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Frederik Leliaert - One of the best experts on this subject based on the ideXlab platform.
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Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models.
Molecular phylogenetics and evolution, 2018Co-Authors: Ling Fang, Frederik Leliaert, Huan Zhu, Guoxiang Liu, Phil M. Novis, Zhenhua Zhang, David Penny, Bojian ZhongAbstract:Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (Blidingia minima NIES-1837, Ulothrix zonata, Halochlorococcum sp. NIES-1838, Scotinosphaera sp. NIES-154, Caulerpa brownii and Cephaleuros sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to reconstruct the optimal phylogenetic relationships by minimizing conflicting signals.
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Taxonomic, ecological, and geographic scope of this book
Freshwater Flora of Central Europe Vol 13: Chlorophyta: Ulvophyceae (Süßwasserflora von Mitteleuropa Bd. 13: Chlorophyta: Ulvophyceae), 2018Co-Authors: Pavel Škaloud, Fabio Rindi, Christian Boedeker, Frederik LeliaertAbstract:This book is in intended to provide a comprehensive overview of Ulvophyceae species diversity in freshwater and (aero)terrestrial habitats in Europe, and a tool for identification of the species, up to the level that species can be recognized or distinguished based on morphological characters. Insights into species diversity based on molecular data, when available, is also discussed.
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Circumscription of the class Ulvophyceae: ultrastructure and morphology
Freshwater Flora of Central Europe Vol 13: Chlorophyta: Ulvophyceae (Süßwasserflora von Mitteleuropa Bd. 13: Chlorophyta: Ulvophyceae), 2018Co-Authors: Pavel Škaloud, Fabio Rindi, Christian Boedeker, Frederik LeliaertAbstract:The Ulvophyceae K. R. Mattox & K. D. Stewart is one of the main classes of green algae, comprising about 1700 species according to AlgaeBase (Guiry 2012, Guiry & Guiry 2017). Most of this diversity is found in marine coastal waters, while a smaller number of species occurs in brackish, freshwater, and terrestrial habitats. The Ulvophyceae are best known for their macroscopic species (Brodie et al. 2007), but a large, less notable diversity comprise of microscopic species, which are found in marine, as well as in freshwater and terrestrial habitats.
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Classification: orders and families
Freshwater Flora of Central Europe Vol 13: Chlorophyta: Ulvophyceae (Süßwasserflora von Mitteleuropa Bd. 13: Chlorophyta: Ulvophyceae), 2018Co-Authors: Pavel Škaloud, Fabio Rindi, Christian Boedeker, Frederik LeliaertAbstract:Current classification of the Ulvophyceae includes 32 families in 8 orders (Leliaert et al. 2015). The present study significantly revises the classification of ulvophytes, in particular the Ulvales and Ulotrichales. One order (Chlorocystidales) is resurrected, and eight families are newly described or resurrected. The Ignatius-clade, which has been recognized as a distinct clade of Ulvophyceae based on ultrastructural and molecular data, is here formally described as a new order and family (Ignatiales, Ignatiaceae). An overview of the order and family level classification, as presented in the current treatment, with indication of habitat type (up to the family level) is given in Table 1.
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Ecology of freshwater and terrestrial ulvophytes
Freshwater Flora of Central Europe Vol 13: Chlorophyta: Ulvophyceae (Süßwasserflora von Mitteleuropa Bd. 13: Chlorophyta: Ulvophyceae), 2018Co-Authors: Pavel Škaloud, Fabio Rindi, Christian Boedeker, Frederik LeliaertAbstract:Although the largest diversity of Ulvophyceae is found in marine habitats, a substantial number of species may be found over a broad salinity range, and occur in brackish to freshwater and semi-terrestrial habitats. For example, some marine Ulva and Blidingia species are able to penetrate into freshwater habitats (Messyasz & Rybak 2011). Other ulvophyte species or genera are entirely confined to brackish (marshes, and estuaries), freshwater, damp terrestrial, or aeroterrestrial habitats.
Monique Turmel - One of the best experts on this subject based on the ideXlab platform.
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Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae.
Scientific reports, 2017Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.
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Mitochondrion-to-Chloroplast DNA Transfers and Intragenomic Proliferation of Chloroplast Group II Introns in Gloeotilopsis Green Algae (Ulotrichales, Ulvophyceae)
Genome biology and evolution, 2016Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:To probe organelle genome evolution in the Ulvales/Ulotrichales clade, the newly sequenced chloroplast and mitochondrial genomes of Gloeotilopsis planctonica and Gloeotilopsis sarcinoidea (Ulotrichales) were compared with those of Pseudendoclonium akinetum (Ulotrichales) and of the few other green algae previously sampled in the Ulvophyceae. At 105,236 bp, the G planctonica mitochondrial DNA (mtDNA) is the largest mitochondrial genome reported so far among chlorophytes, whereas the 221,431-bp G planctonica and 262,888-bp G sarcinoidea chloroplast DNAs (cpDNAs) are the largest chloroplast genomes analyzed among the Ulvophyceae. Gains of non-coding sequences largely account for the expansion of these genomes. Both Gloeotilopsis cpDNAs lack the inverted repeat (IR) typically found in green plants, indicating that two independent IR losses occurred in the Ulvales/Ulotrichales. Our comparison of the Pseudendoclonium and Gloeotilopsis cpDNAs offered clues regarding the mechanism of IR loss in the Ulotrichales, suggesting that internal sequences from the rDNA operon were differentially lost from the two original IR copies during this process. Our analyses also unveiled a number of genetic novelties. Short mtDNA fragments were discovered in two distinct regions of the G sarcinoidea cpDNA, providing the first evidence for intracellular inter-organelle gene migration in green algae. We identified for the first time in green algal organelles, group II introns with LAGLIDADG ORFs as well as group II introns inserted into untranslated gene regions. We discovered many group II introns occupying sites not previously documented for the chloroplast genome and demonstrated that a number of them arose by intragenomic proliferation, most likely through retrohoming.
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The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae
Current Genetics, 2006Co-Authors: Jean-françois Pombert, Claude Lemieux, Christian Otis, Philippe Beauchamp, Monique TurmelAbstract:The mitochondrial genome displays a highly plastic architecture in the green algal division comprising the classes Prasinophyceae, Trebouxiophyceae, Ulvophyceae, and Chlorophyceae (Chlorophyta). The compact mitochondrial DNAs (mtDNAs) of Nephroselmis (Prasinophyceae) and Prototheca (Trebouxiophyceae) encode about 60 genes and have been ascribed an ‘ancestral’ pattern of evolution, whereas those of chlorophycean green algae are much more reduced in gene content and size. Although the mtDNA of the early-diverging ulvophyte Pseudendoclonium contains 57 conserved genes, it differs from ‘ancestral’ chlorophyte mtDNAs by its unusually large size (96 kb) and long intergenic spacers. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we have determined the complete mtDNA sequence of Oltmannsiellopsis viridis , an ulvophyte belonging to a distinct, early-diverging lineage. This 56,761 bp genome harbours 54 conserved genes, numerous repeated sequences, and only three introns. From our comparative analyses with Pseudendoclonium mtDNA, we infer that the mitochondrial genome of the last common ancestor of the two ulvophytes closely resembled that of the trebouxiophyte Prototheca in terms of gene content and gene density. Our results also provide strong evidence for the intracellular, interorganellar transfer of a group I intron and for two distinct events of intercellular, horizontal DNA transfer.
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The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes
BMC Biology, 2006Co-Authors: Jean-françois Pombert, Claude Lemieux, Monique TurmelAbstract:Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis , a representative of a distinct, early diverging lineage. Results The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of Oltmannsiellopsis cpDNA more closely resembles that of Chlorella (Trebouxiophyceae) cpDNA. Conclusion The chloroplast genome of the last common ancestor of Oltmannsiellopsis and Pseudendoclonium contained a minimum of 108 genes, carried only a few group I introns, and featured a distinctive quadripartite architecture. Numerous changes were experienced by the chloroplast genome in the lineages leading to Oltmannsiellopsis and Pseudendoclonium . Our comparative analyses of chlorophyte cpDNAs support the notion that the Ulvophyceae is sister to the Chlorophyceae.
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The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes
BMC biology, 2006Co-Authors: Jean-françois Pombert, Claude Lemieux, Monique TurmelAbstract:The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of Oltmannsiellopsis cpDNA more closely resembles that of Chlorella (Trebouxiophyceae) cpDNA. The chloroplast genome of the last common ancestor of Oltmannsiellopsis and Pseudendoclonium contained a minimum of 108 genes, carried only a few group I introns, and featured a distinctive quadripartite architecture. Numerous changes were experienced by the chloroplast genome in the lineages leading to Oltmannsiellopsis and Pseudendoclonium. Our comparative analyses of chlorophyte cpDNAs support the notion that the Ulvophyceae is sister to the Chlorophyceae.
James T Melton - One of the best experts on this subject based on the ideXlab platform.
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multiple intraspecific variations of mitochondrial genomes in the green tide forming alga ulva compressa linnaeus Ulvophyceae chlorophyta
Frontiers in Marine Science, 2020Co-Authors: Feng Liu, James T Melton, Juan M Lopezbautista, Nansheng ChenAbstract:To gain further insights into intraspecific evolution of Ulva mitochondrial genomes, the mitogenomes of three morphotypes of the green-tide forming alga, Ulva compressa Linnaeus from China and USA, were sequenced and compared with the available data from Ulvophyceae. The U. compressa mitogenomes displayed significantly variable size at intraspecific level ranging from 61,700 to >66,587 bp, due to difference in acquisition of foreign DNA fragments, gain or loss of both group I and II introns, and non-coding intergenic spacer regions. The U. compressa mitogenomes harbored variable gene content ranging from 69 genes (including orfs) in Uco1 to 76 in Uco5, and contained different intron content from 4 introns in Uco3 and Uco4 to 7 in Uco1. A total of 63 genes and only two group IB introns (intron cox1-1107 and cox1-1125) were shared by these five mitogenomes. The U. compressa mitogenomes accumulated much more inverted repeat (IR) elements, ranging from 45 in Uco1 to 88 in Uco2, than that of the other Ulva species (3 - 34). A locally collinear block of eight genes (rps11-rps19-rps4-rpl16-trnR-trnQ-trnE-trnS) with the size of 3,631 bp has been inverted only in Uco1 indicating that the rearrangement event happened after its divergence from Uco2-5 and might be relate to a specific IR element. A majority of the common genes (≈76%) displayed high identity (>98%) among these five mitogenomes, while some low values were observed in six genes mainly due to duplication and insertion/deletion mutations of small DNA fragments. Our study presented the first case of multiple intraspecific variations in ulvophycean mitogenomes, and indicated that the mitogenome will be a valuable tool for understanding the native or nonindigenous nature of the cosmopolitan Ulva species.
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mitochondrial genomes of the green macroalga ulva pertusa Ulvophyceae chlorophyta novel insights into the evolution of mitogenomes in the Ulvophyceae
Journal of Phycology, 2017Co-Authors: James T Melton, Yuping BiAbstract:To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared 2 ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes (PCGs), and 12 open reading frames (ORFs). The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U. pertusa mtDNA (Up2), while the larger mtDNA (Up1) had eight. The larger mtDNA had two additional group II introns in two genes (cox1 and cox2) and tandem duplication mutations in non-coding regions. Our results showed the first case of intra-specific variation in chlorophytan mitogenomes and provided further genomic data for the undersampled Ulvophyceae. This article is protected by copyright. All rights reserved.
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Mitochondrial genomes of the green macroalga Ulva pertusa (Ulvophyceae, Chlorophyta): novel insights into the evolution of mitogenomes in the Ulvophyceae.
Journal of phycology, 2017Co-Authors: Feng Liu, James T MeltonAbstract:To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared two ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes, and 12 open reading frames. The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U. pertusa mtDNA (Up2), while the larger mtDNA (Up1) had eight. The larger mtDNA had two additional group II introns in two genes (cox1 and cox2) and tandem duplication mutations in noncoding regions. Our results showed the first case of intraspecific variation in chlorophytan mitogenomes and provided further genomic data for the undersampled Ulvophyceae.
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RESEARCH ARTICLE The Complete Chloroplast and Mitochondrial Genomes of the
2016Co-Authors: James T Melton, Frederik Leliaert, Ana Tronholm, Juan M. López-bautistaAbstract:Sequencing mitochondrial and chloroplast genomes has become an integral part in under-standing the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mi-tochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping mole-cule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid ge-nome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and fol-lows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA gene
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De novo assembly of the mitochondrial genome of Ulva fasciata Delile (Ulvophyceae, Chlorophyta), a distromatic blade-forming green macroalga
Mitochondrial DNA. Part A DNA mapping sequencing and analysis, 2015Co-Authors: James T Melton, Juan M. López-bautistaAbstract:We present the 61 614 bp circular-mapping mitochondrial genome of Ulva fasciata. Fifty-eight genes were identified including 29 protein-coding genes, 27 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. Four ORFs from the Ulva sp. UNA00071828 mitogenome were conserved compared to the mitogenome of Ulva fasciata. The ∼10 000 bp size difference was mostly due to fewer introns found in U. fasciata mtDNA (4) as compared with the Ulva sp. UNA00071828 mtDNA (10). Introns were annotated in cox1 (3) and nad3 (1). The AT content was similar to Ulva sp. UNA00071828 mtDNA at 67.5%. A phylogenomic anaylsis of 28 chlorophytes and 17 protein-coding genes (14 115 bp alignment) showed that U. fasciata clusters closely with other members of the Ulvophyceae (Ulva sp. UNA00071828, Pseudendoclonium akinetum, and Oltmannsiellopsis viridis). This analysis did not recover a monophyletic Ulvophyceae, however, the Trebouxiophyceae and Chlorophyceae were supported as monophyletic groups.
Olivier De Clerck - One of the best experts on this subject based on the ideXlab platform.
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Marine macroalgal biodiversity of northern Madagascar: morpho-genetic systematics and implications of anthropic impacts for conservation
Biodiversity and Conservation, 2021Co-Authors: Christophe Vieira, Hiroshi Kawai, Antoine Ramon N’yeurt, Faravavy A. Rasoamanendrika, Sofie D’hondt, Lan-anh Thi Tran, Didier Van Den Spiegel, Olivier De ClerckAbstract:A floristic survey of the marine algal biodiversity of Antsiranana Bay, northern Madagascar, was conducted during November 2018. This represents the first inventory encompassing the three major macroalgal classes (Phaeophyceae, Florideophyceae and Ulvophyceae) for the little-known Malagasy marine flora. Combining morphological and DNA-based approaches, we report from our collection a total of 110 species from northern Madagascar, including 30 species of Phaeophyceae, 50 Florideophyceae and 30 Ulvophyceae. Barcoding of the chloroplast-encoded rbc L gene was used for the three algal classes, in addition to tuf A for the Ulvophyceae. This study significantly increases our knowledge of the Malagasy marine biodiversity while augmenting the rbc L and tuf A algal reference libraries for DNA barcoding. These efforts resulted in a total of 72 new species records for Madagascar. Combining our own data with the literature, we also provide an updated catalogue of 442 taxa of marine benthic macroalgae from Madagascar, comprising 85 Phaeophyceae, 1 Compsopogonophyceae, 240 Florideophyceae and 116 Ulvophyceae. This diversity holds 29 (ca. 6.5%) endemic species to Madagascar. Our results are discussed in the context of increasing threats to biodiversity on Madagascar’s coastal reefs from both anthropic and anthropogenic activities including sewage effluent runoffs and unsustainable agricultural practices such as massive deforestation, leading to ecosystem shifts to algal dominance on reefs, which are recommended to be addressed through integrated land-sea management in a Reef-to-Ridge conservation approach.
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Evolution and Cytological Diversification of the Green
2016Co-Authors: Ellen Cocquyt, Heroen Verbruggen, Frederik Leliaert, Olivier De ClerckAbstract:The Ulvophyceae, one of the four classes of the Chlorophyta, is of particular evolutionary interest because it features an unrivaledmorphological and cytological diversity. Morphological types range from unicells and simple multicellular filaments to sheet-like and complex corticated thalli. Cytological layouts range from typical small cells containing a single nucleus and chloroplast to giant cells containing millions of nuclei and chloroplasts. In order to understand the evolution of these morphological and cytological types, the present paper aims to assess whether the Ulvophyceae are monophyletic and elucidate the ancient relationships among its orders. Our approach consists of phylogenetic analyses (maximum likelihood and Bayesian inference) of seven nuclear genes, small subunit nuclear ribosomal DNA and two plastid markers with carefully chosen partitioning strategies, and models of sequence evolution. We introduce a procedure for fast site removal (site stripping) targeted at improving phylogenetic signal in a particular epoch of interest and evaluate the specificity of fast site removal to retain signal about ancient relationships. From our phylogenetic analyses, we conclude that the ancestral ulvophyte likely was a unicellular uninucleate organism and that macroscopic growth was achieved independently in various lineages involving radically different mechanisms: either by evolving multicellularity with coupled mitosis and cytokinesis (Ulvales—Ulotrichales and Trentepohliales), by obtaining a multinucleate siphonocladous organization where every nucleus provides for its own cytoplasmic domain (Cladophorales and Blastophysa), or by developing a siphonous organizatio
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New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data
Frontiers in Ecology and Evolution, 2014Co-Authors: Karolina Fučíková, Louise A. Lewis, Frederik Leliaert, Endymion D. Cooper, Pavel Škaloud, Sofie D'hondt, Olivier De Clerck, Carlos Frederico D. Gurgel, Paul O. Lewis, Juan M. López-bautistaAbstract:Phylogenetic relationships in the green algal phylum Chlorophyta have long been subject to debate, especially at higher taxonomic ranks (order, class). The relationships among three traditionally defined and well-studied classes, Chlorophyceae, Trebouxiophyceae, and Ulvophyceae are of particular interest, as these groups are species-rich and ecologically important worldwide. Different phylogenetic hypotheses have been proposed over the past two decades and the monophyly of the individual classes has been disputed on occasion. Our study seeks to test these hypotheses by combining high throughput sequencing data from the chloroplast genome with increased taxon sampling. Our results suggest that while many of the deep relationships are still problematic to resolve, the classes Trebouxiophyceae and Ulvophyceae are likely not monophyletic as currently defined. Our results also support relationships among several trebouxiophycean taxa that were previously unresolved. Finally, we propose that the common term for the grouping of the three classes, “UTC clade,” be replaced with the term “core Chlorophyta” for the well-supported clade containing Chlorophyceae, taxa belonging to Ulvophyceae and Trebouxiophyceae, and the classes Chlorodendrophyceae and Pedinophyceae.
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RESEARCH ARTICLE Open Access Complex phylogenetic distribution of a noncanonical genetic code in green algae
2013Co-Authors: Ellen Cocquyt, Gillian H Gile, Heroen Verbruggen, Patrick J. Keeling, Frederik Leliaert, Olivier De ClerckAbstract:Background: A non-canonical nuclear genetic code, in which TAG and TAA have been reassigned from stop codons to glutamine, has evolved independently in several eukaryotic lineages, including the ulvophycean green algal orders Dasycladales and Cladophorales. To study the phylogenetic distribution of the standard and noncanonical genetic codes, we generated sequence data of a representative set of ulvophycean green algae and used a robust green algal phylogeny to evaluate different evolutionary scenarios that may account for the origin of the non-canonical code. Results: This study demonstrates that the Dasycladales and Cladophorales share this alternative genetic code with the related order Trentepohliales and the genus Blastophysa, but not with the Bryopsidales, which is sister to the Dasycladales. This complex phylogenetic distribution whereby all but one representative of a single natural lineage possesses an identical deviant genetic code is unique. Conclusions: We compare different evolutionary scenarios for the complex phylogenetic distribution of this noncanonical genetic code. A single transition to the non-canonical code followed by a reversal to the canonical code in the Bryopsidales is highly improbable due to the profound genetic changes that coincide with codon reassignment. Multiple independent gains of the non-canonical code, as hypothesized for ciliates, are also unlikel
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Morphology and Phylogenetic Position of the Freshwater Green Microalgae Chlorochytrium (Chlorophyceae) and Scotinosphaera (Scotinosphaerales, ord. nov., Ulvophyceae).
Journal of phycology, 2013Co-Authors: Pavel Škaloud, Olivier De Clerck, Tomas Kalina, Katarína Nemjová, Frederik LeliaertAbstract:The green algal family Chlorochytriaceae comprises relatively large coccoid algae with secondarily thickened cell walls. Despite its morphological distinctness, the family remained molecularly uncharacterized. In this study, we investigated the morphology and phylogenetic position of 16 strains determined as members of two Chlorochytriaceae genera, Chlorochytrium and Scotinosphaera. The phylogenetic reconstructions were based on the analyses of two data sets, including a broad, concatenated alignment of small subunit rDNA and rbcL sequences, and a 10-gene alignment of 32 selected taxa. All analyses revealed the distant relation of the two genera, segregated in two different classes: Chlorophyceae and Ulvophyceae. Chlorochytrium strains were inferred in two distinct clades of the Stephanosphaerinia clade within the Chlorophyceae. Whereas clade A morphologically fits the description of Chlorochytrium, the strains of clade B coincide with the circumscription of the genus Neospongiococcum. The Scotinosphaera strains formed a distinct and highly divergent clade within the Ulvophyceae, warranting the recognition of a new order, Scotinosphaerales. Morphologically, the order is characterized by large cells bearing local cell wall thickenings, pyrenoid matrix dissected by numerous anastomosing cytoplasmatic channels, sporogenesis comprising the accumulation of secondary carotenoids in the cell periphery and almost simultaneous cytokinesis. The close relationship of the Scotinosphaerales with other early diverging ulvophycean orders enforces the notion that nonmotile unicellular freshwater organisms have played an important role in the early diversification of the Ulvophyceae.
Claude Lemieux - One of the best experts on this subject based on the ideXlab platform.
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Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae.
Scientific reports, 2017Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.
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Mitochondrion-to-Chloroplast DNA Transfers and Intragenomic Proliferation of Chloroplast Group II Introns in Gloeotilopsis Green Algae (Ulotrichales, Ulvophyceae)
Genome biology and evolution, 2016Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:To probe organelle genome evolution in the Ulvales/Ulotrichales clade, the newly sequenced chloroplast and mitochondrial genomes of Gloeotilopsis planctonica and Gloeotilopsis sarcinoidea (Ulotrichales) were compared with those of Pseudendoclonium akinetum (Ulotrichales) and of the few other green algae previously sampled in the Ulvophyceae. At 105,236 bp, the G planctonica mitochondrial DNA (mtDNA) is the largest mitochondrial genome reported so far among chlorophytes, whereas the 221,431-bp G planctonica and 262,888-bp G sarcinoidea chloroplast DNAs (cpDNAs) are the largest chloroplast genomes analyzed among the Ulvophyceae. Gains of non-coding sequences largely account for the expansion of these genomes. Both Gloeotilopsis cpDNAs lack the inverted repeat (IR) typically found in green plants, indicating that two independent IR losses occurred in the Ulvales/Ulotrichales. Our comparison of the Pseudendoclonium and Gloeotilopsis cpDNAs offered clues regarding the mechanism of IR loss in the Ulotrichales, suggesting that internal sequences from the rDNA operon were differentially lost from the two original IR copies during this process. Our analyses also unveiled a number of genetic novelties. Short mtDNA fragments were discovered in two distinct regions of the G sarcinoidea cpDNA, providing the first evidence for intracellular inter-organelle gene migration in green algae. We identified for the first time in green algal organelles, group II introns with LAGLIDADG ORFs as well as group II introns inserted into untranslated gene regions. We discovered many group II introns occupying sites not previously documented for the chloroplast genome and demonstrated that a number of them arose by intragenomic proliferation, most likely through retrohoming.
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The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae
Current Genetics, 2006Co-Authors: Jean-françois Pombert, Claude Lemieux, Christian Otis, Philippe Beauchamp, Monique TurmelAbstract:The mitochondrial genome displays a highly plastic architecture in the green algal division comprising the classes Prasinophyceae, Trebouxiophyceae, Ulvophyceae, and Chlorophyceae (Chlorophyta). The compact mitochondrial DNAs (mtDNAs) of Nephroselmis (Prasinophyceae) and Prototheca (Trebouxiophyceae) encode about 60 genes and have been ascribed an ‘ancestral’ pattern of evolution, whereas those of chlorophycean green algae are much more reduced in gene content and size. Although the mtDNA of the early-diverging ulvophyte Pseudendoclonium contains 57 conserved genes, it differs from ‘ancestral’ chlorophyte mtDNAs by its unusually large size (96 kb) and long intergenic spacers. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we have determined the complete mtDNA sequence of Oltmannsiellopsis viridis , an ulvophyte belonging to a distinct, early-diverging lineage. This 56,761 bp genome harbours 54 conserved genes, numerous repeated sequences, and only three introns. From our comparative analyses with Pseudendoclonium mtDNA, we infer that the mitochondrial genome of the last common ancestor of the two ulvophytes closely resembled that of the trebouxiophyte Prototheca in terms of gene content and gene density. Our results also provide strong evidence for the intracellular, interorganellar transfer of a group I intron and for two distinct events of intercellular, horizontal DNA transfer.
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The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes
BMC Biology, 2006Co-Authors: Jean-françois Pombert, Claude Lemieux, Monique TurmelAbstract:Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis , a representative of a distinct, early diverging lineage. Results The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of Oltmannsiellopsis cpDNA more closely resembles that of Chlorella (Trebouxiophyceae) cpDNA. Conclusion The chloroplast genome of the last common ancestor of Oltmannsiellopsis and Pseudendoclonium contained a minimum of 108 genes, carried only a few group I introns, and featured a distinctive quadripartite architecture. Numerous changes were experienced by the chloroplast genome in the lineages leading to Oltmannsiellopsis and Pseudendoclonium . Our comparative analyses of chlorophyte cpDNAs support the notion that the Ulvophyceae is sister to the Chlorophyceae.
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The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes
BMC biology, 2006Co-Authors: Jean-françois Pombert, Claude Lemieux, Monique TurmelAbstract:The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of Oltmannsiellopsis cpDNA more closely resembles that of Chlorella (Trebouxiophyceae) cpDNA. The chloroplast genome of the last common ancestor of Oltmannsiellopsis and Pseudendoclonium contained a minimum of 108 genes, carried only a few group I introns, and featured a distinctive quadripartite architecture. Numerous changes were experienced by the chloroplast genome in the lineages leading to Oltmannsiellopsis and Pseudendoclonium. Our comparative analyses of chlorophyte cpDNAs support the notion that the Ulvophyceae is sister to the Chlorophyceae.
