
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil.
| | - J Assis
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - M B Batista
- Laboratório de Ficologia, Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-970, Brazil
| | - E A Serrão
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - H C Guabiroba
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - S D T Delfino
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - H T Pinheiro
- Ichthyology Section, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - C R Pimentel
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - L E O Gomes
- Benthic Ecology Group, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - C C Vilar
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - A F Bernardino
- Benthic Ecology Group, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - P Horta
- Laboratório de Ficologia, Departamento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, SC, 88040-970, Brazil
| | - R D Ghisolfi
- Laboratory of Oceanography, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
| | - J-C Joyeux
- Laboratory of Ichthyology, Department of Oceanography, Federal University of Espírito Santo, Vitória, ES, 29075-910, Brazil
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Grant WS, Chenoweth E. Phylogeography of sugar kelp: Northern ice-age refugia in the Gulf of Alaska. Ecol Evol 2021; 11:4670-4687. [PMID: 33976839 PMCID: PMC8093666 DOI: 10.1002/ece3.7368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 11/13/2022] Open
Abstract
Many Northeast (NE) Pacific fishes and invertebrates survived Pleistocene glaciations in northern refugia, but the extent that kelps survived in northern areas is uncertain. Here, we test the hypothesis that populations of sugar kelp (Saccharina latissima) persisted in the Gulf of Alaska during ice-age maxima when the western margin of the Cordilleran ice sheet covered coastal areas around the NE Pacific Ocean. We estimated genetic diversities within and phylogeographical relationships among 14 populations along 2,800 km in the NE Pacific and Bering Sea with partial sequences of mitochondrial DNA 5'-cytochrome oxidase subunit I (COI, bp = 624, n = 543), chloroplast DNA ribulose-1,5-bisphosphate carboxylase large subunit-3' (rbcL, bp = 735, n = 514), and 11 microsatellite loci. Concatenated sequences of rbcL and COI showed moderate levels of within-population genetic diversity (mean h = 0.200) but substantial differences among populations (ΦST = 0.834, p < .0001). Microsatellites showed moderate levels of heterozygosity within populations (mean H E = 0.391). Kelps in the same organellar lineage tended to cluster together, regardless of geographic origins, as indicated in a principal coordinate analysis (PCoA) of microsatellite genotypes. The PCoA also showed evidence of nuclear hybridizations between co-occurring organellar lineages. Individual admixture plots with population clusters of K = 2, 6, and 9 showed increasing complexity with considerable historical admixture between some clusters. A time-calibrated phylogeny placed divergences between rbcL-COI lineages at 1.4 million years at most. The time frames of mutation in the rbcL-COI lineages and microsatellite population clusters differed among locations. The existence of ancient lineages in the Gulf of Alaska, moderate levels of genetic diversity, and the absence of departures from neutrality are consistent with northern refugia during multiple Croll-Milankovitch climate cycles in the Pleistocene Epoch.
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Linardić M, Braybrook SA. Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses. PLoS One 2021; 16:e0233249. [PMID: 33909633 PMCID: PMC8081170 DOI: 10.1371/journal.pone.0233249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/18/2021] [Indexed: 11/19/2022] Open
Abstract
Quantitative gene expression analysis is an important tool in the scientist's belt. The identification of evenly expressed reference genes is necessary for accurate quantitative gene expression analysis, whether by traditional RT-PCR (reverse-transcription polymerase chain reaction) or by qRT-PCR (quantitative real-time PCR; qPCR). In the Stramenopiles (the major line of eukaryotes that includes brown algae) there is a noted lack of known reference genes for such studies, largely due to the absence of available molecular tools. Here we present a set of nine reference genes (Elongation Factor 1 alpha (EF1A), Elongation Factor 2 alpha (EF2A), Elongation Factor 1 beta (EF1B), 14-3-3 Protein, Ubiquitin Conjugating Enzyme (UBCE2), Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH), Actin Related Protein Complex (ARP2/3), Ribosomal Protein (40s; S23), and Actin) for the brown alga Fucus distichus. These reference genes were tested on adult sporophytes across six abiotic stress conditions (desiccation, light and temperature modification, hormone addition, pollutant exposure, nutrient addition, and wounding). Suitability of these genes as reference genes was quantitatively evaluated across conditions using standard methods and the majority of the tested genes were evaluated favorably. However, we show that normalization genes should be chosen on a condition-by-condition basis. We provide a recommendation that at least two reference genes be used per experiment, a list of recommended pairs for the conditions tested here, and a procedure for identifying a suitable set for an experimenter's unique design. With the recent expansion of interest in brown algal biology and accompanied molecular tools development, the variety of experimental conditions tested here makes this study a valuable resource for future work in basic biology and understanding stress responses in the brown algal lineage.
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Affiliation(s)
- Marina Linardić
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Energy Institute of Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Siobhan A. Braybrook
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Energy Institute of Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of Los Angeles, Los Angeles, California, United States of America
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Ni-Ni-Win, Hanyuda T, Kato A, Shimabukuro H, Uchimura M, Kawai H, Tokeshi M. Global Diversity and Geographic Distributions of Padina Species (Dictyotales, Phaeophyceae): New Insights Based on Molecular and Morphological Analyses. JOURNAL OF PHYCOLOGY 2021; 57:454-472. [PMID: 32975311 DOI: 10.1111/jpy.13076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 07/21/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The taxonomic status and species diversity of the brown algal genus Padina (Dictyotales, Phaeophyceae) was assessed based on DNA sequences and the morpho-anatomy of specimens collected worldwide, especially from tropical and subtropical western Pacific regions. Phylogenetic analyses using chloroplast rbcL and mitochondrial cox3 gene sequences demonstrated four distinct clades for newly collected samples with high bootstrap support. Each species clade possesses a suite of morphological features that are not shared by any known species of Padina. These are P. imbricata sp. nov., Padina lutea sp. nov., P. moffittianoides sp. nov., and P. nitida sp. nov. The occurrence of these and other species of Padina clearly points to an elevated diversity of the genus in tropical/subtropical waters of the western Pacific. Phylogenetic analyses provided new insights into biogeographic characteristics of the genus, with many species in the Pacific Ocean showing shared/overlapping distributions, whereas species from the Mediterranean/Atlantic and/or the Indian Ocean tend to be confined to particular regions. Consideration has also been given to the evolutionary time frame of the genus Padina based on molecular time trees: a time tree of the concatenated data set (rbcL + cox3) revealed the estimated divergence time in the mid-Cretaceous, whereas those of cox3 and rbcL showed older estimates pointing to the periods of mid-Jurassic and Early Cretaceous, respectively.
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Affiliation(s)
- Ni-Ni-Win
- Kyushu University Amakusa Marine Biological Laboratory, Reihoku-Amakusa, Kumamoto, 863-2507, Japan
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Rokkodai, Kobe, 657-8501, Japan
| | - Aki Kato
- Takehara Fisheries Research Station, Setouchi Field Science Center, Hiroshima University, Takehara, Hiroshima, 725-0024, Japan
| | - Hiromori Shimabukuro
- National Research Institute of Fisheries and Environment of Inland Sea, Fishery Research Agency, Hatsukaichi, Hiroshima, 739-0452, Japan
| | - Masayuki Uchimura
- Research Institute on Subtropical Ecosystems, 252 Yaga, Nago, Okinawa, 905-1631, Japan
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai, Kobe, 657-8501, Japan
| | - Mutsunori Tokeshi
- Kyushu University Amakusa Marine Biological Laboratory, Reihoku-Amakusa, Kumamoto, 863-2507, Japan
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35
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Graf L, Shin Y, Yang JH, Choi JW, Hwang IK, Nelson W, Bhattacharya D, Viard F, Yoon HS. A genome-wide investigation of the effect of farming and human-mediated introduction on the ubiquitous seaweed Undaria pinnatifida. Nat Ecol Evol 2021; 5:360-368. [PMID: 33495590 PMCID: PMC7929912 DOI: 10.1038/s41559-020-01378-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Human activity is an important driver of ecological and evolutionary change on our planet. In particular, domestication and biological introductions have important and long-lasting effects on species' genomic architecture and diversity. However, genome-wide analysis of independent domestication and introduction events within a single species has not previously been performed. The Pacific kelp Undaria pinnatifida provides such an opportunity because it has been cultivated in its native range in Northeast Asia but also introduced to four other continents in the past 50 years. Here we present the results of a genome-wide analysis of natural, cultivated and introduced populations of U. pinnatifida to elucidate human-driven evolutionary change. We demonstrate that these three categories of origin can be distinguished at the genome level, reflecting the combined influence of neutral (demography and migration) and non-neutral (selection) processes.
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Affiliation(s)
- Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Younhee Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Il Ki Hwang
- Aquaculture Management Division, National Institute of Fisheries Science, Busan, South Korea
| | - Wendy Nelson
- National Institute of Water & Atmospheric Research, Wellington, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Frédérique Viard
- Sorbonne Université, CNRS, AD2M, Station Biologique de Roscoff, Roscoff, France
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea.
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Rana S, Valentin K, Riehl J, Blanfuné A, Reynes L, Thibaut T, Bartsch I, Eichinger L, Glöckner G. Analysis of organellar genomes in brown algae reveals an independent introduction of similar foreign sequences into the mitochondrial genome. Genomics 2021; 113:646-654. [PMID: 33485954 DOI: 10.1016/j.ygeno.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/19/2020] [Accepted: 01/18/2021] [Indexed: 11/21/2022]
Abstract
Kelp species (Laminariales, Phaeophyceae) are globally widespread along temperate to Polar rocky coastal lines. Here we analyse the mitochondrial and chloroplast genomes of Laminaria rodriguezii, in comparison to the organellar genomes of other kelp species. We also provide the complete mitochondrial genome sequence of another endemic kelp species from a Polar habitat, the Arctic Laminaria solidungula. We compare phylogenetic trees derived from twenty complete mitochondrial and seven complete chloroplast kelp genomes. Interestingly, we found a stretch of more than 700 bp in the mitochondrial genome of L.rodriguezii, which is not present in any other yet sequenced member of the Phaeophyceae. This stretch matches a protein coding region in the mitochondrial genome from Desmarestia viridis, another brown seaweed. Their high similarity suggests that these sequences originated through independent introduction into the two species. Their origin could have been by infection by yet unknown similar mitoviruses, currently only known from fungi and plants.
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Affiliation(s)
- Shivani Rana
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Klaus Valentin
- Alfred-Wegener-Institute, Helmholtz-Center for Marine and Polar Research, Bremerhaven, Germany.
| | - Jana Riehl
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Aurélie Blanfuné
- Aix-Marseille University and University of Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Lauric Reynes
- Aix-Marseille University and University of Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Thierry Thibaut
- Aix-Marseille University and University of Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Inka Bartsch
- Alfred-Wegener-Institute, Helmholtz-Center for Marine and Polar Research, Bremerhaven, Germany
| | - Ludwig Eichinger
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany.
| | - Gernot Glöckner
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany
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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. JOURNAL OF PHYCOLOGY 2021; 57:370-378. [PMID: 33179252 DOI: 10.1111/jpy.13100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [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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Li R, Jia X, Zhang J, Jia S, Liu T, Qu J, Wang X. The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:747036. [PMID: 34804089 PMCID: PMC8602799 DOI: 10.3389/fpls.2021.747036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/04/2021] [Indexed: 05/03/2023]
Abstract
Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.
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Affiliation(s)
- Ruoran Li
- College of Life Sciences, Yantai University, Yantai, China
| | - Xuli Jia
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Zhang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Shangang Jia,
| | - Tao Liu
- College of Life Sciences, Yantai University, Yantai, China
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Tao Liu,
| | - Jiangyong Qu
- College of Life Sciences, Yantai University, Yantai, China
- Jiangyong Qu,
| | - Xumin Wang
- College of Life Sciences, Yantai University, Yantai, China
- Xumin Wang,
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39
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Grant WS, Bringloe TT. Pleistocene Ice Ages Created New Evolutionary Lineages, but Limited Speciation in Northeast Pacific Winged Kelp. J Hered 2020; 111:593-605. [PMID: 33252684 DOI: 10.1093/jhered/esaa053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
The extent that Pleistocene climate variability promoted speciation has been much debated. Here, we surveyed genetic markers in winged kelp Alaria in the Gulf of Alaska, Northeast Pacific Ocean to understand how paleoclimates may have influenced diversity in this kelp. The study included wide geographic sampling over 2800 km and large sample sizes compared to previous studies of this kelp. Mitochondrial 5'-COI (664 bp), plastid rbcL-3' (740 bp) and 8 microsatellite markers in 16 populations resolved 5 well-defined lineages. COI-rbcL haplotypes were distributed chaotically among populations around the Gulf of Alaska. Principal Coordinates Analysis of microsatellite genotypes grouped plants largely by organellar lineage instead of geography, indicating reproductive isolation among lineages. However, microsatellite markers detected hybrids at 3 sites where lineages co-occurred. Local adaptation on various time scales may be responsible for some genetic differences between populations located along wave-energy and salinity gradients, but the chaotic pattern of variability over hundreds of kilometers is likely due to isolations in northern refugia during Pleistocene ice ages. The range of divergences between populations indicates that episodic glaciations led to the creation of new lineages, but population turnover (local extinctions and recolonizations) limited the formation of new species in the Northeastern Pacific Ocean.
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Affiliation(s)
- W Stewart Grant
- Genetics Laboratory, Alaska Department of Fish & Game, Anchorage, AK
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, AK
| | - Trevor T Bringloe
- School of BioSciences, University of Melbourne, Parkville Campus, Victoria, Australia
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40
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Algal origin of sponge sterane biomarkers negates the oldest evidence for animals in the rock record. Nat Ecol Evol 2020; 5:165-168. [PMID: 33230256 DOI: 10.1038/s41559-020-01334-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/23/2020] [Indexed: 12/18/2022]
Abstract
The earliest fossils of animal-like organisms occur in Ediacaran rocks that are approximately 571 million years old. Yet 24-isopropylcholestanes and other C30 fossil sterol molecules have been suggested to reflect an important ecological role of demosponges as the first abundant animals by the end of the Cryogenian period (>635 million years ago). Here, we demonstrate that C30 24-isopropylcholestane is not diagnostic for sponges and probably formed in Neoproterozoic sediments through the geological methylation of C29 sterols of chlorophyte algae, the dominant eukaryotes at that time. These findings reconcile biomarker evidence with the geological record and revert the oldest evidence for animals back into the latest Ediacaran.
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41
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Phylogeography of split kelp Hedophyllum nigripes: northern ice-age refugia and trans-Arctic dispersal. Polar Biol 2020. [DOI: 10.1007/s00300-020-02748-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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42
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Yanni D, Jacobeen S, Márquez-Zacarías P, Weitz JS, Ratcliff WC, Yunker PJ. Topological constraints in early multicellularity favor reproductive division of labor. eLife 2020; 9:e54348. [PMID: 32940598 PMCID: PMC7609046 DOI: 10.7554/elife.54348] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 09/17/2020] [Indexed: 12/23/2022] Open
Abstract
Reproductive division of labor (e.g. germ-soma specialization) is a hallmark of the evolution of multicellularity, signifying the emergence of a new type of individual and facilitating the evolution of increased organismal complexity. A large body of work from evolutionary biology, economics, and ecology has shown that specialization is beneficial when further division of labor produces an accelerating increase in absolute productivity (i.e. productivity is a convex function of specialization). Here we show that reproductive specialization is qualitatively different from classical models of resource sharing, and can evolve even when the benefits of specialization are saturating (i.e. productivity is a concave function of specialization). Through analytical theory and evolutionary individual-based simulations, we demonstrate that reproductive specialization is strongly favored in sparse networks of cellular interactions that reflect the morphology of early, simple multicellular organisms, highlighting the importance of restricted social interactions in the evolution of reproductive specialization.
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Affiliation(s)
- David Yanni
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Shane Jacobeen
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Pedro Márquez-Zacarías
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Joshua S Weitz
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Peter J Yunker
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
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Unique biodiversity in Arctic marine forests is shaped by diverse recolonization pathways and far northern glacial refugia. Proc Natl Acad Sci U S A 2020; 117:22590-22596. [PMID: 32843343 DOI: 10.1073/pnas.2002753117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Arctic is experiencing a rapid shift toward warmer regimes, calling for a need to understand levels of biodiversity and ecosystem responses to climate cycles. This study presents genetic data for 109 Arctic marine forest species (seaweeds), which revealed contiguous populations extending from the Bering Sea to the northwest Atlantic, with high levels of genetic diversity in the east Canadian Arctic. One-fifth of the species sampled appeared restricted to Arctic waters. Further supported by hindcasted species distributions during the Last Glacial Maximum, we hypothesize that Arctic coastal systems were recolonized from many geographically disparate refugia leading to enriched diversity levels in the east Canadian Arctic, with important contributions stemming from northerly refugia likely centered along southern Greenland. Our results suggest Arctic marine biomes persisted through cycles of glaciation, leading to unique assemblages in polar waters, rather than being entirely derived from southerly (temperate) areas following glaciation. As such, Arctic marine species are potentially born from selective pressures during Cenozoic global cooling and eventual ice conditions beginning in the Pleistocene. Arctic endemic diversity was likely additionally driven by repeated isolations into globally disparate refugia during glaciation. This study highlights the need to take stock of unique Arctic marine biodiversity. Amplification of warming and loss of perennial ice cover are set to dramatically alter available Arctic coastal habitat, with the potential loss of diversity and decline in ecosystem resilience.
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44
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Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 2020; 5:1026-1039. [PMID: 32451471 DOI: 10.1038/s41564-020-0720-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022]
Abstract
Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.
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Affiliation(s)
- Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany.
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45
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Yip ZT, Quek RZB, Huang D. Historical biogeography of the widespread macroalga Sargassum (Fucales, Phaeophyceae). JOURNAL OF PHYCOLOGY 2020; 56:300-309. [PMID: 31677168 PMCID: PMC7187439 DOI: 10.1111/jpy.12945] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 10/16/2019] [Indexed: 05/13/2023]
Abstract
Sargassum is a cosmopolitan brown algal genus spanning the three ocean basins of the Atlantic, Pacific and Indian Oceans, inhabiting temperate, subtropical and tropical habitats. Sargassum has been postulated to have originated in the Oligocene epoch approximately 30 mya according to a broad phylogenetic analysis of brown macroalgae, but its diversification to become one of the most widespread and speciose macroalgal genera remains unclear. Here, we present a Bayesian molecular clock study, which analyzed data from the order Fucales of the brown algal crown radiation (BACR) group to reconstruct a time-calibrated phylogeny of the Sargassum clade. Our phylogeny included a total of 120 taxa with 99 Sargassum species sampled for three molecular markers - ITS-2, cox3 and rbcLS - calibrated with an unambiguous Sargassaceae fossil from between the lower and middle Miocene. The analysis revealed a much later origin of Sargassum than expected at about 6.7 mya, with the genus diversifying since approximately 4.3 mya. Current geographic distributions of Sargassum species were then analyzed in conjunction with the time-calibrated phylogeny using the dispersal-extinction-cladogenesis (DEC) model to estimate ancestral ranges of clades in the genus. Results strongly support origination of Sargassum in the Central Indo-Pacific (CIP) region with subsequent independent dispersal events into other marine realms. The longer history of diversification in the ancestral CIP range could explain the much greater diversity there relative to other marine areas today. Analyses of these dynamic processes, when fine-tuned to a higher spatial resolution, enable the identification of evolutionary hotspots and provide insights into long-term dispersal patterns.
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Affiliation(s)
- Zhi Ting Yip
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
| | - Randolph Z. B. Quek
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
- Tropical Marine Science InstituteNational University of SingaporeSingapore City119227Singapore
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Choi JW, Graf L, Peters AF, Cock JM, Nishitsuji K, Arimoto A, Shoguchi E, Nagasato C, Choi CG, Yoon HS. Organelle inheritance and genome architecture variation in isogamous brown algae. Sci Rep 2020; 10:2048. [PMID: 32029782 PMCID: PMC7005149 DOI: 10.1038/s41598-020-58817-7] [Citation(s) in RCA: 10] [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: 07/23/2019] [Accepted: 12/26/2019] [Indexed: 11/08/2022] Open
Abstract
Among the brown algal lineages, Ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. In contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. It has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. In contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. To investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDNA) and two mitochondrial genomes (mtDNA) of isogamous species from the Ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDNAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDNAs of oogamous species showed no rearrangements. Our analysis permits the hypothesis that structural rearrangements in ptDNAs may be a consequence of the mode of inheritance.
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Affiliation(s)
- Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | | | - J Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Universités, UPMC, Station Biologique Roscoff, CS 90074, 29688, Roscoff, France
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Onomichi, Hiroshima, 722-0073, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University Muroran, 051-0013, Muroran, Hokkaido, Japan
| | - Chang Geun Choi
- Department of Ecological Engineering, Pukyong National University, Busan, 48513, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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47
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Rugiu L, Panova M, Pereyra RT, Jormalainen V. Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus. BMC Genomics 2020; 21:42. [PMID: 31931708 PMCID: PMC6958763 DOI: 10.1186/s12864-020-6470-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/08/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Rockweeds are among the most important foundation species of temperate rocky littoral shores. In the Baltic Sea, the rockweed Fucus vesiculosus is distributed along a decreasing salinity gradient from the North Atlantic entrance to the low-salinity regions in the north-eastern margins, thus, demonstrating a remarkable tolerance to hyposalinity. The underlying mechanisms for this tolerance are still poorly understood. Here, we exposed F. vesiculosus from two range-margin populations to the hyposaline (2.5 PSU - practical salinity unit) conditions that are projected to occur in the region by the end of this century as a result of climate change. We used transcriptome analysis (RNA-seq) to determine the gene expression patterns associated with hyposalinity acclimation, and examined the variation in these patterns between the sampled populations. RESULTS Hyposalinity induced different responses in the two populations: in one, only 26 genes were differentially expressed between salinity treatments, while the other population demonstrated up- or downregulation in 3072 genes. In the latter population, the projected future hyposalinity induced an acute response in terms of antioxidant production. Genes associated with membrane composition and structure were also heavily involved, with the upregulation of fatty acid and actin production, and the downregulation of ion channels and alginate pathways. Changes in gene expression patterns clearly indicated an inhibition of the photosynthetic machinery, with a consequent downregulation of carbohydrate production. Simultaneously, energy consumption increased, as revealed by the upregulation of genes associated with respiration and ATP synthesis. Overall, the genes that demonstrated the largest increase in expression were ribosomal proteins involved in translation pathways. The fixation rate of SNP:s was higher within genes responding to hyposalinity than elsewhere in the transcriptome. CONCLUSIONS The high fixation rate in the genes coding for salinity acclimation mechanisms implies strong selection for them. The among-population differentiation that we observed in the transcriptomic response to hyposalinity stress suggests that populations of F. vesiculosus may differ in their tolerance to future desalination, possibly as a result of local adaptation to salinity conditions within the Baltic Sea. These results emphasise the importance of considering interspecific genetic variation when evaluating the consequences of environmental change.
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Affiliation(s)
- Luca Rugiu
- Department of Marine Sciences –Tjärnö, University of Gothenburg, SE 452 96 Strömstad, Sweden
| | - Marina Panova
- Department of Marine Sciences –Tjärnö, University of Gothenburg, SE 452 96 Strömstad, Sweden
| | - Ricardo Tomás Pereyra
- Department of Marine Sciences –Tjärnö, University of Gothenburg, SE 452 96 Strömstad, Sweden
| | - Veijo Jormalainen
- Department of Biology, University of Turku, FIN-20014 Turku, Finland
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48
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Rabillé H, Torode TA, Tesson B, Le Bail A, Billoud B, Rolland E, Le Panse S, Jam M, Charrier B. Alginates along the filament of the brown alga Ectocarpus help cells cope with stress. Sci Rep 2019; 9:12956. [PMID: 31506545 PMCID: PMC6736953 DOI: 10.1038/s41598-019-49427-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/23/2019] [Indexed: 11/29/2022] Open
Abstract
Ectocarpus is a filamentous brown alga, which cell wall is composed mainly of alginates and fucans (80%), two non-crystalline polysaccharide classes. Alginates are linear chains of epimers of 1,4-linked uronic acids, β-D-mannuronic acid (M) and α-L-guluronic acid (G). Previous physico-chemical studies showed that G-rich alginate gels are stiffer than M-rich alginate gels when prepared in vitro with calcium. In order to assess the possible role of alginates in Ectocarpus, we first immunolocalised M-rich or G-rich alginates using specific monoclonal antibodies along the filament. As a second step, we calculated the tensile stress experienced by the cell wall along the filament, and varied it with hypertonic or hypotonic solutions. As a third step, we measured the stiffness of the cell along the filament, using cell deformation measurements and atomic force microscopy. Overlapping of the three sets of data allowed to show that alginates co-localise with the stiffest and most stressed areas of the filament, namely the dome of the apical cell and the shanks of the central round cells. In addition, no major distinction between M-rich and G-rich alginate spatial patterns could be observed. Altogether, these results support that both M-rich and G-rich alginates play similar roles in stiffening the cell wall where the tensile stress is high and exposes cells to bursting, and that these roles are independent from cell growth and differentiation.
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Affiliation(s)
- Hervé Rabillé
- CNRS, Sorbonne Université, Laboratoire de Biologie Intégrative des Modèles Marins LBI2M, Station Biologique, Roscoff, France
| | - Thomas A Torode
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, United Kingdom
| | - Benoit Tesson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Aude Le Bail
- CNRS, Sorbonne Université, Laboratoire de Biologie Intégrative des Modèles Marins LBI2M, Station Biologique, Roscoff, France
- Department of Cell Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Bernard Billoud
- CNRS, Sorbonne Université, Laboratoire de Biologie Intégrative des Modèles Marins LBI2M, Station Biologique, Roscoff, France
| | - Elodie Rolland
- CNRS, Sorbonne Université, Laboratoire de Biologie Intégrative des Modèles Marins LBI2M, Station Biologique, Roscoff, France
| | - Sophie Le Panse
- Platform Merimage, FR 2424, CNRS, Station Biologique, Roscoff, France
| | - Murielle Jam
- Marine Glycobiology team, UMR8227, CNRS-UPMC, Station Biologique, Roscoff, France
| | - Bénédicte Charrier
- CNRS, Sorbonne Université, Laboratoire de Biologie Intégrative des Modèles Marins LBI2M, Station Biologique, Roscoff, France.
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49
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Abstract
Algae are photosynthetic eukaryotes whose taxonomic breadth covers a range of life histories, degrees of cellular and developmental complexity, and diverse patterns of sexual reproduction. These patterns include haploid- and diploid-phase sex determination, isogamous mating systems, and dimorphic sexes. Despite the ubiquity of sexual reproduction in algae, their mating-type-determination and sex-determination mechanisms have been investigated in only a limited number of representatives. These include volvocine green algae, where sexual cycles and sex-determining mechanisms have shed light on the transition from mating types to sexes, and brown algae, which are a model for UV sex chromosome evolution in the context of a complex haplodiplontic life cycle. Recent advances in genomics have aided progress in understanding sexual cycles in less-studied taxa including ulvophyte, charophyte, and prasinophyte green algae, as well as in diatoms.
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Affiliation(s)
- James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
| | - Susana Coelho
- Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, CS 90074, F-29688 Roscoff, France;
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50
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Starko S, Soto Gomez M, Darby H, Demes KW, Kawai H, Yotsukura N, Lindstrom SC, Keeling PJ, Graham SW, Martone PT. A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem. Mol Phylogenet Evol 2019; 136:138-150. [PMID: 30980936 DOI: 10.1016/j.ympev.2019.04.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 12/24/2022]
Abstract
Reconstructing phylogenetic topologies and divergence times is essential for inferring the timing of radiations, the appearance of adaptations, and the historical biogeography of key lineages. In temperate marine ecosystems, kelps (Laminariales) drive productivity and form essential habitat but an incomplete understanding of their phylogeny has limited our ability to infer their evolutionary origins and the spatial and temporal patterns of their diversification. Here, we reconstruct the diversification of habitat-forming kelps using a global genus-level phylogeny inferred primarily from organellar genome datasets, and investigate the timing of kelp radiation. We resolve several important phylogenetic features, including relationships among the morphologically simple kelp families and the broader radiation of complex kelps, demonstrating that the initial radiation of the latter resulted from an increase in speciation rate around the Eocene-Oligocene boundary. This burst in speciation rate is consistent with a possible role of recent climatic cooling in triggering the kelp radiation and pre-dates the origin of benthic-foraging carnivores. Historical biogeographical reconstructions point to a northeast Pacific origin of complex kelps, with subsequent colonization of new habitats likely playing an important role in driving their ecological diversification. We infer that complex morphologies associated with modern kelp forests (e.g. branching, pneumatocysts) evolved several times over the past 15-20 MY, highlighting the importance of morphological convergence in establishing modern upright kelp forests. Our phylogenomic findings provide new insights into the geographical and ecological proliferation of kelps and provide a timeline along which feedbacks between kelps and their food-webs could have shaped the structure of temperate ecosystems.
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Affiliation(s)
- Samuel Starko
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield V0R 1B0, Canada; Hakai Institute, Heriot Bay, Quadra Island, Canada.
| | - Marybel Soto Gomez
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Hayley Darby
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Kyle W Demes
- Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Hiroshi Kawai
- Department of Biology, Kobe University, Rokkodaicho 657-8501, Japan
| | - Norishige Yotsukura
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo 060-0809, Japan
| | - Sandra C Lindstrom
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Department of Zoology, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada
| | - Patrick T Martone
- Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield V0R 1B0, Canada; Hakai Institute, Heriot Bay, Quadra Island, Canada
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