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Neiva J, Assis J, Coelho NC, Fernandes F, Pearson GA, Serrão EA. Genes Left Behind: Climate Change Threatens Cryptic Genetic Diversity in the Canopy-Forming Seaweed Bifurcaria bifurcata. PLoS One 2015; 10:e0131530. [PMID: 26177545 PMCID: PMC4503591 DOI: 10.1371/journal.pone.0131530] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 06/03/2015] [Indexed: 11/30/2022] Open
Abstract
The global redistribution of biodiversity will intensify in the coming decades of climate change, making projections of species range shifts and of associated genetic losses important components of conservation planning. Highly-structured marine species, notably brown seaweeds, often harbor unique genetic variation at warmer low-latitude rear edges and thus are of particular concern. Here, a combination of Ecological Niche Models (ENMs) and molecular data is used to forecast the potential near-future impacts of climate change for a warm-temperate, canopy forming seaweed, Bifurcaria bifurcata. ENMs for B. bifurcata were developed using marine and terrestrial climatic variables, and its range projected for 2040-50 and 2090-2100 under two greenhouse emission scenarios. Geographical patterns of genetic diversity were assessed by screening 18 populations spawning the entire distribution for two organelle genes and 6 microsatellite markers. The southern limit of B. bifurcata was predicted to shift northwards to central Morocco by the mid-century. By 2090-2100, depending on the emission scenario, it could either retreat further north to western Iberia or be relocated back to Western Sahara. At the opposing margin, B. bifurcata was predicted to expand its range to Scotland or even Norway. Microsatellite diversity and endemism were highest in Morocco, where a unique and very restricted lineage was also identified. Our results imply that B. bifurcata will maintain a relatively broad latitudinal distribution. Although its persistence is not threatened, the predicted extirpation of a unique southern lineage or even the entire Moroccan diversity hotspot will erase a rich evolutionary legacy and shrink global diversity to current (low) European levels. NW Africa and similarly understudied southern regions should receive added attention if expected range changes and diversity loss of warm-temperate species is not to occur unnoticed.
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Affiliation(s)
- João Neiva
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | - Jorge Assis
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | - Nelson C. Coelho
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | | | - Gareth A. Pearson
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
| | - Ester A. Serrão
- Centro de Ciências do Mar da Universidade do Algarve, Faro, Portugal
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102
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Bennett S, Wernberg T, de Bettignies T, Kendrick GA, Anderson RJ, Bolton JJ, Rodgers KL, Shears NT, Leclerc JC, Lévêque L, Davoult D, Christie HC. Canopy interactions and physical stress gradients in subtidal communities. Ecol Lett 2015; 18:677-86. [PMID: 25975532 DOI: 10.1111/ele.12446] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/15/2014] [Accepted: 04/07/2015] [Indexed: 11/28/2022]
Abstract
Species interactions are integral drivers of community structure and can change from competitive to facilitative with increasing environmental stress. In subtidal marine ecosystems, however, interactions along physical stress gradients have seldom been tested. We observed seaweed canopy interactions across depth and latitudinal gradients to test whether light and temperature stress structured interaction patterns. We also quantified interspecific and intraspecific interactions among nine subtidal canopy seaweed species across three continents to examine the general nature of interactions in subtidal systems under low consumer pressure. We reveal that positive and neutral interactions are widespread throughout global seaweed communities and the nature of interactions can change from competitive to facilitative with increasing light stress in shallow marine systems. These findings provide support for the stress gradient hypothesis within subtidal seaweed communities and highlight the importance of canopy interactions for the maintenance of subtidal marine habitats experiencing environmental stress.
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Affiliation(s)
- Scott Bennett
- School of Plant Biology & UWA Oceans Institute, University of Western Australia, 39 Fairway, Crawley, 6009, WA, Australia
| | - Thomas Wernberg
- School of Plant Biology & UWA Oceans Institute, University of Western Australia, 39 Fairway, Crawley, 6009, WA, Australia
| | - Thibaut de Bettignies
- School of Plant Biology & UWA Oceans Institute, University of Western Australia, 39 Fairway, Crawley, 6009, WA, Australia
| | - Gary A Kendrick
- School of Plant Biology & UWA Oceans Institute, University of Western Australia, 39 Fairway, Crawley, 6009, WA, Australia
| | - Robert J Anderson
- Seaweed Research Unit, Department of Agriculture, forestry and Fisheries, Pvt Bag X2, Roggebaai, 8012, South Africa
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Rondebosch, 7701, South Africa
| | - John J Bolton
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kirsten L Rodgers
- Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, PO Box 349, Warkworth, 0941, New Zealand
| | - Nick T Shears
- Leigh Marine Laboratory, Institute of Marine Science, University of Auckland, PO Box 349, Warkworth, 0941, New Zealand
| | - Jean-Charles Leclerc
- Sorbonne Universités, UPMC Univ Paris 6, Station Biologique, Place Georges Teissier, Roscoff, 29680, France
- CNRS, Station Biologique, Place Georges Teissier, UMR 7144, Roscoff, 29680, France
| | - Laurent Lévêque
- Sorbonne Universités, UPMC Univ Paris 6, Station Biologique, Place Georges Teissier, Roscoff, 29680, France
- CNRS, FR 2424, Station Biologique, Place Georges Teissier, Roscoff, 29680, France
| | - Dominique Davoult
- Sorbonne Universités, UPMC Univ Paris 6, Station Biologique, Place Georges Teissier, Roscoff, 29680, France
- CNRS, Station Biologique, Place Georges Teissier, UMR 7144, Roscoff, 29680, France
| | - Hartvig C Christie
- Section for Marine Biology, Norwegian Institute for Water Research, Oslo, Norway
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103
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Geoffroy A, Mauger S, De Jode A, Le Gall L, Destombe C. Molecular evidence for the coexistence of two sibling species in Pylaiella littoralis (Ectocarpales, Phaeophyceae) along the Brittany coast. JOURNAL OF PHYCOLOGY 2015; 51:480-489. [PMID: 26986664 DOI: 10.1111/jpy.12291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 01/19/2015] [Indexed: 06/05/2023]
Abstract
The great phenotypic variability and the lack of diagnostic characters in the genus Pylaiella render the systematic study of this genus problematic. In this study, we investigated the diversity of Pylaiella littoralis along the Brittany (France) coast using a DNA barcoding multilocus approach with mitochondrial (cox1, nad1, and atp9) and chloroplastic (rbcL and atpB) markers associated with a population genetics approach using 10 microsatellite markers. In addition, spatio-temporal sampling was conducted along the Brittany coast. We sampled 140 individuals from four sites located between Saint-Malo and Concarneau (380 km) from April to October. Mitochondrial sequence data revealed the occurrence of two sibling species, with a minimum of 2.4% divergence between them. Microsatellite genotypic data congruently revealed two well-supported clusters matching the two mitochondrial clades of Pylaiella. Although gene flow is limited between species, occurrence of genetic admixtures in some populations suggested that reproductive isolation is not complete. Our study highlighted the complementarity of barcoding and population genetics approaches to shed light on the evolutionary processes that lead to speciation.
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Affiliation(s)
- Alexandre Geoffroy
- Sorbonne Universités, UPMC Université Paris 06, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Roscoff, 29688, France
- CNRS, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Roscoff, 29688, France
| | - Stéphane Mauger
- Sorbonne Universités, UPMC Université Paris 06, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Roscoff, 29688, France
- CNRS, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Roscoff, 29688, France
| | - Aurélien De Jode
- Sorbonne Universités, UPMC Université Paris 06, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Roscoff, 29688, France
- CNRS, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Roscoff, 29688, France
| | - Line Le Gall
- Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-EPHE-MNHN-UPMC, Equipe Exploration, Espèces, Evolution, case postale No 39, 57 rue Cuvier, 75231, Cedex 05 Paris, France
| | - Christophe Destombe
- Sorbonne Universités, UPMC Université Paris 06, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Roscoff, 29688, France
- CNRS, UMI 3614 Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Roscoff, 29688, France
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104
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Cornwall CE, Revill AT, Hurd CL. High prevalence of diffusive uptake of CO2 by macroalgae in a temperate subtidal ecosystem. PHOTOSYNTHESIS RESEARCH 2015; 124:181-90. [PMID: 25739900 DOI: 10.1007/s11120-015-0114-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/25/2015] [Indexed: 05/19/2023]
Abstract
Productivity of most macroalgae is not currently considered limited by dissolved inorganic carbon (DIC), as the majority of species have CO2-concentrating mechanisms (CCM) allowing the active uptake of DIC. The alternative, diffusive uptake of CO2 (non-CCM), is considered rare (0-9% of all macroalgal cover in a given ecosystem), and identifying species without CCMs is important in understanding factors controlling inorganic carbon use by eukaryotic algae. CCM activity has higher energetic requirements than diffusive CO2 uptake, therefore when light is low, CCM activity is reduced in favour of diffusive CO2 uptake. We hypothesized that the proportional cover of macroalgae without CCMs (red and green macroalgae) would be low (<10%) across four sites in Tasmania, southern Australia at two depths (4-5 and 12-14 m); the proportion of species lacking CCMs would increase with decreasing depth; the δ(13)C values of macroalgae with CCMs would be more depleted with depth. We found the proportion of non-CCM species ranged from 0 to 90% and included species from all three macroalgal phyla: 81% of red (59 species), 14% of brown (three species) and 29% of green macroalgae (two species). The proportion of non-CCM species increased with depth at three of four sites. 35% of species tested had significantly depleted δ(13)C values at deeper depths. Non-CCM macroalgae are more abundant in some temperate reefs than previously thought. If ocean acidification benefits non-CCM species, the ramifications for subtidal macroalgal assemblages could be larger than previously considered.
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Affiliation(s)
- Christopher E Cornwall
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7005, Australia,
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105
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Ye N, Zhang X, Miao M, Fan X, Zheng Y, Xu D, Wang J, Zhou L, Wang D, Gao Y, Wang Y, Shi W, Ji P, Li D, Guan Z, Shao C, Zhuang Z, Gao Z, Qi J, Zhao F. Saccharina genomes provide novel insight into kelp biology. Nat Commun 2015; 6:6986. [PMID: 25908475 PMCID: PMC4421812 DOI: 10.1038/ncomms7986] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/20/2015] [Indexed: 01/28/2023] Open
Abstract
Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome of Saccharina japonica, one of the most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98.5% of the estimated genome, and 18,733 protein-coding genes are predicted and annotated. Gene families related to cell wall synthesis, halogen concentration, development and defence systems were expanded. Functional diversification of the mannuronan C-5-epimerase and haloperoxidase gene families provides insight into the evolutionary adaptation of polysaccharide biosynthesis and iodine antioxidation. Additional sequencing of seven cultivars and nine wild individuals reveal that the genetic diversity within wild populations is greater than among cultivars. All of the cultivars are descendants of a wild S. japonica accession showing limited admixture with S. longissima. This study represents an important advance toward improving yields and economic traits in Saccharina and provides an invaluable resource for plant genome studies.
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Affiliation(s)
- Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Miao Miao
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yi Zheng
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Zhou
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongsheng Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Yuan Gao
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Wenyu Shi
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peifeng Ji
- 1] Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China [2] College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biosystems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zheng Guan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhimeng Zhuang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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106
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Emergence of Ectocarpus as a Model System to Study the Evolution of Complex Multicellularity in the Brown Algae. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-94-017-9642-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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107
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Cock JM, Collén J. Independent Emergence of Complex Multicellularity in the Brown and Red Algae. EVOLUTIONARY TRANSITIONS TO MULTICELLULAR LIFE 2015. [DOI: 10.1007/978-94-017-9642-2_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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108
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Terauchi M, Nagasato C, Motomura T. Plasmodesmata of brown algae. JOURNAL OF PLANT RESEARCH 2015; 128:7-15. [PMID: 25516500 PMCID: PMC4375301 DOI: 10.1007/s10265-014-0677-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/14/2014] [Indexed: 05/29/2023]
Abstract
Plasmodesmata (PD) are intercellular connections in plants which play roles in various developmental processes. They are also found in brown algae, a group of eukaryotes possessing complex multicellularity, as well as green plants. Recently, we conducted an ultrastructural study of PD in several species of brown algae. PD in brown algae are commonly straight plasma membrane-lined channels with a diameter of 10-20 nm and they lack desmotubule in contrast to green plants. Moreover, branched PD could not be observed in brown algae. In the brown alga, Dictyota dichotoma, PD are produced during cytokinesis through the formation of their precursor structures (pre-plasmodesmata, PPD). Clustering of PD in a structure termed "pit field" was recognized in several species having a complex multicellular thallus structure but not in those having uniseriate filamentous or multiseriate one. The pit fields might control cell-to-cell communication and contribute to the establishment of the complex multicellular thallus. In this review, we discuss fundamental morphological aspects of brown algal PD and present questions that remain open.
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Affiliation(s)
- Makoto Terauchi
- />Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810 Japan
- />Research Center for Inland Seas, Kobe University, Kobe, 657-8501 Japan
| | - Chikako Nagasato
- />Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0003 Japan
| | - Taizo Motomura
- />Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0003 Japan
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109
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Valach M, Burger G, Gray MW, Lang BF. Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules. Nucleic Acids Res 2014; 42:13764-77. [PMID: 25429974 PMCID: PMC4267664 DOI: 10.1093/nar/gku1266] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/14/2014] [Accepted: 11/17/2014] [Indexed: 11/13/2022] Open
Abstract
5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator.
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MESH Headings
- Coccidia/genetics
- Databases, Nucleic Acid
- Genes, Mitochondrial
- Genes, rRNA
- Genome, Mitochondrial
- Genome, Plastid
- Nucleic Acid Conformation
- Phaeophyceae/genetics
- RNA/chemistry
- RNA/genetics
- RNA, Mitochondrial
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/classification
- RNA, Ribosomal, 5S/genetics
- Sequence Analysis, RNA
- Stramenopiles/genetics
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Affiliation(s)
- Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4B2, Canada
| | - B Franz Lang
- Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada
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110
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Vieira C, D'hondt S, De Clerck O, Payri CE. Toward an inordinate fondness for stars, beetles and Lobophora? Species diversity of the genus Lobophora (Dictyotales, Phaeophyceae) in New Caledonia. JOURNAL OF PHYCOLOGY 2014; 50:1101-1119. [PMID: 26988791 DOI: 10.1111/jpy.12243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/27/2014] [Indexed: 06/05/2023]
Abstract
Until the recent use of molecular markers, species diversity of Lobophora, an ecologically important brown algal genus with a worldwide distribution in temperate and tropical seas, has been critically underestimated. Using a DNA-based taxonomic approach, we re-examined diversity of the genus from New Caledonia in the Southwest Pacific Ocean. First, species were delineated using general mixed Yule coalescent-based and barcoding gap approaches applied to a mitochondrial cox3 data set. Results were subsequently confirmed using chloroplast psbA and rbcL data sets. Species delimitation analyses agreed well across markers and delimitation algorithms, with the barcoding gap approach being slightly more conservative. Analyses of the cox3 data set resulted in 31-39 molecular operational taxonomic units (MOTUs), four of which are previously described species (L. asiatica, L. crassa, L. nigrescens s.l., L. pachyventera). Of the remaining MOTUs for which we obtained a representative number of sequences and results are corroborated across analyses and genes, we described 10 species de novo: L. abaculusa, L. abscondita, L. densa, L. dimorpha, L. gibbera, L. hederacea, L. monticola, L. petila, L. rosacea, and L. undulata. Our study presents an excellent case of how a traditional morphology-based taxonomy fails to provide accurate estimates of algal diversity. Furthermore, the level of Lobophora diversity unveiled from a single locality in the Pacific Ocean raises important questions with respect to the global diversity of the genus, the distributions and range sizes of the individual species, as well as the mechanisms facilitating coexistence.
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Affiliation(s)
- Christophe Vieira
- CoRéUs, LabEx-CORAIL, U227 "Biocomplexité des écosystèmes coralliens", Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, 75252, Paris Cedex 05, France
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Sofie D'hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Claude E Payri
- CoRéUs, LabEx-CORAIL, U227 "Biocomplexité des écosystèmes coralliens", Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France
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111
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Deniaud-Bouët E, Kervarec N, Michel G, Tonon T, Kloareg B, Hervé C. Chemical and enzymatic fractionation of cell walls from Fucales: insights into the structure of the extracellular matrix of brown algae. ANNALS OF BOTANY 2014; 114:1203-16. [PMID: 24875633 PMCID: PMC4195554 DOI: 10.1093/aob/mcu096] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 04/09/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Brown algae are photosynthetic multicellular marine organisms evolutionarily distant from land plants, with a distinctive cell wall. They feature carbohydrates shared with plants (cellulose), animals (fucose-containing sulfated polysaccharides, FCSPs) or bacteria (alginates). How these components are organized into a three-dimensional extracellular matrix (ECM) still remains unclear. Recent molecular analysis of the corresponding biosynthetic routes points toward a complex evolutionary history that shaped the ECM structure in brown algae. METHODS Exhaustive sequential extractions and composition analyses of cell wall material from various brown algae of the order Fucales were performed. Dedicated enzymatic degradations were used to release and identify cell wall partners. This approach was complemented by systematic chromatographic analysis to study polymer interlinks further. An additional structural assessment of the sulfated fucan extracted from Himanthalia elongata was made. KEY RESULTS The data indicate that FCSPs are tightly associated with proteins and cellulose within the walls. Alginates are associated with most phenolic compounds. The sulfated fucans from H. elongata were shown to have a regular α-(1→3) backbone structure, while an alternating α-(1→3), (1→4) structure has been described in some brown algae from the order Fucales. CONCLUSIONS The data provide a global snapshot of the cell wall architecture in brown algae, and contribute to the understanding of the structure-function relationships of the main cell wall components. Enzymatic cross-linking of alginates by phenols may regulate the strengthening of the wall, and sulfated polysaccharides may play a key role in the adaptation to osmotic stress. The emergence and evolution of ECM components is further discussed in relation to the evolution of multicellularity in brown algae.
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Affiliation(s)
- Estelle Deniaud-Bouët
- Sorbonne Universités, UPMC Université Paris 06, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Nelly Kervarec
- Service RMN-RPE, UFR Sciences et Techniques, Université de Bretagne Occidentale (UBO), Avenue Le Gorgeu, 29200 Brest, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Université Paris 06, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Thierry Tonon
- Sorbonne Universités, UPMC Université Paris 06, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Bernard Kloareg
- Sorbonne Universités, UPMC Université Paris 06, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Cécile Hervé
- Sorbonne Universités, UPMC Université Paris 06, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
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112
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Ahmed S, Cock JM, Pessia E, Luthringer R, Cormier A, Robuchon M, Sterck L, Peters AF, Dittami SM, Corre E, Valero M, Aury JM, Roze D, Van de Peer Y, Bothwell J, Marais GAB, Coelho SM. A haploid system of sex determination in the brown alga Ectocarpus sp. Curr Biol 2014; 24:1945-57. [PMID: 25176635 DOI: 10.1016/j.cub.2014.07.042] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 02/11/2014] [Accepted: 07/15/2014] [Indexed: 11/15/2022]
Abstract
BACKGROUND A common feature of most genetic sex-determination systems studied so far is that sex is determined by nonrecombining genomic regions, which can be of various sizes depending on the species. These regions have evolved independently and repeatedly across diverse groups. A number of such sex-determining regions (SDRs) have been studied in animals, plants, and fungi, but very little is known about the evolution of sexes in other eukaryotic lineages. RESULTS We report here the sequencing and genomic analysis of the SDR of Ectocarpus, a brown alga that has been evolving independently from plants, animals, and fungi for over one giga-annum. In Ectocarpus, sex is expressed during the haploid phase of the life cycle, and both the female (U) and the male (V) sex chromosomes contain nonrecombining regions. The U and V of this species have been diverging for more than 70 mega-annum, yet gene degeneration has been modest, and the SDR is relatively small, with no evidence for evolutionary strata. These features may be explained by the occurrence of strong purifying selection during the haploid phase of the life cycle and the low level of sexual dimorphism. V is dominant over U, suggesting that femaleness may be the default state, adopted when the male haplotype is absent. CONCLUSIONS The Ectocarpus UV system has clearly had a distinct evolutionary trajectory not only to the well-studied XY and ZW systems but also to the UV systems described so far. Nonetheless, some striking similarities exist, indicating remarkable universality of the underlying processes shaping sex chromosome evolution across distant lineages.
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Affiliation(s)
- Sophia Ahmed
- Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France; Medical Biology Centre, Queens University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - J Mark Cock
- Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Eugenie Pessia
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, Centre National de la Recherche Scientifique, Université Lyon 1, 69622 Villeurbanne, France
| | - Remy Luthringer
- Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Alexandre Cormier
- Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Marine Robuchon
- Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France; Evolutionary Biology and Ecology of Algae, CNRS UMI 3604, Sorbonne Université, UPMC, PUCCh, UACH, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Lieven Sterck
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052 Gent, Belgium
| | | | - Simon M Dittami
- Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Erwan Corre
- ABiMS Platform, FR2424, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS UMI 3604, Sorbonne Université, UPMC, PUCCh, UACH, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, 91000 Evry, France
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS UMI 3604, Sorbonne Université, UPMC, PUCCh, UACH, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Yves Van de Peer
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052 Gent, Belgium; Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - John Bothwell
- Medical Biology Centre, Queens University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, Centre National de la Recherche Scientifique, Université Lyon 1, 69622 Villeurbanne, France
| | - Susana M Coelho
- Integrative Biology of Marine Models, CNRS UMR 8227, Sorbonne Universités, UPMC Université Paris 6, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
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113
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Fu G, Nagasato C, Oka S, Cock JM, Motomura T. Proteomics analysis of heterogeneous flagella in brown algae (stramenopiles). Protist 2014; 165:662-75. [PMID: 25150613 DOI: 10.1016/j.protis.2014.07.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 10/25/2022]
Abstract
Flagella are conserved organelles among eukaryotes and they are composed of many proteins, which are necessary for flagellar assembly, maintenance and function. Stramenopiles, which include brown algae, diatoms and oomycetes, possess two laterally inserted flagella. The anterior flagellum (AF) extends forward and bears tripartite mastigonemes, whilst the smooth posterior flagellum (PF) often has a paraflagellar body structure. These heterogeneous flagella have served as crucial structures in algal studies especially from a viewpoint of phylogeny. However, the protein compositions of the flagella are still largely unknown. Here we report a LC-MS/MS based proteomics analysis of brown algal flagella. In total, 495 flagellar proteins were identified. Functional annotation of the proteome data revealed that brown algal flagellar proteins were associated with cell motility, signal transduction and various metabolic activities. We separately isolated AF and PF and analyzed their protein compositions. This analysis led to the identification of several AF- and PF-specific proteins. Among the PF-specific proteins, we found a candidate novel blue light receptor protein involved in phototaxis, and named it HELMCHROME because of the steering function of PF. Immunological analysis revealed that this protein was localized along the whole length of the PF and concentrated in the paraflagellar body.
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Affiliation(s)
- Gang Fu
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Hokkaido, Japan
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Hokkaido, Japan
| | - Seiko Oka
- Instrumental Analysis Division, Equipment Management Center, Creative Research Institution, Hokkaido University, Sapporo 001-0021, Hokkaido, Japan
| | - J Mark Cock
- University Pierre et Marie Curie and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, 29682 Roscoff Cedex, France
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Hokkaido, Japan.
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114
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Dittami SM, Barbeyron T, Boyen C, Cambefort J, Collet G, Delage L, Gobet A, Groisillier A, Leblanc C, Michel G, Scornet D, Siegel A, Tapia JE, Tonon T. Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae. Front Genet 2014; 5:241. [PMID: 25120558 PMCID: PMC4110880 DOI: 10.3389/fgene.2014.00241] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The “Ca. P. ectocarpi” genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, “Ca. P. ectocarpi” has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus “Phaeomarinobacter” may comprise several species, which may colonize different niches.
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Affiliation(s)
- Simon M Dittami
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Jeanne Cambefort
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Guillaume Collet
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Ludovic Delage
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Agnès Groisillier
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Leblanc
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Delphine Scornet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Anne Siegel
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Javier E Tapia
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Thierry Tonon
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
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115
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Kohli BA, Speer KA, Kilpatrick CW, Batsaikhan N, Damdinbazar D, Cook JA. Multilocus systematics and non-punctuated evolution of Holarctic Myodini (Rodentia: Arvicolinae). Mol Phylogenet Evol 2014; 76:18-29. [PMID: 24594062 DOI: 10.1016/j.ympev.2014.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 02/06/2014] [Accepted: 02/18/2014] [Indexed: 11/17/2022]
Abstract
The tribe Myodini consists of five genera of forest and alpine voles (Alticola, Caryomys, Eothenomys, Hyperacrius and Myodes) distributed throughout the Holarctic. Because mitochondrial evidence has revealed paraphyly and polyphyly among genera, we apply the first multilocus tests to clarify taxonomy and phylogenetic relationships. Our analyses of 28 of 36 species within Myodini, including three not previously sequenced (A. montosa, A. albicaudus, and H. fertilis), identify four distinct clades and provide the first molecular evidence that Hyperacrius may not belong in Myodini. Myodes is paraphyletic, while polyphyly of Alticola reflects apparent ancient mitochondrial introgression. Diversification in this tribe was hypothesized to be tightly linked to Late Cenozoic climatic events, however, lineage through time analysis indicates diversification over the last 4 My was gradual and not strongly punctuated.
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Affiliation(s)
- Brooks A Kohli
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA.
| | - Kelly A Speer
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA
| | | | - Nyamsuren Batsaikhan
- Department of Zoology, Faculty of Biology, National University of Mongolia, Ulaan Bataar, Mongolia
| | - Darmaa Damdinbazar
- Department of Zoology, Faculty of Biology, National University of Mongolia, Ulaan Bataar, Mongolia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA
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116
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Cock JM, Godfroy O, Macaisne N, Peters AF, Coelho SM. Evolution and regulation of complex life cycles: a brown algal perspective. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:1-6. [PMID: 24507487 DOI: 10.1016/j.pbi.2013.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 09/22/2013] [Indexed: 05/24/2023]
Abstract
The life cycle of an organism is one of its fundamental features, influencing many aspects of its biology. The brown algae exhibit a diverse range of life cycles indicating that transitions between life cycle types may have been key adaptive events in the evolution of this group. Life cycle mutants, identified in the model organism Ectocarpus, are providing information about how life cycle progression is regulated at the molecular level in brown algae. We explore some of the implications of the phenotypes of the life cycle mutants described to date and draw comparisons with recent insights into life cycle regulation in the green lineage. Given the importance of coordinating growth and development with life cycle progression, we suggest that the co-option of ancient life cycle regulators to control key developmental events may be a common feature in diverse groups of multicellular eukaryotes.
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Affiliation(s)
- J Mark Cock
- UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France; CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France.
| | - Olivier Godfroy
- UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France; CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
| | - Nicolas Macaisne
- UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France; CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
| | | | - Susana M Coelho
- UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France; CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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117
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Yang EC, Peters AF, Kawai H, Stern R, Hanyuda T, Bárbara I, Müller DG, Strittmatter M, van Reine WFP, Küpper FC. Ligulate Desmarestia (Desmarestiales, Phaeophyceae) revisited: D. japonica sp. nov. and D. dudresnayi differ from D. ligulata. JOURNAL OF PHYCOLOGY 2014; 50:149-166. [PMID: 26988016 DOI: 10.1111/jpy.12148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 09/11/2013] [Indexed: 06/05/2023]
Abstract
The phylogeny of ligulate and sulfuric-acid containing species of Desmarestia, occurring worldwide from polar to temperate regions, was revised using a multigenic and polyphasic approach. Sequence data, gametophyte characteristics, and sporophyte morphology support reducing a total of 16 taxa to four different species. (1) D. herbacea, containing broad-bladed and highly branched forms, has dioecious gametophytes. The three other species have monoecious gametophytes: (2) D. ligulata which is profusely branched and, except for one subspecies, narrow-bladed, (3) Japanese ligulate Desmarestia, here described as D. japonica sp. nov., which is morphologically similar to D. ligulata but genetically distant from all other ligulate taxa. This species may have conserved the morphology of original ligulate Desmarestia. (4) D. dudresnayi, including unbranched or little branched broad-bladed taxa. A figure of the holotype of D. dudresnayi, which was lost for decades, was relocated. The taxonomy is complemented by a comparison of internal transcribed spacer and cytochrome c oxidase subunit I (cox1) as potential barcode loci, with cox1 offering good resolution, reflecting species delimitations within the genus Desmarestia.
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Affiliation(s)
- Eun Chan Yang
- Culture Collection of Algae and Protozoa (CCAP), The Scottish Association for Marine Science Dunstaffnage Marine Laboratory, Oban, Argyll, Scotland, PA37 1QA, UK
- Marine Ecosystem Research Division, Korea Institute of Ocean Science & Technology, 787 Haeanro, Ansan, 426-744, Korea
| | - Akira F Peters
- Bezhin Rosko, 40 rue des pêcheurs, 29250, Santec, Brittany, France
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai, Nadaku, Kobe, 657-8501, Japan
| | - Rowena Stern
- SAHFOS, The Laboratory, Citadel Hill, The Hoe, Plymouth, PL1 2PB, UK
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Rokkodai, Nadaku, Kobe, 657-8501, Japan
| | - Ignacio Bárbara
- Coastal Biology Research Group, Facultad de Ciencias, Universidad de A Coruña, Campus de la Zapateira, A Coruña, 15071, Spain
| | | | - Martina Strittmatter
- Culture Collection of Algae and Protozoa (CCAP), The Scottish Association for Marine Science Dunstaffnage Marine Laboratory, Oban, Argyll, Scotland, PA37 1QA, UK
| | - Willem F Prud'Homme van Reine
- Netherlands Centre for Biodiversity Naturalis, Leiden University (section NHN), P.O. Box 9514, RA Leiden, 2300, The Netherlands
| | - Frithjof C Küpper
- Culture Collection of Algae and Protozoa (CCAP), The Scottish Association for Marine Science Dunstaffnage Marine Laboratory, Oban, Argyll, Scotland, PA37 1QA, UK
- Oceanlab, University of Aberdeen, Main Street, Newburgh, Scotland, AB41 6AA, UK
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118
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Groisillier A, Shao Z, Michel G, Goulitquer S, Bonin P, Krahulec S, Nidetzky B, Duan D, Boyen C, Tonon T. Mannitol metabolism in brown algae involves a new phosphatase family. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:559-70. [PMID: 24323504 DOI: 10.1093/jxb/ert405] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Brown algae belong to a phylogenetic lineage distantly related to green plants and animals, and are found predominantly in the intertidal zone, a harsh and frequently changing environment. Because of their unique evolutionary history and of their habitat, brown algae feature several peculiarities in their metabolism. One of these is the mannitol cycle, which plays a central role in their physiology, as mannitol acts as carbon storage, osmoprotectant, and antioxidant. This polyol is derived directly from the photoassimilate fructose-6-phosphate via the action of a mannitol-1-phosphate dehydrogenase and a mannitol-1-phosphatase (M1Pase). Genome analysis of the brown algal model Ectocarpus siliculosus allowed identification of genes potentially involved in the mannitol cycle. Among these, two genes coding for haloacid dehalogenase (HAD)-like enzymes were suggested to correspond to M1Pase activity, and thus were named EsM1Pase1 and EsM1Pase2, respectively. To test this hypothesis, both genes were expressed in Escherichia coli. Recombinant EsM1Pase2 was shown to hydrolyse the phosphate group from mannitol-1-phosphate to produce mannitol but was not active on the hexose monophosphates tested. Gene expression analysis showed that transcription of both E. siliculosus genes was under the influence of the diurnal cycle. Sequence analysis and three-dimensional homology modelling indicated that EsM1Pases, and their orthologues in Prasinophytes, should be seen as founding members of a new family of phosphatase with original substrate specificity within the HAD superfamily of proteins. This is the first report describing the characterization of a gene encoding M1Pase activity in photosynthetic organisms.
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Affiliation(s)
- Agnès Groisillier
- UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
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119
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Stevens K, Weynberg K, Bellas C, Brown S, Brownlee C, Brown MT, Schroeder DC. A novel evolutionary strategy revealed in the phaeoviruses. PLoS One 2014; 9:e86040. [PMID: 24465858 PMCID: PMC3897601 DOI: 10.1371/journal.pone.0086040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/04/2013] [Indexed: 11/18/2022] Open
Abstract
Phaeoviruses infect the brown algae, which are major contributors to primary production of coastal waters and estuaries. They exploit a Persistent evolutionary strategy akin to a K- selected life strategy via genome integration and are the only known representatives to do so within the giant algal viruses that are typified by r- selected Acute lytic viruses. In screening the genomes of five species within the filamentous brown algal lineage, here we show an unprecedented diversity of viral gene sequence variants especially amongst the smaller phaeoviral genomes. Moreover, one variant shares features from both the two major sub-groups within the phaeoviruses. These phaeoviruses have exploited the reduction of their giant dsDNA genomes and accompanying loss of DNA proofreading capability, typical of an Acute life strategist, but uniquely retain a Persistent life strategy.
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Affiliation(s)
- Kim Stevens
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Karen Weynberg
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Christopher Bellas
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Sonja Brown
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Colin Brownlee
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Murray T. Brown
- School of Marine Science and Engineering, University of Plymouth, Plymouth, Devon, United Kingdom
| | - Declan C. Schroeder
- Cell and Molecular Department, Marine Biological Association, Plymouth, Devon, United Kingdom
- * E-mail:
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120
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Li TY, Qu JQ, Feng YJ, Liu C, Chi S, Liu T. Complete mitochondrial genome of Undaria pinnatifida (Alariaceae, Laminariales, Phaeophyceae). MITOCHONDRIAL DNA 2014; 26:953-4. [PMID: 24409911 DOI: 10.3109/19401736.2013.865172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Undaria pinnatifida is one of the most important economic marine algae and key components of coastal ecosystems. Undaria pinnatifida owns a typical heteromorphic, diplohaplontic life cycle. We present the complete sequence of mitochondrial genome of U. pinnatifida, focusing on genome organization and phylogenetic relationship between different brown algae lineages. The size of U. pinnatifida mitochondrial DNA is 37,402 bp, including 3 rRNAs, 25 tRNAs, 35 proteins, as well as 3 ORFs. No intron is found and most genes are encoded on the H-strand. The phylogenetic trees (BI) constructed on 35 protein-coding genes from 17 species proved that Saccharina has a closer relationship with Laminaria than that with Undaria. The results supported the conclusion that Alariaceae is sister genus to the Laminariaceae. Above researches will facilitate the understanding of evolutionary relationship within brown algae.
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Affiliation(s)
- Tian-Yong Li
- a College of Marine Life Sciences, Ocean University of China , Qingdao , Shandong , People's Republic of China
| | - Jie-Qiong Qu
- a College of Marine Life Sciences, Ocean University of China , Qingdao , Shandong , People's Republic of China
| | - Yan-Jing Feng
- a College of Marine Life Sciences, Ocean University of China , Qingdao , Shandong , People's Republic of China
| | - Cui Liu
- a College of Marine Life Sciences, Ocean University of China , Qingdao , Shandong , People's Republic of China
| | - Shan Chi
- a College of Marine Life Sciences, Ocean University of China , Qingdao , Shandong , People's Republic of China
| | - Tao Liu
- a College of Marine Life Sciences, Ocean University of China , Qingdao , Shandong , People's Republic of China
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121
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Massoni J, Forest F, Sauquet H. Increased sampling of both genes and taxa improves resolution of phylogenetic relationships within Magnoliidae, a large and early-diverging clade of angiosperms. Mol Phylogenet Evol 2014; 70:84-93. [DOI: 10.1016/j.ympev.2013.09.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 08/30/2013] [Accepted: 09/11/2013] [Indexed: 11/25/2022]
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Lipinska AP, D’hondt S, Van Damme EJM, De Clerck O. Uncovering the genetic basis for early isogamete differentiation: a case study of Ectocarpus siliculosus. BMC Genomics 2013; 14:909. [PMID: 24359479 PMCID: PMC3879662 DOI: 10.1186/1471-2164-14-909] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 12/17/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The phenomenon of sexual reproduction characterizes nearly all eukaryotes, with anisogamy being the most prevalent form of gamete discrimination. Since dimorphic gametes most likely descend from equal-sized specialized germ cells, identifying the genetic bases of the early functional diversification in isogametes can provide better understanding of the evolution of sexual dimorphism. However, despite the potential importance to the evolutionary biology field, no comprehensive survey of the transcriptome profiling in isomorphic gametes has been reported hitherto. RESULTS Gamete differentiation on the genomic level was investigated using Ectocarpus siliculosus, a model organism for brown algal lineage which displays an isogamous sexual reproduction cycle. Transcriptome libraries of male and female gametes were generated using Next Generation Sequencing technology (SOLiD) and analyzed to identify differentially regulated genes and pathways with potential roles in fertilization and gamete specialization. Gamete transcriptomes showed a high level of complexity with a large portion of gender specific gene expression. Our results indicate that over 4,000 of expressed genes are differentially regulated between male and female, including sequences related to cell movement, carbohydrate and lipid metabolism, signaling, transport and RNA processing. CONCLUSIONS This first comprehensive transcriptomic study of protist isogametes describes considerable adaptation to distinct sexual roles, suggesting that functional anisogamy precedes morphological differentiation. Several sex-biased genes and pathways with a putative role in reproduction were identified, providing the basis for more detailed investigations of the mechanisms underlying evolution of mating types and sexual dimorphism.
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Affiliation(s)
- Agnieszka P Lipinska
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
| | - Sofie D’hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
| | - Els JM Van Damme
- Department of Molecular Biotechnology, Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
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123
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Molecular phylogeny and barcoding of Caulerpa (Bryopsidales) based on the tufA, rbcL, 18S rDNA and ITS rDNA genes. PLoS One 2013; 8:e82438. [PMID: 24340028 PMCID: PMC3855484 DOI: 10.1371/journal.pone.0082438] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2013] [Indexed: 11/19/2022] Open
Abstract
The biodiversity assessment of different taxa of the genus Caulerpa is of interest from the context of morphological plasticity, invasive potential of some species and biotechnological and pharmacological applications. The present study investigated the identification and molecular phylogeny of different species of Caulerpa occurring along the Indian coast inferred from tufA, rbcL, 18S rDNA and ITS rDNA nucleotide sequences. Molecular data confirmed the identification of 10 distinct Caulerpa species: C. veravalensis, C. verticillata, C. racemosa, C. microphysa, C. taxifolia, C. sertularioides, C. scalpelliformis, C. serrulata, C. peltata and C. mexicana. All datasets significantly supported the sister relationship between C. veravalensis and C. racemosa var. cylindracea. It was also concluded from the results that the specimen identified previously as C. microphysa and C. lentillifera could not be considered as separate species. The molecular data revealed the presence of multiple lineages for C. racemosa which can be resolved into separate species. All four markers were used to ascertain their utility for DNA barcoding. The tufA gene proved a better marker with monophyletic association as the main criteria for identification at the species level. The results also support the use of 18S rDNA insertion sequences to delineate the Caulerpa species through character-based barcoding. The ITS rDNA (5.8S-ITS2) phylogenetic analysis also served as another supporting tool. Further, more sequences from additional Caulerpa specimens will need to be analysed in order to support the role of these two markers (ITS rDNA and 18S insertion sequence) in identification of Caulerpa species. The present study revealed the phylogeny of Caulerpa as complete as possible using the currently available data, which is the first comprehensive report illustrating the molecular phylogeny and barcoding of the genus Caulerpa from Indian waters.
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124
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Fraser CI, Zuccarello GC, Spencer HG, Salvatore LC, Garcia GR, Waters JM. Genetic affinities between trans-oceanic populations of non-buoyant macroalgae in the high latitudes of the Southern Hemisphere. PLoS One 2013; 8:e69138. [PMID: 23894421 PMCID: PMC3718832 DOI: 10.1371/journal.pone.0069138] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022] Open
Abstract
Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships – even shared haplotypes – were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.
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Affiliation(s)
- Ceridwen I Fraser
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand.
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125
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Kumari P, Bijo AJ, Mantri VA, Reddy CRK, Jha B. Fatty acid profiling of tropical marine macroalgae: an analysis from chemotaxonomic and nutritional perspectives. PHYTOCHEMISTRY 2013; 86:44-56. [PMID: 23168246 DOI: 10.1016/j.phytochem.2012.10.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 10/18/2012] [Accepted: 10/22/2012] [Indexed: 05/24/2023]
Abstract
The lipid and fatty acid (FA) compositions for 100 marine macroalgae were determined and discussed from the context of chemotaxonomic and nutritional perspectives. In general, the lipid contents in macroalgae were low (2.3-20 mg/g fr. wt.) but with substantially high amounts of nutritionally important polyunsaturated fatty acids (PUFAs) such as LA, ALA, STA, AA, EPA and DHA, that ranged from 10% to 70% of TFAs. More than 90% of the species showed nutritionally beneficial n6/n3 ratio (0.1:1-3.6:1) (p≤0.001). A closer look at the FA data revealed characteristic chemotaxonomic features with C18 PUFAs (LA, ALA and STA) being higher in Chlorophyta, C20 PUFAs (AA and EPA) in Rhodophyta while Phaeophyta depicted evenly distribution of C18 and C20 PUFAs. The ability of macroalgae to produce long-chain PUFAs could be attributed to the coupling of chloroplastic FA desaturase enzyme system from a photosynthetic endosymbiont to the FA desaturase/elongase enzyme system of a non-photosynthetic eukaryotic protist host. Further, the principal component analysis segregated the three macroalgal groups with a marked distinction of different genera, families and orders, Hierarchical cluster analyses substantiated the phylogenetic relationships of all orders investigated except for those red algal taxa belonging to Gigartinales, Ceramiales, Halymeniales and Rhodymeniales for which increased sampling effort is required to infer a conclusion. Also, the groups deduced from FA compositions were congruent with the clades inferred from nuclear and plastid genome sequences. This study further indicates that FA signatures could be employed as a valid chemotaxonomic tool to differentiate macroalgae at higher taxonomic levels such as family and orders.
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Affiliation(s)
- Puja Kumari
- Discipline of Marine Biotechnology and Ecology, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat 364002, India
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126
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Silberfeld T, Bittner L, Fernández-García C, Cruaud C, Rousseau F, de Reviers B, Leliaert F, Payri CE, De Clerck O. Species Diversity, Phylogeny and Large Scale Biogeographic Patterns of the Genus Padina (Phaeophyceae, Dictyotales). JOURNAL OF PHYCOLOGY 2013; 49:130-142. [PMID: 27008395 DOI: 10.1111/jpy.12027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 07/10/2012] [Indexed: 06/05/2023]
Abstract
The brown algal genus Padina (Dictyotales, Phaeophyceae) is distributed worldwide in tropical and temperate seas. Global species diversity and distribution ranges, however, remain largely unknown. Species-level diversity was reassessed using DNA-based, algorithmic species delineation techniques based on cox3 and rbcL sequence data from 221 specimens collected worldwide. This resulted in estimates ranging from 39 to 61 putative species (ESUs), depending on the technique as well as the locus. We discuss the merits, potential pitfalls, and evolutionary and biogeographic significance of algorithmic species delineation. We unveil patterns whereby ESUs are in all but one case restricted to either the Atlantic or Indo-Pacific Ocean. Within ocean basins we find evidence for the vast majority of ESUs to be confined to a single marine realm. Exceptions, whereby ESUs span up to three realms, are located in the Indo-Pacific Ocean. Patterns of range-restricted species likely arise by repeated founder events and subsequent peripatric speciation, hypothesized to dominate speciation mechanisms for coastal marine organisms in the Indo-Pacific. Using a three-gene (cox3, psaA and rbcL), relaxed molecular clock phylogenetic analysis we estimated divergence times, providing a historical framework to interpret biogeographic patterns.
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Affiliation(s)
- Thomas Silberfeld
- UMR 7138, UPMC, MNHN, CNRS, IRD: Systématique, adaptation, évolution, Département Systématique & évolution, Muséum National d'Histoire Naturelle, 57 rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - Lucie Bittner
- UMR 7138, UPMC, MNHN, CNRS, IRD: Systématique, adaptation, évolution, Département Systématique & évolution, Muséum National d'Histoire Naturelle, 57 rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - Cindy Fernández-García
- Programa en Botánica Marina, Posgrado en Ciencias Marinas y Costeras, UABCS, La Paz, México
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, 2060, Costa Rica
| | - Corinne Cruaud
- Genoscope, Centre national de séquençage, 2 rue Gaston Crémieux, CP 5706, 91057, Évry Cedex, France
| | - Florence Rousseau
- UMR 7138, UPMC, MNHN, CNRS, IRD: Systématique, adaptation, évolution, Département Systématique & évolution, Muséum National d'Histoire Naturelle, 57 rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - Bruno de Reviers
- UMR 7138, UPMC, MNHN, CNRS, IRD: Systématique, adaptation, évolution, Département Systématique & évolution, Muséum National d'Histoire Naturelle, 57 rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - Frederik Leliaert
- Phycology Research Group, Ghent University, Krijgslaan 281, Building S8, 9000, Ghent, Belgium
| | - Claude E Payri
- U227, Biocomplexité des écosystèmes coralliens de l'Indo-Pacifique, Institut de Recherche pour le Développement, BP A5, 98848, Nouméa Cedex, New Caledonia
| | - Olivier De Clerck
- Phycology Research Group, Ghent University, Krijgslaan 281, Building S8, 9000, Ghent, Belgium
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127
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Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH, McManus H, Mitchell EAD, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Shadwick L, Schoch CL, Smirnov A, Spiegel FW. The revised classification of eukaryotes. J Eukaryot Microbiol 2013; 59:429-93. [PMID: 23020233 DOI: 10.1111/j.1550-7408.2012.00644.x] [Citation(s) in RCA: 908] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.
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Affiliation(s)
- Sina M Adl
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
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128
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Abstract
Brown algae are an extremely interesting, but surprisingly poorly explored, group of organisms. They are one of only five eukaryotic lineages to have independently evolved complex multicellularity, which they express through a wide variety of morphologies ranging from uniseriate branched filaments to complex parenchymatous thalli with multiple cell types. Despite their very distinct evolutionary history, brown algae and land plants share a striking amount of developmental features. This has led to an interest in several aspects of brown algal development, including embryogenesis, polarity, cell cycle, asymmetric cell division and a putative role for plant hormone signalling. This review describes how investigations using brown algal models have helped to increase our understanding of the processes controlling early embryo development, in particular polarization, axis formation and asymmetric cell division. Additionally, the diversity of life cycles in the brown lineage and the emergence of Ectocarpus as a powerful model organism, are affording interesting insights on the molecular mechanisms underlying haploid-diploid life cycles. The use of these and other emerging brown algal models will undoubtedly add to our knowledge on the mechanisms that regulate development in multicellular photosynthetic organisms.
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Affiliation(s)
- Kenny A Bogaert
- Phycology Research Group, Department of Biology, Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
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129
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Meyer M, Griffiths H. Origins and diversity of eukaryotic CO2-concentrating mechanisms: lessons for the future. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:769-86. [PMID: 23345319 DOI: 10.1093/jxb/ers390] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The importance of the eukaryotic algal CO(2)-concentrating mechanism (CCM) is considered in terms of global productivity as well as molecular phylogeny and diversity. The three major constituents comprising the CCM in the majority of eukaryotes are described. These include: (i) likely plasma- and chloroplast-membrane inorganic carbon transporters; (ii) a suite of carbonic anhydrase enzymes in strategic locations; and usually (iii) a microcompartment in which most Rubisco aggregates (the chloroplast pyrenoid). The molecular diversity of known CCM components are set against the current green algal model for their probable operation. The review then focuses on the kinetic and cystallographic interactions of Rubisco, which permit pyrenoid formation and CCM function. Firstly, we consider observations that surface residues of the Rubisco small subunit directly condition Rubisco aggregation and pyrenoid formation. Secondly, we reanalyse the phylogenetic progression in green Rubisco kinetic properties, and suggest that Rubisco substrate selectivity (the specificity factor, S(rel), and affinity for CO(2), K(c)) demonstrate a systematic relaxation, which directly relates to the origins and effectiveness of a CCM. Finally, we consider the implications of eukaryotic CCM regulation and minimum components needed for introduction into higher plants as a possible means to enhance crop productivity in the future.
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Affiliation(s)
- Moritz Meyer
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
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130
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Kawai H, Hanyuda T, Ridgway LM, Holser K. Ancestral reproductive structure in basal kelp Aureophycus aleuticus. Sci Rep 2013; 3:2491. [PMID: 23966101 PMCID: PMC3749548 DOI: 10.1038/srep02491] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 08/07/2013] [Indexed: 11/24/2022] Open
Abstract
Laminarialean species (so-called kelps) are the largest photosynthetic organisms in aquatic environments, constituting significant ecological components of coastal ecosystems. The largest kelps such as Macrocystis exhibit differentiation between stipe and blade, as well as buoyancy to maintain the distal portion at the water's surface for photosynthesis, while bearing reproductive structures only near the base on special blades (sporophylls). There is a considerable gap between basic kelps such as Chorda and derived kelps, and the evolution of kelp specialization remains unclear. Here we report novel reproductive adaptations in the recently discovered species Aureophycus aleuticus; unlike any known kelps, A. aleuticus forms zoidangia only on the expanded, disc-shaped holdfast. Molecular phylogeny suggests that A. aleuticus is most basal among derived kelps. Because Aureophycus lacks any of the elaborate anatomical structures found in other derived kelps, we suggest that it exhibits some of the most ancestral morphological features of kelps.
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Affiliation(s)
- Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai, Kobe 657-8501, Japan
| | - Takeaki Hanyuda
- Kobe University Research Center for Inland Seas, Rokkodai, Kobe 657-8501, Japan
| | | | - Karin Holser
- St. George Island Research Institute, St. George Island, AK 99801, U.S.A
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131
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Abstract
It is now well established that plants have an important place in studies of sex chromosome evolution because of the repeated independent evolution of separate sexes and sex chromosomes. There has been considerable recent progress in studying plant sex chromosomes. In this review, I focus on how these recent studies have helped clarify or answer several important questions about sex chromosome evolution, and I shall also try to clarify some common misconceptions. I also outline future work that will be needed to make further progress, including testing some important ideas by genetic, molecular, and developmental approaches. Systems with different ages can clearly help show the time course of events during changes from an ancestral co-sexual state (hermaphroditism or monoecy), and I will also explain how different questions can be studied in lineages whose dioecy or sex chromosomes evolved at different times in the past.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
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133
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Dittami SM, Gravot A, Goulitquer S, Rousvoal S, Peters AF, Bouchereau A, Boyen C, Tonon T. Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:366-77. [PMID: 22394375 DOI: 10.1111/j.1365-313x.2012.04982.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Colonizations of freshwater by marine species are rare events, and little information is known about the underlying mechanisms. Brown algae are an independent lineage of photosynthetic and multicellular organisms from which few species inhabit freshwater. As a marine alga that is also found in freshwater, Ectocarpus is of particular interest for studying the transition between these habitats. To gain insights into mechanisms of the transition, we examined salinity tolerance and adaptations to low salinities in a freshwater strain of Ectocarpus on physiological and molecular levels. We show that this isolate belongs to a widely distributed and highly stress-resistant clade, and differed from the genome-sequenced marine strain in its tolerance of low salinities. It also exhibited profound, but reversible, morphological, physiological, and transcriptomic changes when transferred to seawater. Although gene expression profiles were similar in both strains under identical conditions, metabolite and ion profiles differed strongly, the freshwater strain exhibiting e.g. higher cellular contents of amino acids and nitrate, higher contents of n-3 fatty acids, and lower intracellular mannitol and sodium concentrations. Moreover, several stress markers were noted in the freshwater isolate in seawater. This finding suggests that, while high stress tolerance and plasticity may be prerequisites for the colonization of freshwater, genomic alterations have occurred that produced permanent changes in the metabolite profiles to stabilize the transition.
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Affiliation(s)
- Simon M Dittami
- UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
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134
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Charrier B, Le Bail A, de Reviers B. Plant Proteus: brown algal morphological plasticity and underlying developmental mechanisms. TRENDS IN PLANT SCIENCE 2012; 17:468-77. [PMID: 22513108 DOI: 10.1016/j.tplants.2012.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 03/05/2012] [Accepted: 03/05/2012] [Indexed: 05/13/2023]
Abstract
Brown algae are multicellular photosynthetic marine organisms, ubiquitous on rocky intertidal shores at cold and temperate latitudes. Nevertheless, little is known about many aspects of their biology, particularly their development. Given their phylogenetic distance (1.6 billion years) from other plant organisms (land plants, and green and red algae), brown algae harbor a high, as-yet undiscovered diversity of biological mechanisms governing their development. They also show great morphological plasticity, responding to specific environmental constraints, such as sea currents, reduced light availability, grazer attacks, desiccation and UV exposure. Here, we show that brown algal morphogenesis is rather simple and flexible, and review recent genomic data on the cellular and molecular mechanisms known to date that can possibly account for this developmental strategy.
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Affiliation(s)
- Bénédicte Charrier
- Marine Biological Station, UMR7139 CNRS-UPMC 'Marine Plants and Biomolecules', Place Georges Teissier, 29682 Roscoff Cedex, France.
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135
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Balakirev ES, Krupnova TN, Ayala FJ. DNA variation in the phenotypically-diverse brown alga Saccharina japonica. BMC PLANT BIOLOGY 2012; 12:108. [PMID: 22784095 PMCID: PMC3490969 DOI: 10.1186/1471-2229-12-108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 06/21/2012] [Indexed: 05/17/2023]
Abstract
BACKGROUND Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica. RESULTS The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events. CONCLUSION Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
- A. V. Zhirmunsky Institute of Marine Biology, Far Eastern Branch of the Russian Academy of Science, Vladivostok, 690059, Russia
| | - Tatiana N Krupnova
- Pacific Research Fisheries Centre (TINRO-Centre), Vladivostok, 690600, Russia
| | - Francisco J Ayala
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA
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136
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Coelho SM, Scornet D, Rousvoal S, Peters NT, Dartevelle L, Peters AF, Cock JM. Ectocarpus: a model organism for the brown algae. Cold Spring Harb Protoc 2012; 2012:193-8. [PMID: 22301644 DOI: 10.1101/pdb.emo065821] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The brown algae are an interesting group of organisms from several points of view. They are the dominant organisms in many coastal ecosystems, where they often form large, underwater forests. They also have an unusual evolutionary history, being members of the stramenopiles, which are very distantly related to well-studied animal and green plant models. As a consequence of this history, brown algae have evolved many novel features, for example in terms of their cell biology and metabolic pathways. They are also one of only a small number of eukaryotic groups to have independently evolved complex multicellularity. Despite these interesting features, the brown algae have remained a relatively poorly studied group. This situation has started to change over the last few years, however, with the emergence of the filamentous brown alga Ectocarpus as a model system that is amenable to the genomic and genetic approaches that have proved to be so powerful in more classical model organisms such as Drosophila and Arabidopsis.
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Affiliation(s)
- Susana M Coelho
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, BP74, 29682 Roscoff Cedex, France
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137
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Cock JM, Arun A, Godfroy O, Macaisne N, Strittmatter M, Peters AF, Coelho SM. Genomics of brown algae: current advances and future prospects. Genes Genomics 2012. [DOI: 10.1007/s13258-010-0225-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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138
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Tronholm A, Leliaert F, Sansón M, Afonso-Carrillo J, Tyberghein L, Verbruggen H, De Clerck O. Contrasting geographical distributions as a result of thermal tolerance and long-distance dispersal in two allegedly widespread tropical brown algae. PLoS One 2012; 7:e30813. [PMID: 22292046 PMCID: PMC3266907 DOI: 10.1371/journal.pone.0030813] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 12/21/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Many tropical marine macroalgae are reported from all three ocean basins, though these very wide distributions may simply be an artifact resulting from inadequate taxonomy that fails to take into account cryptic diversity. Alternatively, pantropical distributions challenge the belief of limited intrinsic dispersal capacity of marine seaweeds and the effectiveness of the north-south oriented continents as dispersal barriers. We aimed to re-assess the distribution of two allegedly circumtropical brown algae, Dictyota ciliolata and D. crenulata, and interpret the realized geographical range of the respective species in relation to their thermal tolerance and major tectonic and climatic events during the Cenozoic. METHODOLOGY/PRINCIPAL FINDINGS Species delimitation was based on 184 chloroplast encoded psbA sequences, using a Generalized Mixed Yule Coalescent method. Phylogenetic relationships were inferred by analyzing a six-gene dataset. Divergence times were estimated using relaxed molecular clock methods and published calibration data. Distribution ranges of the species were inferred from DNA-confirmed records, complemented with credible literature data and herbarium vouchers. Temperature tolerances of the species were determined by correlating distribution records with local SST values. We found considerable conflict between traditional and DNA-based species definitions. Dictyota crenulata consists of several pseudocryptic species, which have restricted distributions in the Atlantic Ocean and Pacific Central America. In contrast, the pantropical distribution of D. ciliolata is confirmed and linked to its significantly wider temperature tolerance. CONCLUSIONS/SIGNIFICANCE Tectonically driven rearrangements of physical barriers left an unequivocal imprint on the current diversity patterns of marine macroalgae, as witnessed by the D. crenulata-complex. The nearly circumglobal tropical distribution of D. ciliolata, however, demonstrates that the north-south oriented continents do not present absolute dispersal barriers for species characterized by wide temperature tolerances.
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Affiliation(s)
- Ana Tronholm
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
- Departamento de Biología Vegetal (Botánica), Universidad de La Laguna, La Laguna, Canary Islands, Spain
| | - Frederik Leliaert
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Marta Sansón
- Departamento de Biología Vegetal (Botánica), Universidad de La Laguna, La Laguna, Canary Islands, Spain
| | - Julio Afonso-Carrillo
- Departamento de Biología Vegetal (Botánica), Universidad de La Laguna, La Laguna, Canary Islands, Spain
| | - Lennert Tyberghein
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Heroen Verbruggen
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Centre for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
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Cánovas FG, Mota CF, Serrão EA, Pearson GA. Driving south: a multi-gene phylogeny of the brown algal family Fucaceae reveals relationships and recent drivers of a marine radiation. BMC Evol Biol 2011; 11:371. [PMID: 22188734 PMCID: PMC3292578 DOI: 10.1186/1471-2148-11-371] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/21/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the processes driving speciation in marine ecosystems remained a challenge until recently, due to the unclear nature of dispersal boundaries. However, recent evidence for marine adaptive radiations and ecological speciation, as well as previously undetected patterns of cryptic speciation is overturning this view. Here, we use multi-gene phylogenetics to infer the family-level evolutionary history of Fucaceae (intertidal brown algae of the northern Pacific and Atlantic) in order to investigate recent and unique patterns of radiative speciation in the genus Fucus in the Atlantic, in contrast with the mainly monospecific extant genera. RESULTS We developed a set of markers from 13 protein coding genes based on polymorphic cDNA from EST libraries, which provided novel resolution allowing estimation of ancestral character states and a detailed reconstruction of the recent radiative history. Phylogenetic reconstructions yielded similar topologies and revealed four independent trans-Arctic colonization events by Fucaceae lineages, two of which also involved transitions from hermaphroditism to dioecy associated with Atlantic invasions. More recently, reversion of dioecious ancestral lineages towards hermaphroditism has occurred in the genus Fucus, particularly coinciding with colonization of more extreme habitats. Novel lineages in the genus Fucus were also revealed in association with southern habitats. These most recent speciation events occurred during the Pleistocene glaciations and coincided with a shift towards selfing mating systems, generally southward shifts in distribution, and invasion of novel habitats. CONCLUSIONS Diversification of the family occurred in the Late-Mid Miocene, with at least four independent trans-Artic lineage crossings coincident with two reproductive mode transitions. The genus Fucus arose in the Pliocene but radiated within a relatively short time frame about 2.5 million years ago. Current species distributions of Fucus suggest that climatic factors promoted differentiation between the two major clades, while the recent and rapid species radiation in the temperate clade during Pleistocene glacial cycles coincided with several potential speciation drivers.
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Affiliation(s)
- Fernando G Cánovas
- CCMAR, CIMAR-Laboratório Associado, Universidade do Algarve, Faro, Portugal.
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Tonon T, Eveillard D, Prigent S, Bourdon J, Potin P, Boyen C, Siegel A. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:883-92. [PMID: 22136637 DOI: 10.1089/omi.2011.0089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.
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Affiliation(s)
- Thierry Tonon
- UPMC Univ Paris 6 , UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France.
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Phillips N, Kapraun DF, Gómez Garreta A, Ribera Siguan MA, Rull JL, Salvador Soler N, Lewis R, Kawai H. Estimates of nuclear DNA content in 98 species of brown algae (Phaeophyta). AOB PLANTS 2011; 2011:plr001. [PMID: 22476472 PMCID: PMC3064507 DOI: 10.1093/aobpla/plr001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 11/12/2010] [Accepted: 01/13/2011] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Brown algae are critical components of marine ecosystems around the world. However, the genome of only one species of the class has so far been sequenced. This contrasts with numerous sequences available for model organisms such as higher plants, flies or worms. The present communication expands our coverage of DNA content information to 98 species of brown algae with a view to facilitating further genomic investigations of the class. METHODOLOGY The DNA-localizing fluorochrome DAPI (4',6-diamidino-2-phenylindole) and the red blood cell (chicken erythrocyte) standard were used to estimate 2C values by static microspectrophotometry. PRINCIPAL RESULTS 2C DNA contents are reported for 98 species of brown algae, almost doubling the number of estimates available for the class. The present results also expand the reported DNA content range to 0.2-3.6 pg, with several species of Fucales and Laminariales containing apparent polyploid genomes with 2C = 1.8-3.6 pg. CONCLUSIONS The data provide DNA content values for 12 of the 19 recognized orders of brown algae spanning the breadth of the class. Despite earlier contentions concerning DNA content and the presence of oogamy, the present results do not support a correlation between phylogenetic placement and genome size. The closest sister groups to the brown algae have genome sizes on the order of 0.3 pg (e.g. Schizocladiophyceae), suggesting that this may be the ancestral genome size. However, DNA content ranges widely across the class.
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Affiliation(s)
- Naomi Phillips
- Department of Biology, Arcadia University, 450 South Easton Road, Glenside, PA 19038, USA
- Corresponding author's e-mail address:
| | - Donald F. Kapraun
- Department of Biology & Marine Biology, University of North Carolina Wilmington, 601 South College Road, Wilmington, NC 28403-3915, USA
| | - Amelia Gómez Garreta
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona 08028, Spain
| | - M. Antonia Ribera Siguan
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona 08028, Spain
| | - Jorde L. Rull
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona 08028, Spain
| | - Noemi Salvador Soler
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona 08028, Spain
| | - Raymond Lewis
- Department of Biology, Wheaton College, Wheaton, IL 60187, USA
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas Rokkodai, Nadaku, Kobe 657-8501, Japan
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Fraser CI, Winter DJ, Spencer HG, Waters JM. Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales). Mol Phylogenet Evol 2010; 57:1301-11. [PMID: 20971197 DOI: 10.1016/j.ympev.2010.10.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 10/15/2010] [Accepted: 10/15/2010] [Indexed: 10/18/2022]
Abstract
Durvillaea (southern bull-kelp) is an economically and ecologically important brown algal genus that dominates many exposed, rocky coasts in the cold-temperate Southern Hemisphere. Of its five currently-recognized species, four are non-buoyant and restricted to the south-western Pacific, whereas one is both buoyant and widely distributed. Durvillaea has had an unsettled taxonomic history. Although its position within the brown algae (Phaeophyceae) has now been largely resolved through the use of molecular techniques, the taxonomic status of several Durvillaea species/morphotypes remains unresolved. Previous molecular phylogenetic studies of phaeophycean taxa have included few Durvillaea samples, and have consequently paid little or no attention to variation within this genus. The current study presents phylogenetic analyses of four genetic markers (mitchondrial: COI; chloroplast: rbcL; and nuclear: 18S and 28S) to resolve phylogenetic relationships within Durvillaea. Results support the monophyly of solid-bladed taxa D. willana, D. potatorum, and D. sp. A (an undescribed species from the Antipodes Islands), whereas the widespread, buoyant D. antarctica is paraphyletic, with solid-bladed D.chathamensis placed sister to a D. antarctica clade from northern NZ but within D. antarctica sensu lato. The phylogenetic and ecological diversity detected within D. antarctica indicate that it is a species complex of five deeply divergent clades. Under a phylogenetic species concept, Durvillaea can be interpreted as a complex of nine distinct evolutionary lineages, only one of which has an intercontinental distribution ('subantarctic'D. antarctica).
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Affiliation(s)
- Ceridwen I Fraser
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, 340 Great King St., Dunedin 9016, New Zealand.
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