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Yamagishi T, Müller DG, Kawai H. Comparative transcriptome analysis of Discosporangium mesarthrocarpum (Phaeophyceae), Schizocladia ischiensis (Schizocladiophyceae), and Phaeothamnion confervicola (Phaeothamniophyceae), with special reference to cell wall-related genes. JOURNAL OF PHYCOLOGY 2014; 50:543-551. [PMID: 26988326 DOI: 10.1111/jpy.12190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 02/24/2014] [Indexed: 06/05/2023]
Abstract
Within the stramenopile lineage, only brown algae (Phaeophyceae) have evolved complex multicellularity, although some other members of the lineage (e.g., Schizocladia in Schizocladiophyceae; Phaeothamnion in Phaeothamniophyceae) also develop simple multicellular thalli. The development of an adherent extracellular matrix (ECM) is considered to be one of the key steps in the evolution of multicellularity, because ECM is involved in adhesion of cells to each other and in cell-cell communication essential for developmental, reproductive, and sophisticated defense systems. Because there are no unicellular organisms within brown algae, we considered that comparison of other stramenopile taxa closely related to brown algae and having multicellular thalli could yield clues to elucidate the evolution of multicellularity in brown algae. In this study, we investigated transcriptomes involved in cell wall polysaccharide metabolism of three stramenopile species, Discosporangium mesarthrocarpum, which is suggested to be one of the most basal taxa within Phaeophyceae, S. ischiensis, and P. confervicola. We employed 454-FLX high-throughput pyrosequencing to generate expressed sequence tag (EST) databases for these species, and performed comparative analyses between these databases and the genome sequence of the brown alga Ectocarpus siliculosus. Results indicate that cell wall polysaccharide metabolism pathways of D. mesarthrocarpum are similar to E. siliculosus, whereas those of S. ischiensis and P. confervicola are significantly different from E. siliculosus, suggesting that the components of the cell wall in S. ischiensis and P. confervicola are likely to be different from those of E. siliculosus.
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Affiliation(s)
| | - Dieter G Müller
- Faculty of Biology, University of Konstanz, Konstanz, D-78434, Germany
| | - Hiroshi Kawai
- Research Center for Inland Seas, Kobe University, Kobe, 657-8501, Japan
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Matari NH, Blair JE. A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models. BMC Evol Biol 2014; 14:101. [PMID: 24884411 PMCID: PMC4030286 DOI: 10.1186/1471-2148-14-101] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be particularly useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits. Here we have used a Bayesian molecular clock method under three distinct clock models to estimate divergence times within oomycetes, a group of fungal-like eukaryotes that are ubiquitous in the environment and include a number of devastating pathogenic species. The earliest fossil evidence for oomycetes comes from the Lower Devonian (~400 Ma), however the taxonomic affinities of these fossils are unclear. RESULTS Complete genome sequences were used to identify orthologous proteins among oomycetes, diatoms, and a brown alga, with a focus on conserved regulators of gene expression such as DNA and histone modifiers and transcription factors. Our molecular clock estimates place the origin of oomycetes by at least the mid-Paleozoic (~430-400 Ma), with the divergence between two major lineages, the peronosporaleans and saprolegnialeans, in the early Mesozoic (~225-190 Ma). Divergence times estimated under the three clock models were similar, although only the strict and random local clock models produced reliable estimates for most parameters. CONCLUSIONS Our molecular timescale suggests that modern pathogenic oomycetes diverged well after the origin of their respective hosts, indicating that environmental conditions or perhaps horizontal gene transfer events, rather than host availability, may have driven lineage diversification. Our findings also suggest that the last common ancestor of oomycetes possessed a full complement of eukaryotic regulatory proteins, including those involved in histone modification, RNA interference, and tRNA and rRNA methylation; interestingly no match to canonical DNA methyltransferases could be identified in the oomycete genomes studied here.
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Affiliation(s)
| | - Jaime E Blair
- Department of Biology, Franklin & Marshall College, Lancaster, PA, USA.
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Green JJ, Cordero Cervantes D, Peters NT, Logan KO, Kropf DL. Dynamic microtubules and endomembrane cycling contribute to polarity establishment and early development of Ectocarpus mitospores. PROTOPLASMA 2013; 250:1035-43. [PMID: 23322087 DOI: 10.1007/s00709-012-0476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
Many zygotes and spores of brown algae are photosensitive and establish a developmental axis in accordance with directional light cues. Ectocarpus siliculosus is being advanced as a genetic and genomic model organism for investigating brown alga development, and this report investigates photopolarization of the growth axis of mitospores. When exposed to unidirectional light, mitospores photopolarized and established a growth axis such that germination was preferentially localized to the shaded hemisphere of the spore body. The roles of the microtubule cytoskeleton and endomembrane cycling in the photopolarization process were investigated using pharmacological agents. Disruption of microtubule dynamics progressively reduced the percentage of mitospores that photopolarized, while inhibition of vesicle secretion blocked photopolarization nearly completely. Chronic treatment with these pharmacological agents severely affected algal morphogenesis. Microtubules in mitospores and algal filaments were imaged by confocal microscopy. Mitospores contained a radial microtubule array, emanating from a centrosome associated with the nuclear envelope. At germination, the radial array gradually transitioned into a longitudinal array with microtubules extending into the emerging apex. At mitosis, spindles were aligned with the growth axis of cylindrical cells in the filament, and the division plane bisected the spindle axis. These studies demonstrate that dynamic membrane cycling and microtubule assembly play fundamental roles in photopolarization and provide a foundation for future genetic and genomic investigations of this important developmental process.
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Affiliation(s)
- Jeffrey J Green
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
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Konotchick T, Dupont CL, Valas RE, Badger JH, Allen AE. Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season. THE NEW PHYTOLOGIST 2013; 198:398-407. [PMID: 23488966 PMCID: PMC3644879 DOI: 10.1111/nph.12160] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/10/2012] [Indexed: 05/30/2023]
Abstract
To increase knowledge of transcript diversity for the giant kelp, Macrocystis pyrifera, and assess gene expression across naturally occurring depth gradients in light, temperature and nutrients, we sequenced four cDNA libraries created from blades collected at the sea surface and at 18 m depth during the winter and summer. Comparative genomics cluster analyses revealed novel gene families (clusters) in existing brown alga expressed sequence tag data compared with other related algal groups, a pattern also seen with the addition of M. pyrifera sequences. Assembly of 228 Mbp of sequence generated c. 9000 isotigs and c. 12,000 open reading frames. Annotations were assigned using families of hidden Markov models for c. 11% of open reading frames; M. pyrifera had highest similarity to other members of the Phaeophyceae, namely Ectocarpus siliculosus and Laminaria digitata. Quantitative polymerase chain reaction of transcript targets verified depth-related differences in gene expression; stress response and light-harvesting transcripts, especially members of the LI818 (also known as LHCSR) family, showed high expression in the surface compared with 18 m depth, while some nitrogen acquisition transcripts (e.g. nitrite reductase) were upregulated at depth compared with the surface, supporting a conceptual biological model of depth-dependent physiology.
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Affiliation(s)
- Talina Konotchick
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
| | | | - Ruben E Valas
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
| | - Jonathan H Badger
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
| | - Andrew E Allen
- J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
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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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Bothwell JH, Marie D, Peters AF, Cock JM, Coelho SM. Role of endoreduplication and apomeiosis during parthenogenetic reproduction in the model brown alga Ectocarpus. THE NEW PHYTOLOGIST 2010; 188:111-21. [PMID: 20618911 DOI: 10.1111/j.1469-8137.2010.03357.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
• The filamentous brown alga Ectocarpus has a complex life cycle, involving alternation between independent and morphologically distinct sporophyte and gametophyte generations. In addition to this basic haploid-diploid life cycle, gametes can germinate parthenogenetically to produce parthenosporophytes. This article addresses the question of how parthenosporophytes, which are derived from a haploid progenitor cell, are able to produce meiospores in unilocular sporangia, a process that normally involves a reductive meiotic division. • We used flow cytometry, multiphoton imaging, culture studies and a bioinformatics survey of the recently sequenced Ectocarpus genome to describe its life cycle under laboratory conditions and the nuclear DNA changes which accompany key developmental transitions. • Endoreduplication occurs during the first cell cycle in about one-third of parthenosporophytes. The production of meiospores by these diploid parthenosporophytes involves a meiotic division similar to that observed in zygote-derived sporophytes. By contrast, meiospore production in parthenosporophytes that fail to endoreduplicate occurs via a nonreductive apomeiotic event. • Our results highlight Ectocarpus's reproductive and developmental plasticity and are consistent with previous work showing that its life cycle transitions are controlled by genetic mechanisms and are independent of ploidy.
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Affiliation(s)
- John H Bothwell
- Queen's University Belfast, School of Biological Sciences, 97 Lisburn Road, Belfast, BT9 7BL, UK
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Brown JW, Sorhannus U. A molecular genetic timescale for the diversification of autotrophic stramenopiles (Ochrophyta): substantive underestimation of putative fossil ages. PLoS One 2010; 5:e12759. [PMID: 20862282 PMCID: PMC2940848 DOI: 10.1371/journal.pone.0012759] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 08/20/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Stramenopiles constitute a large and diverse eukaryotic clade that is currently poorly characterized from both phylogenetic and temporal perspectives at deeper taxonomic levels. To better understand this group, and in particular the photosynthetic stramenopiles (Ochrophyta), we analyzed sequence data from 135 taxa representing most major lineages. Our analytical approach utilized several recently developed methods that more realistically model the temporal evolutionary process. METHODOLOGY/PRINCIPAL FINDINGS Phylogenetic reconstruction employed a Bayesian joint rate- and pattern-heterogeneity model to reconstruct the evolutionary history of these taxa. Inferred phylogenetic resolution was generally high at all taxonomic levels, sister-class relationships in particular receiving good statistical support. A signal for heterotachy was detected in clustered portions of the tree, although this does not seem to have had a major influence on topological inference. Divergence time estimates, assuming a lognormally-distributed relaxed molecular clock while accommodating topological uncertainty, were broadly congruent over alternative temporal prior distributions. These data suggest that Ochrophyta originated near the Proterozoic-Phanerozoic boundary, diverging from their sister-taxon Oomycota. The evolution of the major ochrophyte lineages appears to have proceeded gradually thereafter, with most lineages coming into existence by ∼200 million years ago. CONCLUSIONS/SIGNIFICANCE The evolutionary timescale of the autotrophic stramenopiles reconstructed here is generally older than previously inferred from molecular clocks. However, this more ancient timescale nevertheless casts serious doubt on the taxonomic validity of putative xanthophyte/phaeophyte fossils from the Proterozoic, which predate by as much as a half billion years or more the age suggested by our molecular genetic data. If these fossils truly represent crown stramenopile lineages, then this would imply that molecular rate evolution in this group proceeds in a fashion that is fundamentally incompatible with the relaxed molecular clock model employed here. A more likely scenario is that there is considerable convergent morphological evolution within Heterokonta, and that these fossils have been taxonomically misdiagnosed.
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Affiliation(s)
- Joseph W. Brown
- Museum of Zoology and Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ulf Sorhannus
- Department of Biology & Health Services, Edinboro University of Pennsylvania, Edinboro, Pennsylvania, United States of America
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Silberfeld T, Leigh JW, Verbruggen H, Cruaud C, de Reviers B, Rousseau F. A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the "brown algal crown radiation". Mol Phylogenet Evol 2010; 56:659-74. [PMID: 20412862 DOI: 10.1016/j.ympev.2010.04.020] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 04/09/2010] [Accepted: 04/13/2010] [Indexed: 11/27/2022]
Abstract
The most conspicuous feature in previous phaeophycean phylogenies is a large polytomy known as the brown algal crown radiation (BACR). The BACR encompasses 10 out of the 17 currently recognized brown algal orders. A recent study has been able to resolve a few nodes of the BACR, suggesting that it may be a soft polytomy caused by a lack of signal in molecular markers. The present work aims to refine relationships within the BACR and investigate the nature and timeframe of the diversification in question using a dual approach. A multi-marker phylogeny of the brown algae was built from 10 mitochondrial, plastid and nuclear loci (>10,000 nt) of 72 phaeophycean taxa, resulting in trees with well-resolved inter-ordinal relationships within the BACR. Using Bayesian relaxed molecular clock analysis, it is shown that the BACR is likely to represent a gradual diversification spanning most of the Lower Cretaceous rather than a sudden radiation. Non-molecular characters classically used in ordinal delimitation were mapped on the molecular topology to study their evolutionary history.
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Affiliation(s)
- Thomas Silberfeld
- UMR 7138, UPMC, MNHN, CNRS, IRD: Systématique, adaptation, évolution, Département Systématique & évolution, USM 603, Muséum National d'Histoire Naturelle, 75231 Paris cedex 05, France.
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La Barre S, Potin P, Leblanc C, Delage L. The halogenated metabolism of brown algae (Phaeophyta), its biological importance and its environmental significance. Mar Drugs 2010; 8:988-1010. [PMID: 20479964 PMCID: PMC2866472 DOI: 10.3390/md8040988] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 03/13/2010] [Accepted: 03/25/2010] [Indexed: 11/16/2022] Open
Abstract
Brown algae represent a major component of littoral and sublittoral zones in temperate and subtropical ecosystems. An essential adaptive feature of this independent eukaryotic lineage is the ability to couple oxidative reactions resulting from exposure to sunlight and air with the halogenations of various substrates, thereby addressing various biotic and abiotic stresses i.e., defense against predators, tissue repair, holdfast adhesion, and protection against reactive species generated by oxidative processes. Whereas marine organisms mainly make use of bromine to increase the biological activity of secondary metabolites, some orders of brown algae such as Laminariales have also developed a striking capability to accumulate and to use iodine in physiological adaptations to stress. We review selected aspects of the halogenated metabolism of macrophytic brown algae in the light of the most recent results, which point toward novel functions for iodide accumulation in kelps and the importance of bromination in cell wall modifications and adhesion properties of brown algal propagules. The importance of halogen speciation processes ranges from microbiology to biogeochemistry, through enzymology, cellular biology and ecotoxicology.
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Affiliation(s)
- Stéphane La Barre
- Université Pierre et Marie Curie-Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France; E-Mails:
(P.P.);
(C.L.);
(L.D.)
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France
| | - Philippe Potin
- Université Pierre et Marie Curie-Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France; E-Mails:
(P.P.);
(C.L.);
(L.D.)
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France
| | - Catherine Leblanc
- Université Pierre et Marie Curie-Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France; E-Mails:
(P.P.);
(C.L.);
(L.D.)
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France
| | - Ludovic Delage
- Université Pierre et Marie Curie-Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France; E-Mails:
(P.P.);
(C.L.);
(L.D.)
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique F-29682, Roscoff, France
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On the origin of chloroplasts, import mechanisms of chloroplast-targeted proteins, and loss of photosynthetic ability — review. Folia Microbiol (Praha) 2009; 54:303-21. [DOI: 10.1007/s12223-009-0048-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 03/31/2009] [Indexed: 10/20/2022]
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