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Claude Lemieux - One of the best experts on this subject based on the ideXlab platform.
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Complete mitogenome of the streptophyte green alga Coleochaete scutata (Coleochaetophyceae)
Mitochondrial DNA. Part B Resources, 2019Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:We have sequenced the mitogenome of Coleochaete scutata strain SAG 110.80M. This mitogenome is the largest among the streptophyte green algae examined to date. At 242,024 bp, it is 4.3-fold larger than the mitogenome of Chaetosphaeridium globosum, the only other mitogenome available for the Coleochaetophyceae. This size difference is mainly explained by differences in the abundance of introns and in the length of intergenic regions containing vestiges of coding sequences thought to be of foreign origin. With 31 group I and 26 group II introns, the C. scutata mitogenome is the most intron-rich organelle genome known among streptophyte algae.
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Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae
Frontiers in plant science, 2016Co-Authors: Claude Lemieux, Christian Otis, Monique TurmelAbstract:The Streptophyta comprises all land plants and six main lineages of freshwater green algae: Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Charophyceae, Coleochaetophyceae and Zygnematophyceae. Previous comparisons of the chloroplast genome from nine streptophyte algae (including four zygnematophyceans) revealed that, although land plant chloroplast DNAs (cpDNAs) inherited most of their highly conserved structural features from green algal ancestors, considerable cpDNA changes took place during the evolution of the Zygnematophyceae, the sister group of land plants. To gain deeper insights into the evolutionary dynamics of the chloroplast genome in streptophyte algae, we sequenced the cpDNAs of nine additional taxa: two klebsormidiophyceans (Entransia fimbriata and Klebsormidium sp. SAG 51.86), one coleocheatophycean (Coleochaete scutata) and six zygnematophyceans (Cylindrocystis brebissonii, Netrium digitus, Roya obtusa, Spirogyra maxima, Cosmarium botrytis and Closterium baillyanum). Our comparative analyses of these genomes with their streptophyte algal counterparts indicate that the large inverted repeat (IR) encoding the rDNA operon experienced loss or expansion/contraction in all three sampled classes and that genes were extensively shuffled in both the Klebsormidiophyceae and Zygnematophyceae. The klebsormidiophycean genomes boast greatly expanded IRs, with the Entransia 60,590-bp IR being the largest known among green algae. The 206,025-bp Entransia cpDNA, which is one of the largest genome among streptopytes, encodes 118 standard genes, i.e. four additional genes compared to its Klebsormidium flaccidum homolog. We inferred that seven of the 21 group II introns usually found in land plants were already present in the common ancestor of the Klebsormidiophyceae and its sister lineages. At 107,236 bp and with 117 standard genes, the Coleochaete IR-less genome is both the smallest and most compact among the streptophyte algal cpDNAs analyzed thus far; it lacks eight genes relative to its Chaetosphaeridium globosum homolog, four of which represent unique events in the evolutionary scenario of gene losses we reconstructed for streptophyte algae. The ten compared zygnematophycean cpDNAs display tremendous variations at all levels, except gene content. During zygnematophycean evolution, the IR disappeared a minimum of five times, the rDNA operon was broken at four distinct sites, group II introns were lost on at least 43 occasions, and putative foreign genes, mainly of phage/viral origin, were gained.
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An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus
BMC Genomics, 2007Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens . Results The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL (gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara , Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma , due to analytical problems arising from accelerated sequence evolution in this lineage. Conclusion The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.
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An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus
BMC genomics, 2007Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens. The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL(gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara, Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma, due to analytical problems arising from accelerated sequence evolution in this lineage. The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.
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The Chloroplast Genome Sequence of Chara vulgaris Sheds New Light into the Closest Green Algal Relatives of Land Plants
Molecular Biology and Evolution, 2006Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:: The phylum Streptophyta comprises all land plants and six monophyletic groups of charophycean green algae (Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales, and Charales). Phylogenetic analyses of four genes encoded in three cellular compartments suggest that the Charales are sister to land plants and that charophycean green algae evolved progressively toward an increasing cellular complexity. To validate this phylogenetic hypothesis and to understand how and when the highly conservative pattern displayed by land plant chloroplast DNAs (cpDNAs) originated in the Streptophyta, we have determined the complete chloroplast genome sequence (184,933 bp) of a representative of the Charales, Chara vulgaris, and compared this genome to those of Mesostigma (Mesostigmatales), Chlorokybus (Chlorokybales), Staurastrum and Zygnema (Zygnematales), Chaetosphaeridium (Coleochaetales), and selected land plants. The phylogenies we inferred from 76 cpDNA-encoded proteins and genes using various methods favor the hypothesis that the Charales diverged before the Coleochaetales and Zygnematales. The Zygnematales were identified as sister to land plants in the best tree topology (T1), whereas Chaetosphaeridium (T2) or a clade uniting the Zygnematales and Chaetosphaeridium (T3) occupied this position in alternative topologies. Chara remained at the same basal position in trees including more land plant taxa and inferred from 56 proteins/genes. Phylogenetic inference from gene order data yielded two most parsimonious trees displaying the T1 and T3 topologies. Analyses of additional structural cpDNA features (gene order, gene content, intron content, and indels in coding regions) provided better support for T1 than for the topology of the above-mentioned four-gene tree. Our structural analyses also revealed that many of the features conserved in land plant cpDNAs were inherited from their green algal ancestors. The intron content data predicted that at least 15 of the 21 land plant group II introns were gained early during the evolution of streptophytes and that a single intron was acquired during the transition from charophycean green algae to land plants. Analyses of genome rearrangements based on inversions predicted no alteration in gene order during the transition from charophycean green algae to land plants.
Monique Turmel - One of the best experts on this subject based on the ideXlab platform.
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Complete mitogenome of the streptophyte green alga Coleochaete scutata (Coleochaetophyceae)
Mitochondrial DNA. Part B Resources, 2019Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:We have sequenced the mitogenome of Coleochaete scutata strain SAG 110.80M. This mitogenome is the largest among the streptophyte green algae examined to date. At 242,024 bp, it is 4.3-fold larger than the mitogenome of Chaetosphaeridium globosum, the only other mitogenome available for the Coleochaetophyceae. This size difference is mainly explained by differences in the abundance of introns and in the length of intergenic regions containing vestiges of coding sequences thought to be of foreign origin. With 31 group I and 26 group II introns, the C. scutata mitogenome is the most intron-rich organelle genome known among streptophyte algae.
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Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae
Frontiers in plant science, 2016Co-Authors: Claude Lemieux, Christian Otis, Monique TurmelAbstract:The Streptophyta comprises all land plants and six main lineages of freshwater green algae: Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Charophyceae, Coleochaetophyceae and Zygnematophyceae. Previous comparisons of the chloroplast genome from nine streptophyte algae (including four zygnematophyceans) revealed that, although land plant chloroplast DNAs (cpDNAs) inherited most of their highly conserved structural features from green algal ancestors, considerable cpDNA changes took place during the evolution of the Zygnematophyceae, the sister group of land plants. To gain deeper insights into the evolutionary dynamics of the chloroplast genome in streptophyte algae, we sequenced the cpDNAs of nine additional taxa: two klebsormidiophyceans (Entransia fimbriata and Klebsormidium sp. SAG 51.86), one coleocheatophycean (Coleochaete scutata) and six zygnematophyceans (Cylindrocystis brebissonii, Netrium digitus, Roya obtusa, Spirogyra maxima, Cosmarium botrytis and Closterium baillyanum). Our comparative analyses of these genomes with their streptophyte algal counterparts indicate that the large inverted repeat (IR) encoding the rDNA operon experienced loss or expansion/contraction in all three sampled classes and that genes were extensively shuffled in both the Klebsormidiophyceae and Zygnematophyceae. The klebsormidiophycean genomes boast greatly expanded IRs, with the Entransia 60,590-bp IR being the largest known among green algae. The 206,025-bp Entransia cpDNA, which is one of the largest genome among streptopytes, encodes 118 standard genes, i.e. four additional genes compared to its Klebsormidium flaccidum homolog. We inferred that seven of the 21 group II introns usually found in land plants were already present in the common ancestor of the Klebsormidiophyceae and its sister lineages. At 107,236 bp and with 117 standard genes, the Coleochaete IR-less genome is both the smallest and most compact among the streptophyte algal cpDNAs analyzed thus far; it lacks eight genes relative to its Chaetosphaeridium globosum homolog, four of which represent unique events in the evolutionary scenario of gene losses we reconstructed for streptophyte algae. The ten compared zygnematophycean cpDNAs display tremendous variations at all levels, except gene content. During zygnematophycean evolution, the IR disappeared a minimum of five times, the rDNA operon was broken at four distinct sites, group II introns were lost on at least 43 occasions, and putative foreign genes, mainly of phage/viral origin, were gained.
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An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus
BMC Genomics, 2007Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens . Results The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL (gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara , Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma , due to analytical problems arising from accelerated sequence evolution in this lineage. Conclusion The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.
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An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus
BMC genomics, 2007Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens. The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL(gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara, Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma, due to analytical problems arising from accelerated sequence evolution in this lineage. The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.
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The Chloroplast Genome Sequence of Chara vulgaris Sheds New Light into the Closest Green Algal Relatives of Land Plants
Molecular Biology and Evolution, 2006Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:: The phylum Streptophyta comprises all land plants and six monophyletic groups of charophycean green algae (Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales, and Charales). Phylogenetic analyses of four genes encoded in three cellular compartments suggest that the Charales are sister to land plants and that charophycean green algae evolved progressively toward an increasing cellular complexity. To validate this phylogenetic hypothesis and to understand how and when the highly conservative pattern displayed by land plant chloroplast DNAs (cpDNAs) originated in the Streptophyta, we have determined the complete chloroplast genome sequence (184,933 bp) of a representative of the Charales, Chara vulgaris, and compared this genome to those of Mesostigma (Mesostigmatales), Chlorokybus (Chlorokybales), Staurastrum and Zygnema (Zygnematales), Chaetosphaeridium (Coleochaetales), and selected land plants. The phylogenies we inferred from 76 cpDNA-encoded proteins and genes using various methods favor the hypothesis that the Charales diverged before the Coleochaetales and Zygnematales. The Zygnematales were identified as sister to land plants in the best tree topology (T1), whereas Chaetosphaeridium (T2) or a clade uniting the Zygnematales and Chaetosphaeridium (T3) occupied this position in alternative topologies. Chara remained at the same basal position in trees including more land plant taxa and inferred from 56 proteins/genes. Phylogenetic inference from gene order data yielded two most parsimonious trees displaying the T1 and T3 topologies. Analyses of additional structural cpDNA features (gene order, gene content, intron content, and indels in coding regions) provided better support for T1 than for the topology of the above-mentioned four-gene tree. Our structural analyses also revealed that many of the features conserved in land plant cpDNAs were inherited from their green algal ancestors. The intron content data predicted that at least 15 of the 21 land plant group II introns were gained early during the evolution of streptophytes and that a single intron was acquired during the transition from charophycean green algae to land plants. Analyses of genome rearrangements based on inversions predicted no alteration in gene order during the transition from charophycean green algae to land plants.
Christian Otis - One of the best experts on this subject based on the ideXlab platform.
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Complete mitogenome of the streptophyte green alga Coleochaete scutata (Coleochaetophyceae)
Mitochondrial DNA. Part B Resources, 2019Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:We have sequenced the mitogenome of Coleochaete scutata strain SAG 110.80M. This mitogenome is the largest among the streptophyte green algae examined to date. At 242,024 bp, it is 4.3-fold larger than the mitogenome of Chaetosphaeridium globosum, the only other mitogenome available for the Coleochaetophyceae. This size difference is mainly explained by differences in the abundance of introns and in the length of intergenic regions containing vestiges of coding sequences thought to be of foreign origin. With 31 group I and 26 group II introns, the C. scutata mitogenome is the most intron-rich organelle genome known among streptophyte algae.
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Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae
Frontiers in plant science, 2016Co-Authors: Claude Lemieux, Christian Otis, Monique TurmelAbstract:The Streptophyta comprises all land plants and six main lineages of freshwater green algae: Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Charophyceae, Coleochaetophyceae and Zygnematophyceae. Previous comparisons of the chloroplast genome from nine streptophyte algae (including four zygnematophyceans) revealed that, although land plant chloroplast DNAs (cpDNAs) inherited most of their highly conserved structural features from green algal ancestors, considerable cpDNA changes took place during the evolution of the Zygnematophyceae, the sister group of land plants. To gain deeper insights into the evolutionary dynamics of the chloroplast genome in streptophyte algae, we sequenced the cpDNAs of nine additional taxa: two klebsormidiophyceans (Entransia fimbriata and Klebsormidium sp. SAG 51.86), one coleocheatophycean (Coleochaete scutata) and six zygnematophyceans (Cylindrocystis brebissonii, Netrium digitus, Roya obtusa, Spirogyra maxima, Cosmarium botrytis and Closterium baillyanum). Our comparative analyses of these genomes with their streptophyte algal counterparts indicate that the large inverted repeat (IR) encoding the rDNA operon experienced loss or expansion/contraction in all three sampled classes and that genes were extensively shuffled in both the Klebsormidiophyceae and Zygnematophyceae. The klebsormidiophycean genomes boast greatly expanded IRs, with the Entransia 60,590-bp IR being the largest known among green algae. The 206,025-bp Entransia cpDNA, which is one of the largest genome among streptopytes, encodes 118 standard genes, i.e. four additional genes compared to its Klebsormidium flaccidum homolog. We inferred that seven of the 21 group II introns usually found in land plants were already present in the common ancestor of the Klebsormidiophyceae and its sister lineages. At 107,236 bp and with 117 standard genes, the Coleochaete IR-less genome is both the smallest and most compact among the streptophyte algal cpDNAs analyzed thus far; it lacks eight genes relative to its Chaetosphaeridium globosum homolog, four of which represent unique events in the evolutionary scenario of gene losses we reconstructed for streptophyte algae. The ten compared zygnematophycean cpDNAs display tremendous variations at all levels, except gene content. During zygnematophycean evolution, the IR disappeared a minimum of five times, the rDNA operon was broken at four distinct sites, group II introns were lost on at least 43 occasions, and putative foreign genes, mainly of phage/viral origin, were gained.
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An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus
BMC Genomics, 2007Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens . Results The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL (gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara , Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma , due to analytical problems arising from accelerated sequence evolution in this lineage. Conclusion The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.
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An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus
BMC genomics, 2007Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:The Streptophyta comprises all land plants and six groups of charophycean green algae. The scaly biflagellate Mesostigma viride (Mesostigmatales) and the sarcinoid Chlorokybus atmophyticus (Chlorokybales) represent the earliest diverging lineages of this phylum. In trees based on chloroplast genome data, these two charophycean green algae are nested in the same clade. To validate this relationship and gain insight into the ancestral state of the mitochondrial genome in the Charophyceae, we sequenced the mitochondrial DNA (mtDNA) of Chlorokybus and compared this genome sequence with those of three other charophycean green algae and the bryophytes Marchantia polymorpha and Physcomitrella patens. The Chlorokybus genome differs radically from its 42,424-bp Mesostigma counterpart in size, gene order, intron content and density of repeated elements. At 201,763-bp, it is the largest mtDNA yet reported for a green alga. The 70 conserved genes represent 41.4% of the genome sequence and include nad10 and trnL(gag), two genes reported for the first time in a streptophyte mtDNA. At the gene order level, the Chlorokybus genome shares with its Chara, Chaetosphaeridium and bryophyte homologues eight to ten gene clusters including about 20 genes. Notably, some of these clusters exhibit gene linkages not previously found outside the Streptophyta, suggesting that they originated early during streptophyte evolution. In addition to six group I and 14 group II introns, short repeated sequences accounting for 7.5% of the genome were identified. Mitochondrial trees were unable to resolve the correct position of Mesostigma, due to analytical problems arising from accelerated sequence evolution in this lineage. The Chlorokybus and Mesostigma mtDNAs exemplify the marked fluidity of the mitochondrial genome in charophycean green algae. The notion that the mitochondrial genome was constrained to remain compact during charophycean evolution is no longer tenable. Our data raise the possibility that the emergence of land plants was not associated with a substantial gain of intergenic sequences by the mitochondrial genome.
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The Chloroplast Genome Sequence of Chara vulgaris Sheds New Light into the Closest Green Algal Relatives of Land Plants
Molecular Biology and Evolution, 2006Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:: The phylum Streptophyta comprises all land plants and six monophyletic groups of charophycean green algae (Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales, and Charales). Phylogenetic analyses of four genes encoded in three cellular compartments suggest that the Charales are sister to land plants and that charophycean green algae evolved progressively toward an increasing cellular complexity. To validate this phylogenetic hypothesis and to understand how and when the highly conservative pattern displayed by land plant chloroplast DNAs (cpDNAs) originated in the Streptophyta, we have determined the complete chloroplast genome sequence (184,933 bp) of a representative of the Charales, Chara vulgaris, and compared this genome to those of Mesostigma (Mesostigmatales), Chlorokybus (Chlorokybales), Staurastrum and Zygnema (Zygnematales), Chaetosphaeridium (Coleochaetales), and selected land plants. The phylogenies we inferred from 76 cpDNA-encoded proteins and genes using various methods favor the hypothesis that the Charales diverged before the Coleochaetales and Zygnematales. The Zygnematales were identified as sister to land plants in the best tree topology (T1), whereas Chaetosphaeridium (T2) or a clade uniting the Zygnematales and Chaetosphaeridium (T3) occupied this position in alternative topologies. Chara remained at the same basal position in trees including more land plant taxa and inferred from 56 proteins/genes. Phylogenetic inference from gene order data yielded two most parsimonious trees displaying the T1 and T3 topologies. Analyses of additional structural cpDNA features (gene order, gene content, intron content, and indels in coding regions) provided better support for T1 than for the topology of the above-mentioned four-gene tree. Our structural analyses also revealed that many of the features conserved in land plant cpDNAs were inherited from their green algal ancestors. The intron content data predicted that at least 15 of the 21 land plant group II introns were gained early during the evolution of streptophytes and that a single intron was acquired during the transition from charophycean green algae to land plants. Analyses of genome rearrangements based on inversions predicted no alteration in gene order during the transition from charophycean green algae to land plants.
Charles F. Delwiche - One of the best experts on this subject based on the ideXlab platform.
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PHYLOGENY OF THE GENUS COLEOCHAETE (COLEOCHAETALES, CHAROPHYTA) AND RELATED TAXA INFERRED BY ANALYSIS OF THE CHLOROPLAST GENE rbcL 1
Journal of Phycology, 2002Co-Authors: Charles F. Delwiche, Matthew T. Cimino, Kenneth G. Karol, Kenneth J. SytsmaAbstract:The genus Coleochaete Breb. is considered to be a key taxon in the evolution of green algae and embryophytes (land plants), but only a few of the approximately 15 species have been studied with molecular phylogenetic methods. We report here the sequences of the gene rbcL from six new cultures of Coleochaete and two of Chaetosphaeridium Klebahn. These sequences were combined with 32 additional sequences, and phylogenetic analyses were performed with maximum likelihood, distance optimality, and parsimony methods. Important subgroups within Coleochaete include two primary lineages, one marked by fully corticated zygotes and the other by naked or weakly corticated zygotes. In the first lineage there is a subclade with tightly joined filaments and distinctive (“T-shaped”) cell division, an assemblage of strains that resembles the endophytic species Coleochaete nitellarum Jost, and a clade with loosely joined filaments and “Y-shaped” cell divisions. Consistent with recent multigene phylogenies, these analyses support the monophyly of the Coleochaetales, place the Charales as the sister taxon to land plants, and indicate that Chaetosphaeridium is far more closely related to Coleochaete than to Mesostigma Lauterborn.
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phylogenetic relationship of coleochaete and chaeto sphaeridium coleochaetales based on the chloroplast genes rbcl and atpb
Journal of Phycology, 2000Co-Authors: Kenneth G. Karol, J. D. Lewandowski, Charles F. DelwicheAbstract:The freshwater green algal genera Coleochaete and Chaetosphaeridium form the order Coleochaetales sensu Mattox and Stewart (Charophyceae). To test the monophyly of this order, a data set was compiled consisting of the chloroplast genes rbcL and atpB from nine species of Coleochaete, six strains of Chaetosphaeridium, and other representative green algae and embryophytes. Phylogenetic analyses of these data indicate that Coleochaete and Chaetosphaeridium form a monophyletic group that diverged late in basal streptophyte evolution. By contrast, published analyses of nuclear encoded small subunit ribosomal DNA (rDNA) data for similar taxa do not support a monophyletic Coleochaetales. These analyses suggest Chaetosphaeridium is an early branching lineage within Streptophyta and/or that Chaetosphaeridium forms a lineage with the unicellular flagellate Mesostigma (Mesostigmatophyceae). A close relationship of Chaetosphaeridium and Mesostigma is not supported by the rbcL and atpB data. Reexamination of morphological characters suggests a monophyletic Coleochaetales is supported by several characters that include branching filamentous habit, unicellular apical growth, sheathed hairs, and rotating plastids.
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BUILDING A SPECIES PHYLOGENY FOR THE GENUS COLEOCHAETE (COLEOCHAETALES) USING THE GENES RBCL AND ATPB
Journal of Phycology, 2000Co-Authors: Cimino, Charles F. DelwicheAbstract:The freshwater green alga Coleochaete Breb. (Coleochaetaceae; Coleochaetales) is a key streptophyte genus and is important to the understanding of the evolutionary origin of embryophytes (land plants). To date only a few species have been available from public culture collections. To facilitate research on this genus we have isolated 17 previously uncultured species of Coloechaete from material collected in the United States, Puerto Rico, and the Dominican Republic. Sequences for the genes rbcL and atpB were determined for these new isolates of Coleochaete (and for existing cultures) and combined with sequences from representative other streptophytes. Phylogenetic analyses indicate that Coleochaete, along with Chaetosphaeridium and Chara, are closely related to embryophytes and constitute a ‘higher streptophyte’ clade. At least four well-supported lineages exist within Coleochaete. Characteristic growth forms have been identified for these four lineages, with important characters including aspects of thallus establishment, thallus habit, zygote development and hair sheath position. These data provide an improved understanding of species diversity and character evolution in the genus Coleochaete, and facilitate examination of hypotheses concerning character evolution in the streptophytes.
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PHYLOGENETIC RELATIONSHIP OF COLEOCHAETE AND CHAETO‐SPHAERIDIUM (COLEOCHAETALES) BASED ON THE CHLOROPLAST GENES RBCL AND ATPB
Journal of Phycology, 2000Co-Authors: Cimino, J. D. Lewandowski, Kenneth G. Karol, Charles F. DelwicheAbstract:The freshwater green algal genera Coleochaete and Chaetosphaeridium form the order Coleochaetales sensu Mattox and Stewart (Charophyceae). To test the monophyly of this order, a data set was compiled consisting of the chloroplast genes rbcL and atpB from nine species of Coleochaete, six strains of Chaetosphaeridium, and other representative green algae and embryophytes. Phylogenetic analyses of these data indicate that Coleochaete and Chaetosphaeridium form a monophyletic group that diverged late in basal streptophyte evolution. By contrast, published analyses of nuclear encoded small subunit ribosomal DNA (rDNA) data for similar taxa do not support a monophyletic Coleochaetales. These analyses suggest Chaetosphaeridium is an early branching lineage within Streptophyta and/or that Chaetosphaeridium forms a lineage with the unicellular flagellate Mesostigma (Mesostigmatophyceae). A close relationship of Chaetosphaeridium and Mesostigma is not supported by the rbcL and atpB data. Reexamination of morphological characters suggests a monophyletic Coleochaetales is supported by several characters that include branching filamentous habit, unicellular apical growth, sheathed hairs, and rotating plastids.
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GRAPPLING WITH CONFLICT AMONG INFORMATION SOURCES IN RECONSTRUCTION OF THE EARLY EVOLUTION OF LAND PLANTS
Journal of Phycology, 2000Co-Authors: Charles F. Delwiche, Kenneth G. Karol, Cimino, Richard M. MccourtAbstract:Although a close relationship between embryophytes (land plants) and charophycean green algae has been discussed for over a hundred years, the precise nature of this relationship remains uncertain. This is largely because of difficulty reconstructing the phylogeny of the basal members of this group. Recent analyses of SSU rDNA, rbcL, and concatenated chloroplast genes have all produced different phylogenies, and none is fully compatible with morphological data. Noteworthy conflict is apparent in the positions of the unicellular flagellate Mesostigma and the filamentous epiphyte Chaetosphaeridium. Several phenomena could result in such incongruence, including problems with the underlying data (taxon ID, sequence determination, alignment, etc.), choice of analytical method, lack of resolution with one or more of the datasets, unrecognized paralogy, and horizontal gene transfer. We have examined each of these possible sources of incongruence, and have determined that several factors underlie the apparent conflict among phylogenies. When these factors are taken into account a consensus molecular phylogeny begins to emerge. Despite the long divergence time in question, the prospects for reconstruction of land plant phylogeny are good.
Kenneth G. Karol - One of the best experts on this subject based on the ideXlab platform.
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PHYLOGENY OF THE GENUS COLEOCHAETE (COLEOCHAETALES, CHAROPHYTA) AND RELATED TAXA INFERRED BY ANALYSIS OF THE CHLOROPLAST GENE rbcL 1
Journal of Phycology, 2002Co-Authors: Charles F. Delwiche, Matthew T. Cimino, Kenneth G. Karol, Kenneth J. SytsmaAbstract:The genus Coleochaete Breb. is considered to be a key taxon in the evolution of green algae and embryophytes (land plants), but only a few of the approximately 15 species have been studied with molecular phylogenetic methods. We report here the sequences of the gene rbcL from six new cultures of Coleochaete and two of Chaetosphaeridium Klebahn. These sequences were combined with 32 additional sequences, and phylogenetic analyses were performed with maximum likelihood, distance optimality, and parsimony methods. Important subgroups within Coleochaete include two primary lineages, one marked by fully corticated zygotes and the other by naked or weakly corticated zygotes. In the first lineage there is a subclade with tightly joined filaments and distinctive (“T-shaped”) cell division, an assemblage of strains that resembles the endophytic species Coleochaete nitellarum Jost, and a clade with loosely joined filaments and “Y-shaped” cell divisions. Consistent with recent multigene phylogenies, these analyses support the monophyly of the Coleochaetales, place the Charales as the sister taxon to land plants, and indicate that Chaetosphaeridium is far more closely related to Coleochaete than to Mesostigma Lauterborn.
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phylogenetic relationship of coleochaete and chaeto sphaeridium coleochaetales based on the chloroplast genes rbcl and atpb
Journal of Phycology, 2000Co-Authors: Kenneth G. Karol, J. D. Lewandowski, Charles F. DelwicheAbstract:The freshwater green algal genera Coleochaete and Chaetosphaeridium form the order Coleochaetales sensu Mattox and Stewart (Charophyceae). To test the monophyly of this order, a data set was compiled consisting of the chloroplast genes rbcL and atpB from nine species of Coleochaete, six strains of Chaetosphaeridium, and other representative green algae and embryophytes. Phylogenetic analyses of these data indicate that Coleochaete and Chaetosphaeridium form a monophyletic group that diverged late in basal streptophyte evolution. By contrast, published analyses of nuclear encoded small subunit ribosomal DNA (rDNA) data for similar taxa do not support a monophyletic Coleochaetales. These analyses suggest Chaetosphaeridium is an early branching lineage within Streptophyta and/or that Chaetosphaeridium forms a lineage with the unicellular flagellate Mesostigma (Mesostigmatophyceae). A close relationship of Chaetosphaeridium and Mesostigma is not supported by the rbcL and atpB data. Reexamination of morphological characters suggests a monophyletic Coleochaetales is supported by several characters that include branching filamentous habit, unicellular apical growth, sheathed hairs, and rotating plastids.
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PHYLOGENETIC RELATIONSHIP OF COLEOCHAETE AND CHAETO‐SPHAERIDIUM (COLEOCHAETALES) BASED ON THE CHLOROPLAST GENES RBCL AND ATPB
Journal of Phycology, 2000Co-Authors: Cimino, J. D. Lewandowski, Kenneth G. Karol, Charles F. DelwicheAbstract:The freshwater green algal genera Coleochaete and Chaetosphaeridium form the order Coleochaetales sensu Mattox and Stewart (Charophyceae). To test the monophyly of this order, a data set was compiled consisting of the chloroplast genes rbcL and atpB from nine species of Coleochaete, six strains of Chaetosphaeridium, and other representative green algae and embryophytes. Phylogenetic analyses of these data indicate that Coleochaete and Chaetosphaeridium form a monophyletic group that diverged late in basal streptophyte evolution. By contrast, published analyses of nuclear encoded small subunit ribosomal DNA (rDNA) data for similar taxa do not support a monophyletic Coleochaetales. These analyses suggest Chaetosphaeridium is an early branching lineage within Streptophyta and/or that Chaetosphaeridium forms a lineage with the unicellular flagellate Mesostigma (Mesostigmatophyceae). A close relationship of Chaetosphaeridium and Mesostigma is not supported by the rbcL and atpB data. Reexamination of morphological characters suggests a monophyletic Coleochaetales is supported by several characters that include branching filamentous habit, unicellular apical growth, sheathed hairs, and rotating plastids.
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GRAPPLING WITH CONFLICT AMONG INFORMATION SOURCES IN RECONSTRUCTION OF THE EARLY EVOLUTION OF LAND PLANTS
Journal of Phycology, 2000Co-Authors: Charles F. Delwiche, Kenneth G. Karol, Cimino, Richard M. MccourtAbstract:Although a close relationship between embryophytes (land plants) and charophycean green algae has been discussed for over a hundred years, the precise nature of this relationship remains uncertain. This is largely because of difficulty reconstructing the phylogeny of the basal members of this group. Recent analyses of SSU rDNA, rbcL, and concatenated chloroplast genes have all produced different phylogenies, and none is fully compatible with morphological data. Noteworthy conflict is apparent in the positions of the unicellular flagellate Mesostigma and the filamentous epiphyte Chaetosphaeridium. Several phenomena could result in such incongruence, including problems with the underlying data (taxon ID, sequence determination, alignment, etc.), choice of analytical method, lack of resolution with one or more of the datasets, unrecognized paralogy, and horizontal gene transfer. We have examined each of these possible sources of incongruence, and have determined that several factors underlie the apparent conflict among phylogenies. When these factors are taken into account a consensus molecular phylogeny begins to emerge. Despite the long divergence time in question, the prospects for reconstruction of land plant phylogeny are good.