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Claude Lemieux - One of the best experts on this subject based on the ideXlab platform.
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evolution of the plastid genome in green algae
2018Co-Authors: Monique Turmel, Claude LemieuxAbstract:Abstract Comparative analyses of green algal plastid genomes (plastomes) have flourished in the past decade. In addition to improving our understanding of the phylogenetic relationships among green algal lineages, the expanded collection of plastome sequences has provided new insights into the ancestral architecture of this genome in the common ancestor of all green algae and into the changes that it underwent during lineage diversification in the two major divisions of the Viridiplantae (Chlorophyta and Streptophyta). The level of plastome diversity is much greater in the Chlorophyta than in the Streptophyta, with important variations seen at several levels—including genome size, presence/absence and size of the large inverted repeat encoding the rRNA operon, pattern of gene partitioning among single-copy regions, gene content, gene order, intron content, and amount of repetitive sequences—both within and across the main lineages of these two divisions. Here, we present an overview of the structural changes that sustained the plastome during the evolution of both chlorophyte and streptophyte algae. We begin by examining the range of variations observed at the above-mentioned levels in 112 chlorophyte taxa and then summarize what we learned for the Streptophyta based on the plastomes of 17 taxa. The chapter ends with a presentation of issues that need to be resolved in future studies.
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distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae scherffelia dubia and tetraselmis sp ccmp 881
PLOS ONE, 2016Co-Authors: Monique Turmel, Christian Otis, Jeancharles De Cambiaire, Claude LemieuxAbstract:The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.
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the chloroplast genomes of the green algae pedinomonas minor parachlorella kessleri and oocystis solitaria reveal a shared ancestry between the pedinomonadales and chlorellales
Molecular Biology and Evolution, 2009Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The green algae belonging to the Chlorophyta-the lineage sister to that comprising the land plants and their charophycean green algal relatives (Streptophyta)-have been subdivided into four classes (Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae). Yet the Pedinomonadales, an assemblage consisting of tiny, naked uniflagellates with a second basal body, has no clear affiliation with these classes and the branching order of the crown chlorophytes remains unknown. To gain an insight into the phylogenetic position of the Pedinomonadales and the relationships among the recognized chlorophyte classes, we have sequenced the chloroplast genomes of Pedinomonas minor (Pedinomonadales) and of two trebouxiophyceans belonging to the Chlorellales, Parachlorella kessleri (Chlorellaceae) and Oocystis solitaria (Oocystaceae), and compared these genomes with those of previously examined streptophytes and chlorophytes, including Chlorella vulgaris (Chlorellaceae). Unlike their Chlorella homolog, the three newly investigated chloroplast DNAs (cpDNAs) carry a large rRNA-encoding inverted repeat (IR) that divides the genome into large and small single-copy regions. In contrast to the situation found for ulvophycean and chlorophycean cpDNAs, the gene contents of the IR and single-copy regions are strikingly similar to that inferred for the common ancestor of chlorophytes and streptophytes. The intronless 98,340-bp Pedinomonas genome is among the chlorophyte cpDNAs featuring the smallest size and most ancestral gene organization. All 105 conserved genes encoded by this genome are included in the gene repertoires of Oocystis (111 genes) and Chlorella (113 genes), with just trnR(ccg) missing from Parachlorella cpDNA. Trees inferred from 71 cpDNA-encoded genes/proteins of 16 chlorophytes and nine streptophytes showed that Pedinomonas is nested in the Chlorellales, a group of algae lacking flagella. This phylogenetic conclusion is independently supported by uniquely shared gene linkages. We hypothesize that chlorellalean and pedinomonadalean green algae are reduced forms of a distant biflagellate ancestor that might have also given rise to the other known trebouxiophycean lineages. Our structural cpDNA data suggest that the Chlorellales and Pedinomonadales represent a deep branch of core chlorophytes, strengthening the notion that the Trebouxiophyceae emerged before the Ulvophyceae and Chlorophyceae. Our results further emphasize the importance of secondary reduction at both the cellular and genome levels during chlorophyte evolution.
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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 Chloroplast Genome Sequence of the Green Alga Pseudendoclonium akinetum (Ulvophyceae) Reveals Unusual Structural Features and New Insights into the Branching Order of Chlorophyte Lineages
Molecular biology and evolution, 2005Co-Authors: Jean-françois Pombert, Claude Lemieux, Christian Otis, Monique TurmelAbstract:One major lineage of green plants, the Chlorophyta, is represented by the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The Prasinophyceae occupies the most basal position in the Chlorophyta, but the branching order of the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae remains unresolved. The chloroplast genome sequences currently available for representatives of three chlorophyte classes have revealed that this genome is highly plastic, with Chlamydomonas (Chlorophyceae) and Chlorella (Trebouxiophyceae) showing fewer ancestral features than Nephroselmis (Prasinophyceae). We report the 195,867-bp chloroplast DNA (cpDNA) sequence of Pseudendoclonium akinetum (Ulvophyceae), a member of the class that has not been previously examined for detailed cpDNA analysis. This genome shares common evolutionary trends with its Chlorella and Chlamydomonas homologs. The gene content, number of ancestral gene clusters, and abundance of short dispersed repeats in Pseudendoclonium cpDNA are intermediate between those observed for Chlorella and Chlamydomonas cpDNAs. Although Pseudendoclonium cpDNA features a large inverted repeat, its quadripartite structure is unusual in displaying an rRNA operon transcribed toward the large single-copy (LSC) region and a small single-copy region containing 14 genes that are normally found in the LSC region. Twenty-seven group I introns lie in nine genes and fall within four subgroups (IA1, IA2, IA3, and IB); 19 encode putative homing endonucleases, and 7 have homologs at identical insertion sites in other chlorophyte or streptophyte organelle genomes. The high similarity observed among the 14 IA1 and 7 IA2 introns and their encoded endonucleases suggests that many introns arose from intragenomic proliferation of a few founding introns in the lineage leading to Pseudendoclonium. Interestingly, one intron (in atpA) and some of the dispersed repeats also reside in Pseudendoclonium mitochondria, providing strong evidence for interorganellar lateral transfer of these genetic elements. Phylogenetic analyses of 58 cpDNA-encoded proteins and genes support the hypothesis that the Ulvophyceae is sister to the Trebouxiophyceae but cannot eliminate the hypothesis that the Ulvophyceae is sister to the Chlorophyceae. We favor the latter hypothesis because it is strongly supported by phylogenetic analyses of gene order data and by independent structural evidence based on shared gene losses and rearrangement break points within ancestrally conserved gene clusters.
Monique Turmel - One of the best experts on this subject based on the ideXlab platform.
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evolution of the plastid genome in green algae
2018Co-Authors: Monique Turmel, Claude LemieuxAbstract:Abstract Comparative analyses of green algal plastid genomes (plastomes) have flourished in the past decade. In addition to improving our understanding of the phylogenetic relationships among green algal lineages, the expanded collection of plastome sequences has provided new insights into the ancestral architecture of this genome in the common ancestor of all green algae and into the changes that it underwent during lineage diversification in the two major divisions of the Viridiplantae (Chlorophyta and Streptophyta). The level of plastome diversity is much greater in the Chlorophyta than in the Streptophyta, with important variations seen at several levels—including genome size, presence/absence and size of the large inverted repeat encoding the rRNA operon, pattern of gene partitioning among single-copy regions, gene content, gene order, intron content, and amount of repetitive sequences—both within and across the main lineages of these two divisions. Here, we present an overview of the structural changes that sustained the plastome during the evolution of both chlorophyte and streptophyte algae. We begin by examining the range of variations observed at the above-mentioned levels in 112 chlorophyte taxa and then summarize what we learned for the Streptophyta based on the plastomes of 17 taxa. The chapter ends with a presentation of issues that need to be resolved in future studies.
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distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae scherffelia dubia and tetraselmis sp ccmp 881
PLOS ONE, 2016Co-Authors: Monique Turmel, Christian Otis, Jeancharles De Cambiaire, Claude LemieuxAbstract:The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.
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the chloroplast genomes of the green algae pedinomonas minor parachlorella kessleri and oocystis solitaria reveal a shared ancestry between the pedinomonadales and chlorellales
Molecular Biology and Evolution, 2009Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The green algae belonging to the Chlorophyta-the lineage sister to that comprising the land plants and their charophycean green algal relatives (Streptophyta)-have been subdivided into four classes (Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae). Yet the Pedinomonadales, an assemblage consisting of tiny, naked uniflagellates with a second basal body, has no clear affiliation with these classes and the branching order of the crown chlorophytes remains unknown. To gain an insight into the phylogenetic position of the Pedinomonadales and the relationships among the recognized chlorophyte classes, we have sequenced the chloroplast genomes of Pedinomonas minor (Pedinomonadales) and of two trebouxiophyceans belonging to the Chlorellales, Parachlorella kessleri (Chlorellaceae) and Oocystis solitaria (Oocystaceae), and compared these genomes with those of previously examined streptophytes and chlorophytes, including Chlorella vulgaris (Chlorellaceae). Unlike their Chlorella homolog, the three newly investigated chloroplast DNAs (cpDNAs) carry a large rRNA-encoding inverted repeat (IR) that divides the genome into large and small single-copy regions. In contrast to the situation found for ulvophycean and chlorophycean cpDNAs, the gene contents of the IR and single-copy regions are strikingly similar to that inferred for the common ancestor of chlorophytes and streptophytes. The intronless 98,340-bp Pedinomonas genome is among the chlorophyte cpDNAs featuring the smallest size and most ancestral gene organization. All 105 conserved genes encoded by this genome are included in the gene repertoires of Oocystis (111 genes) and Chlorella (113 genes), with just trnR(ccg) missing from Parachlorella cpDNA. Trees inferred from 71 cpDNA-encoded genes/proteins of 16 chlorophytes and nine streptophytes showed that Pedinomonas is nested in the Chlorellales, a group of algae lacking flagella. This phylogenetic conclusion is independently supported by uniquely shared gene linkages. We hypothesize that chlorellalean and pedinomonadalean green algae are reduced forms of a distant biflagellate ancestor that might have also given rise to the other known trebouxiophycean lineages. Our structural cpDNA data suggest that the Chlorellales and Pedinomonadales represent a deep branch of core chlorophytes, strengthening the notion that the Trebouxiophyceae emerged before the Ulvophyceae and Chlorophyceae. Our results further emphasize the importance of secondary reduction at both the cellular and genome levels during chlorophyte evolution.
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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 Chloroplast Genome Sequence of the Green Alga Pseudendoclonium akinetum (Ulvophyceae) Reveals Unusual Structural Features and New Insights into the Branching Order of Chlorophyte Lineages
Molecular biology and evolution, 2005Co-Authors: Jean-françois Pombert, Claude Lemieux, Christian Otis, Monique TurmelAbstract:One major lineage of green plants, the Chlorophyta, is represented by the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The Prasinophyceae occupies the most basal position in the Chlorophyta, but the branching order of the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae remains unresolved. The chloroplast genome sequences currently available for representatives of three chlorophyte classes have revealed that this genome is highly plastic, with Chlamydomonas (Chlorophyceae) and Chlorella (Trebouxiophyceae) showing fewer ancestral features than Nephroselmis (Prasinophyceae). We report the 195,867-bp chloroplast DNA (cpDNA) sequence of Pseudendoclonium akinetum (Ulvophyceae), a member of the class that has not been previously examined for detailed cpDNA analysis. This genome shares common evolutionary trends with its Chlorella and Chlamydomonas homologs. The gene content, number of ancestral gene clusters, and abundance of short dispersed repeats in Pseudendoclonium cpDNA are intermediate between those observed for Chlorella and Chlamydomonas cpDNAs. Although Pseudendoclonium cpDNA features a large inverted repeat, its quadripartite structure is unusual in displaying an rRNA operon transcribed toward the large single-copy (LSC) region and a small single-copy region containing 14 genes that are normally found in the LSC region. Twenty-seven group I introns lie in nine genes and fall within four subgroups (IA1, IA2, IA3, and IB); 19 encode putative homing endonucleases, and 7 have homologs at identical insertion sites in other chlorophyte or streptophyte organelle genomes. The high similarity observed among the 14 IA1 and 7 IA2 introns and their encoded endonucleases suggests that many introns arose from intragenomic proliferation of a few founding introns in the lineage leading to Pseudendoclonium. Interestingly, one intron (in atpA) and some of the dispersed repeats also reside in Pseudendoclonium mitochondria, providing strong evidence for interorganellar lateral transfer of these genetic elements. Phylogenetic analyses of 58 cpDNA-encoded proteins and genes support the hypothesis that the Ulvophyceae is sister to the Trebouxiophyceae but cannot eliminate the hypothesis that the Ulvophyceae is sister to the Chlorophyceae. We favor the latter hypothesis because it is strongly supported by phylogenetic analyses of gene order data and by independent structural evidence based on shared gene losses and rearrangement break points within ancestrally conserved gene clusters.
Christian Otis - One of the best experts on this subject based on the ideXlab platform.
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distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae scherffelia dubia and tetraselmis sp ccmp 881
PLOS ONE, 2016Co-Authors: Monique Turmel, Christian Otis, Jeancharles De Cambiaire, Claude LemieuxAbstract:The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.
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the chloroplast genomes of the green algae pedinomonas minor parachlorella kessleri and oocystis solitaria reveal a shared ancestry between the pedinomonadales and chlorellales
Molecular Biology and Evolution, 2009Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The green algae belonging to the Chlorophyta-the lineage sister to that comprising the land plants and their charophycean green algal relatives (Streptophyta)-have been subdivided into four classes (Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae). Yet the Pedinomonadales, an assemblage consisting of tiny, naked uniflagellates with a second basal body, has no clear affiliation with these classes and the branching order of the crown chlorophytes remains unknown. To gain an insight into the phylogenetic position of the Pedinomonadales and the relationships among the recognized chlorophyte classes, we have sequenced the chloroplast genomes of Pedinomonas minor (Pedinomonadales) and of two trebouxiophyceans belonging to the Chlorellales, Parachlorella kessleri (Chlorellaceae) and Oocystis solitaria (Oocystaceae), and compared these genomes with those of previously examined streptophytes and chlorophytes, including Chlorella vulgaris (Chlorellaceae). Unlike their Chlorella homolog, the three newly investigated chloroplast DNAs (cpDNAs) carry a large rRNA-encoding inverted repeat (IR) that divides the genome into large and small single-copy regions. In contrast to the situation found for ulvophycean and chlorophycean cpDNAs, the gene contents of the IR and single-copy regions are strikingly similar to that inferred for the common ancestor of chlorophytes and streptophytes. The intronless 98,340-bp Pedinomonas genome is among the chlorophyte cpDNAs featuring the smallest size and most ancestral gene organization. All 105 conserved genes encoded by this genome are included in the gene repertoires of Oocystis (111 genes) and Chlorella (113 genes), with just trnR(ccg) missing from Parachlorella cpDNA. Trees inferred from 71 cpDNA-encoded genes/proteins of 16 chlorophytes and nine streptophytes showed that Pedinomonas is nested in the Chlorellales, a group of algae lacking flagella. This phylogenetic conclusion is independently supported by uniquely shared gene linkages. We hypothesize that chlorellalean and pedinomonadalean green algae are reduced forms of a distant biflagellate ancestor that might have also given rise to the other known trebouxiophycean lineages. Our structural cpDNA data suggest that the Chlorellales and Pedinomonadales represent a deep branch of core chlorophytes, strengthening the notion that the Trebouxiophyceae emerged before the Ulvophyceae and Chlorophyceae. Our results further emphasize the importance of secondary reduction at both the cellular and genome levels during chlorophyte evolution.
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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 Chloroplast Genome Sequence of the Green Alga Pseudendoclonium akinetum (Ulvophyceae) Reveals Unusual Structural Features and New Insights into the Branching Order of Chlorophyte Lineages
Molecular biology and evolution, 2005Co-Authors: Jean-françois Pombert, Claude Lemieux, Christian Otis, Monique TurmelAbstract:One major lineage of green plants, the Chlorophyta, is represented by the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The Prasinophyceae occupies the most basal position in the Chlorophyta, but the branching order of the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae remains unresolved. The chloroplast genome sequences currently available for representatives of three chlorophyte classes have revealed that this genome is highly plastic, with Chlamydomonas (Chlorophyceae) and Chlorella (Trebouxiophyceae) showing fewer ancestral features than Nephroselmis (Prasinophyceae). We report the 195,867-bp chloroplast DNA (cpDNA) sequence of Pseudendoclonium akinetum (Ulvophyceae), a member of the class that has not been previously examined for detailed cpDNA analysis. This genome shares common evolutionary trends with its Chlorella and Chlamydomonas homologs. The gene content, number of ancestral gene clusters, and abundance of short dispersed repeats in Pseudendoclonium cpDNA are intermediate between those observed for Chlorella and Chlamydomonas cpDNAs. Although Pseudendoclonium cpDNA features a large inverted repeat, its quadripartite structure is unusual in displaying an rRNA operon transcribed toward the large single-copy (LSC) region and a small single-copy region containing 14 genes that are normally found in the LSC region. Twenty-seven group I introns lie in nine genes and fall within four subgroups (IA1, IA2, IA3, and IB); 19 encode putative homing endonucleases, and 7 have homologs at identical insertion sites in other chlorophyte or streptophyte organelle genomes. The high similarity observed among the 14 IA1 and 7 IA2 introns and their encoded endonucleases suggests that many introns arose from intragenomic proliferation of a few founding introns in the lineage leading to Pseudendoclonium. Interestingly, one intron (in atpA) and some of the dispersed repeats also reside in Pseudendoclonium mitochondria, providing strong evidence for interorganellar lateral transfer of these genetic elements. Phylogenetic analyses of 58 cpDNA-encoded proteins and genes support the hypothesis that the Ulvophyceae is sister to the Trebouxiophyceae but cannot eliminate the hypothesis that the Ulvophyceae is sister to the Chlorophyceae. We favor the latter hypothesis because it is strongly supported by phylogenetic analyses of gene order data and by independent structural evidence based on shared gene losses and rearrangement break points within ancestrally conserved gene clusters.
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The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes
Proceedings of the National Academy of Sciences of the United States of America, 1999Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Green plants seem to form two sister lineages: Chlorophyta, comprising the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae, and Streptophyta, comprising the Charophyceae and land plants. We have determined the complete chloroplast DNA (cpDNA) sequence (200,799 bp) of Nephroselmis olivacea, a member of the class (Prasinophyceae) thought to include descendants of the earliest-diverging green algae. The 127 genes identified in this genome represent the largest gene repertoire among the green algal and land plant cpDNAs completely sequenced to date. Of the Nephroselmis genes, 2 (ycf81 and ftsI, a gene involved in peptidoglycan synthesis) have not been identified in any previously investigated cpDNA; 5 genes [ftsW, rnE, ycf62, rnpB, and trnS(cga)] have been found only in cpDNAs of nongreen algae; and 10 others (ndh genes) have been described only in land plant cpDNAs. Nephroselmis and land plant cpDNAs share the same quadripartite structure—which is characterized by the presence of a large rRNA-encoding inverted repeat and two unequal single-copy regions—and very similar sets of genes in corresponding genomic regions. Given that our phylogenetic analyses place Nephroselmis within the Chlorophyta, these structural characteristics were most likely present in the cpDNA of the common ancestor of chlorophytes and streptophytes. Comparative analyses of chloroplast genomes indicate that the typical quadripartite architecture and gene-partitioning pattern of land plant cpDNAs are ancient features that may have been derived from the genome of the cyanobacterial progenitor of chloroplasts. Our phylogenetic data also offer insight into the chlorophyte ancestor of euglenophyte chloroplasts.
Okolodkov, Yuri B. - One of the best experts on this subject based on the ideXlab platform.
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New records of green (Chlorophyta) and brown algae (Phaeophyceae) for cabezo reef, national park sistema arrecifal veracruzano, gulf of mexico
'Instituto de Ecologia A.C.', 2012Co-Authors: Robinson, Néstor M., Galicia García Citlalli, Okolodkov, Yuri B.Abstract:Descriptions of 13 green and 12 brown algal species from 20 genera and 15 families collected on Cabezo Reef of the National Park Sistema Arrecifal Veracruzano in the southwestern Gulf of Mexico, which are new records for the reef, are given. The species belong to the chlorophyte genera Caulerpa, Cladophoropsis, Codium, Dictyosphaeria, Ernodesmis, Halimeda, Neomeris, Parvocaulis, Percursaria and Rhipocephalus and the phaeophycean genera Canistrocarpus, Colpomenia, Cladosiphon, Dictyerpa, Dictyota, Ectocarpus, Padina, Rosenvingea, Sargassum and Sphacelaria. The family Dictyotaceae contained the largest number of species (6). The descriptions include morphometric and biological data and are accompanied by photographs and line drawings for each species. Data on the geographic distribution in the State of Veracruz, park and the Gulf of Mexico in general are also given. Percursaria percursa is a new record for the park, while Dictyerpa jamaicensis, Sargassum furcatum, Caulerpa racemosa var. occidentalis and Codium isthmocladum subsp. clavatum are new records for the State of Veracruz. Most of the specimens of Chlorophyta were found in the vegetative stage, whereas all the brown algal species except Dictyerpa jamaicensis and Sphacelaria rigidula possessed gametangia or sporangia.Se presentan las descripciones de 13 especies de algas verdes y 12 de algas pardas de 20 géneros y 15 familias, que son nuevos registros para el arrecife Cabezo ubicado en la parte sureste del Parque Nacional Sistema Arrecifal Veracruzano en el suroeste del Golfo de México. Las especies pertenecen a los géneros de clorofitas Caulerpa, Cladophoropsis, Codium, Dictyosphaeria, Ernodesmis, Halimeda, Neomeris, Parvocaulis, Percursaria y Rhipocephalus, y los géneros de algas pardas Canistrocarpus, Colpomenia, Cladosiphon, Dictyerpa, Dictyota, Ectocarpus, Padina, Rosenvingea, Sargassum y Sphacelaria. La familia Dictyotaceae fue la mejor representada en cuanto al número de especies (6). Las descripciones incluyen datos morfométricos y biológicos y están acompañadas con fotografías y dibujos a línea para cada especie. También se presenta la información sobre la distribución de las especies en el estado de Veracruz, el parque y el Golfo de México en general. Percursaria percursa es un nuevo registro para el parque, mientras Dictyerpa jamaicensis, Sargassum furcatum, Caulerpa racemosa var. occidentalis y Codium isthmocladum subsp. clavatum lo son para el estado de Veracruz. La mayor proporción de ejemplares pertenecientes a Chlorophyta se encontraron en estado vegetativo, mientras que los especímenes de algas pardas excluyendo a las especies Dictyerpa jamaicensis y Sphacelaria rigidula, se encontraron ya sea con gametangios o esporangios
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New Records of green (Chlorophyta) and brown algae (Phaeophyta) for Cabezo Reef, National Park Sistema Arrecifal Veracruzano, Gulf of Mexico
'Instituto de Ecologia A.C.', 2012Co-Authors: Robinson, Néstor M., Galicia García Citlalli, Okolodkov, Yuri B.Abstract:Descriptions of 13 green and 12 brown algal species from 20 genera and 15 families collected on Cabezo Reef of the National Park Sistema Arrecifal Veracruzano in the southwestern Gulf of Mexico, which are new records for the reef, are given. The species belong to the chlorophyte genera Caulerpa, Cladophoropsis, Codium, Dictyosphaeria, Ernodesmis, Halimeda, Neomeris, Parvocaulis, Percursaria and Rhipocephalus and the phaeophycean generaCanistrocarpus, Colpomenia, Cladosiphon, Dictyerpa, Dictyota, Ectocarpus, Padina, Rosenvingea, Sargassum and Sphacelaria. The family Dictyotaceae contained the largest number of species (6). The descriptions include morphometric and biological data and are accompanied by photographs and line drawings for each species. Data on the geographic distribution in the State of Veracruz, park and the Gulf of Mexico in general are also given.Percursaria percursa is a new record for the park, while Dictyerpa jamaicensis, Sargassum furcatum, Caulerpa racemosa var. occidentalis and Codium isthmocladum subsp.clavatum are new records for the State of Veracruz. Most of the specimens of Chlorophyta were found in the vegetative stage, whereas all the brown algal species except Dictyerpa jamaicensis and Sphacelaria rigidula possessed gametangia or sporangia.Se presentan las descripciones de 13 especies de algas verdes y 12 de algas pardas de 20 géneros y 15 familias, que son nuevos registros para el arrecife Cabezo ubicado en la parte sureste del Parque Nacional Sistema Arrecifal Veracruzano en el suroeste del Golfo de México. Las especies pertenecen a los géneros de clorofitas Caulerpa, Cladophoropsis, Codium, Dictyosphaeria, Ernodesmis, Halimeda, Neomeris, Parvocaulis, Percursaria yRhipocephalus, y los géneros de algas pardas Canistrocarpus, Colpomenia, Cladosiphon, Dictyerpa, Dictyota, Ectocarpus, Padina, Rosenvingea, Sargassum y Sphacelaria. La familia Dictyotaceae fue la mejor representada en cuanto al número de especies (6). Las descripciones incluyen datos morfométricos y biológicos y están acompañadas con fotografías y dibujos a línea para cada especie. También se presenta la información sobre la distribución de las especies en el estado de Veracruz, el parque y el Golfo de México en general. Percursaria percursa es un nuevo registro para el parque, mientras Dictyerpa jamaicensis, Sargassum furcatum, Caulerpa racemosa var. occidentalis y Codium isthmocladum subsp. clavatumlo son para el estado de Veracruz. La mayor proporción de ejemplares pertenecientes a Chlorophyta se encontraron en estado vegetativo, mientras que los especímenes de algas pardas excluyendo a las especies Dictyerpa jamaicensis y Sphacelaria rigidula, se encontraron ya sea con gametangios o esporangios
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Flora ficologica da plataforma continental do litoral setentrional da bacia potiguar (RN), Brasil, com ênfase em Chlorophyta
Universidade Federal de Pernambuco, 2009Co-Authors: De Lourdes Montenegro Cocentino AdilmaAbstract:Foram estudadas as macroalgas marinhas bentônicas de um habitat pouco explorado (Bacia Potiguar, Rio Grande do Norte, Nordeste do Brasil) e cuja informação florística é rara, para se conhecer a diversidade taxonômica e padrões de distribuição em um infralitoral tropical, onde vários empreendimentos estão em fase de instalação, sendo enfatizadas as Chlorophyta, como indicadoras da qualidade ambiental. Amostragens de macroalgas bentônicas foram feitas, com dois tipos de dragas e uma rede de arrasto do tipo porta, durante quatro campanhas: julho de 2002, maio e novembro de 2003 e maio de 2004, em 43 estações. Foram identificados 196 táxons de macroalgas (incluindo variedades e formas), distribuídos nos filos Chlorophyta (29%), Ochrophyta (17%) e Rhodophyta (54%). Três espécies de Rhodophyta, Halopthys schottii (W. R. Taylor) L.E. Philips & De Clerck (63,9%), Bryothamnion seaforthii (Turner) Kütz. (62,5%), Osmundaria obtusiloba (C. Agardh) R. E. Norris (47,2%) e uma Ochrophyta, Dictyopteris delicatula J. V. Lamour. ( 43,1%) foram classificadas como as mais frequentes na área. Os táxons pouco frequentes (frequência de ocorrência entre 11,1% e 34,7%) distribuíram-se em 19 Rhodophyta, oito Ochrophyta e duas Chlorophyta. Na categoria dos táxons de frequência de ocorrência esporádica com menos de 10%, foram identificadas 39 espécies de Rhodophyta, e Chlorophyta e 16 Ochrophyta. Chlorophyta esteve representado por 54 táxons. A família mais frequente foi Caulerpaceae, e o gênero mais diversificado foi Caulerpa J. V. Lamour., com 11 espécies. Do total dos táxons identificados, uma espécie de Rhodophyta, Palisada poiteaui (J. V. Lamour.) K. W. Nam var. gemmifera (Harvey) Sentíes, M. T. Fujii & Díaz teve a sua ocorrência confirmada para o litoral brasileiro e 14 espécies estão sendo citadas pela primeira vez para o litoral Potiguar, sendo sete Rhodophyta: Ptilothamnion speluncarum (Collins & Herv.) D. L. Ballant., Ceramium brasiliense A. B. Joly, C. COCENTINO, A. L. M. Flora Ficológica da Plataforma Continental do Litoral Setentrional... 16 comptum Børgesen, C. flaccidum (Kütz.) Ardiss., C. nitens (C. Agardh.) J. Agardh., Chodrophycus furcatus (Cord. - Mar. & M. T. Fujii) M. T. Fujii & Sentíes, Wrightiella tumanowiczii (Gatty ex Harv.) F. Schmitz; três espécies de Chlorophyta: Cladophora coelothrix Kütz., Caulerpella ambígua (Okamura) Prud homme & Lokhorst, Halimeda simulans M. Howe; e cinco espécies de Ochrophyta: Dictyota bartayresiana J. V. Lamour., D. pulchella Hörnig & Schenetter, Ralfisia expansa (J. Agardh.) J. Agardh, Padina sanctae-crucis Børgesen e P. boergesenii Allender & Kraft. Dentre as Chlorophyta a espécie mais frequente foi Caulerpa prolifera (Forsskål) J. V. Lamour., ocorrendo em quase todas as estações da plataforma costeira e interna, durante todas as campanhas. A distribuição das espécies de Chlorophyta por profundidade mostrou que o maior número de táxons ocorreu entre 10 e 20m, e uma ampla distribuição vertical foi registrada para Anadyomene stellata (Wulfen in Jacq.) C. Agardh, Chamaedoris peniculum (J. Ellis & Solander) Kuntze, Codium isthmocladum Vickers, Microdictyon vanbosseae Setch., Udotea occidentalis A. Gepp & E. Gepp e Ventricaria ventricosa (J. Agardh) J. L. Olsen & J. A. West. Das amostras coletadas por draga nas quatro faixas de profundidade, o transecto T3 (faixa de 20 a 50m) apresentou o maior número de espécies (114 táxons), seguida por T2 (10 a 20m) com 111 táxons. Em geral, Rhodophyta apresentou uma maior distribuição em relação às diversas profundidades, principalmente as algas calcárias não articuladas, com 29% de frequência de ocorrência. Padrão sazonal na comunidade das macroalgas não foi observado em nenhuma das quatro campanhas realizadas. Apesar das atividades petrolíferas que ocorrem na área não foram observadas espécies consideradas bioindicadoras de alterações ambientais com frequências significativasUniversidade Federal de Pernambuc
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Flora ficologica da plataforma continental do litoral setentrional da bacia potiguar (RN), Brasil, com ênfase em Chlorophyta
Universidade Federal de Pernambuco, 2009Co-Authors: De Lourdes Montenegro Cocentino AdilmaAbstract:Foram estudadas as macroalgas marinhas bentônicas de um habitat pouco explorado (Bacia Potiguar, Rio Grande do Norte, Nordeste do Brasil) e cuja informação florística é rara, para se conhecer a diversidade taxonômica e padrões de distribuição em um infralitoral tropical, onde vários empreendimentos estão em fase de instalação, sendo enfatizadas as Chlorophyta, como indicadoras da qualidade ambiental. Amostragens de macroalgas bentônicas foram feitas, com dois tipos de dragas e uma rede de arrasto do tipo porta, durante quatro campanhas: julho de 2002, maio e novembro de 2003 e maio de 2004, em 43 estações. Foram identificados 196 táxons de macroalgas (incluindo variedades e formas), distribuídos nos filos Chlorophyta (29%), Ochrophyta (17%) e Rhodophyta (54%). Três espécies de Rhodophyta, Halopthys schottii (W. R. Taylor) L.E. Philips & De Clerck (63,9%), Bryothamnion seaforthii (Turner) Kütz. (62,5%), Osmundaria obtusiloba (C. Agardh) R. E. Norris (47,2%) e uma Ochrophyta, Dictyopteris delicatula J. V. Lamour. ( 43,1%) foram classificadas como as mais frequentes na área. Os táxons pouco frequentes (frequência de ocorrência entre 11,1% e 34,7%) distribuíram-se em 19 Rhodophyta, oito Ochrophyta e duas Chlorophyta. Na categoria dos táxons de frequência de ocorrência esporádica com menos de 10%, foram identificadas 39 espécies de Rhodophyta, e Chlorophyta e 16 Ochrophyta. Chlorophyta esteve representado por 54 táxons. A família mais frequente foi Caulerpaceae, e o gênero mais diversificado foi Caulerpa J. V. Lamour., com 11 espécies. Do total dos táxons identificados, uma espécie de Rhodophyta, Palisada poiteaui (J. V. Lamour.) K. W. Nam var. gemmifera (Harvey) Sentíes, M. T. Fujii & Díaz teve a sua ocorrência confirmada para o litoral brasileiro e 14 espécies estão sendo citadas pela primeira vez para o litoral Potiguar, sendo sete Rhodophyta: Ptilothamnion speluncarum (Collins & Herv.) D. L. Ballant., Ceramium brasiliense A. B. Joly, C. COCENTINO, A. L. M. Flora Ficológica da Plataforma Continental do Litoral Setentrional... 16 comptum Børgesen, C. flaccidum (Kütz.) Ardiss., C. nitens (C. Agardh.) J. Agardh., Chodrophycus furcatus (Cord. - Mar. & M. T. Fujii) M. T. Fujii & Sentíes, Wrightiella tumanowiczii (Gatty ex Harv.) F. Schmitz; três espécies de Chlorophyta: Cladophora coelothrix Kütz., Caulerpella ambígua (Okamura) Prud homme & Lokhorst, Halimeda simulans M. Howe; e cinco espécies de Ochrophyta: Dictyota bartayresiana J. V. Lamour., D. pulchella Hörnig & Schenetter, Ralfisia expansa (J. Agardh.) J. Agardh, Padina sanctae-crucis Børgesen e P. boergesenii Allender & Kraft. Dentre as Chlorophyta a espécie mais frequente foi Caulerpa prolifera (Forsskål) J. V. Lamour., ocorrendo em quase todas as estações da plataforma costeira e interna, durante todas as campanhas. A distribuição das espécies de Chlorophyta por profundidade mostrou que o maior número de táxons ocorreu entre 10 e 20m, e uma ampla distribuição vertical foi registrada para Anadyomene stellata (Wulfen in Jacq.) C. Agardh, Chamaedoris peniculum (J. Ellis & Solander) Kuntze, Codium isthmocladum Vickers, Microdictyon vanbosseae Setch., Udotea occidentalis A. Gepp & E. Gepp e Ventricaria ventricosa (J. Agardh) J. L. Olsen & J. A. West. Das amostras coletadas por draga nas quatro faixas de profundidade, o transecto T3 (faixa de 20 a 50m) apresentou o maior número de espécies (114 táxons), seguida por T2 (10 a 20m) com 111 táxons. Em geral, Rhodophyta apresentou uma maior distribuição em relação às diversas profundidades, principalmente as algas calcárias não articuladas, com 29% de frequência de ocorrência. Padrão sazonal na comunidade das macroalgas não foi observado em nenhuma das quatro campanhas realizadas. Apesar das atividades petrolíferas que ocorrem na área não foram observadas espécies consideradas bioindicadoras de alterações ambientais com frequências significativa