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Monique Turmel - One of the best experts on this subject based on the ideXlab platform.
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Complete mitogenomes of the chlorophycean green algae Bulbochaete rectangularis var. hiloensis (Oedogoniales) and Stigeoclonium helveticum (Chaetophorales) provide insight into the sequence of events that led to the acquisition of a reduced-derived p
Mitochondrial DNA. Part B Resources, 2020Co-Authors: Monique Turmel, Anne-sophie Bélanger, Christian Otis, Claude LemieuxAbstract:Mitogenome evolution in the Chlorophyceae is characterized by the acquisition of a reduced-derived pattern by the Chlamydomonadales + Sphaeropleales clade. Because no mitogenomes are available for ...
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complete mitogenomes of the chlorophycean green algae bulbochaete rectangularis var hiloensis oedogoniales and stigeoclonium helveticum chaetophorales provide insight into the sequence of events that led to the acquisition of a reduced derived patter
Mitochondrial DNA Part B, 2020Co-Authors: Monique Turmel, Anne-sophie Bélanger, Christian Otis, Claude LemieuxAbstract:AbstractMitogenome evolution in the Chlorophyceae is characterized by the acquisition of a reduced-derived pattern by the Chlamydomonadales + Sphaeropleales clade. Because no mitogenomes are availa...
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Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)
PeerJ Inc., 2016Co-Authors: Jean-simon Brouard, Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site. Discussion Our results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites
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chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the sphaeropleales Chlorophyceae
BMC Evolutionary Biology, 2015Co-Authors: Claude Lemieux, Christian Otis, Antony T Vincent, Aurelie Labarre, Monique TurmelAbstract:The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis and the Crucicarteria, and was followed by the Radicarteria and then by the Chloromonadinia. The latter lineage was sister to two superclades, one consisting of the Oogamochlamydinia and Reinhardtinia and the other of the Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the two spine-bearing green algae belonging to the Golenkinia and Treubaria genera were recovered in a highly supported monophyletic group that also included three taxa representing distinct families of the Sphaeropleales (Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae). Our phylogenomic study advances our knowledge regarding the circumscription and internal structure of the Chlamydomonadales, suggesting that a previously unrecognized lineage is sister to the Sphaeropleales. In addition, it offers new insights into the flagellar structures of the founding members of both the Chlamydomonadales and Sphaeropleales.
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The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae
Genome Biology and Evolution, 2010Co-Authors: Jean-simon Brouard, Christian Otis, Claude Lemieux, Monique TurmelAbstract:The Chlorophyceae, an advanced class of chlorophyte green algae, comprises five lineages that form two major clades (Chlamydomonadales + Sphaeropleales and Oedogoniales + Chaetopeltidales + Chaetophorales). The four complete chloroplast DNA (cpDNA) sequences currently available for chlorophyceans uncovered an extraordinarily fluid genome architecture as well as many structural features distinguishing this group from other green algae. We report here the 521,168-bp cpDNA sequence from a member of the Chaetopeltidales (Floydiella terrestris), the sole chlorophycean lineage not previously sampled for chloroplast genome analysis. This genome, which contains 97 conserved genes and 26 introns (19 group I and 7 group II introns), is the largest chloroplast genome ever sequenced. Intergenic regions account for 77.8% of the genome size and are populated by short repeats. Numerous genomic features are shared with the cpDNA of the chaetophoralean Stigeoclonium helveticum, notably the absence of a large inverted repeat and the presence of unique gene clusters and trans-spliced group II introns. Although only one of the Floydiella group I introns encodes a homing endonuclease gene, our finding of five free-standing reading frames having similarity with such genes suggests that chloroplast group I introns endowed with mobility were once more abundant in the Floydiella lineage. Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. An evolutionary scenario of the molecular events that shaped the chloroplast genome in the Chlorophyceae is presented.
Claude Lemieux - One of the best experts on this subject based on the ideXlab platform.
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Complete mitogenomes of the chlorophycean green algae Bulbochaete rectangularis var. hiloensis (Oedogoniales) and Stigeoclonium helveticum (Chaetophorales) provide insight into the sequence of events that led to the acquisition of a reduced-derived p
Mitochondrial DNA. Part B Resources, 2020Co-Authors: Monique Turmel, Anne-sophie Bélanger, Christian Otis, Claude LemieuxAbstract:Mitogenome evolution in the Chlorophyceae is characterized by the acquisition of a reduced-derived pattern by the Chlamydomonadales + Sphaeropleales clade. Because no mitogenomes are available for ...
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complete mitogenomes of the chlorophycean green algae bulbochaete rectangularis var hiloensis oedogoniales and stigeoclonium helveticum chaetophorales provide insight into the sequence of events that led to the acquisition of a reduced derived patter
Mitochondrial DNA Part B, 2020Co-Authors: Monique Turmel, Anne-sophie Bélanger, Christian Otis, Claude LemieuxAbstract:AbstractMitogenome evolution in the Chlorophyceae is characterized by the acquisition of a reduced-derived pattern by the Chlamydomonadales + Sphaeropleales clade. Because no mitogenomes are availa...
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Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)
PeerJ Inc., 2016Co-Authors: Jean-simon Brouard, Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site. Discussion Our results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites
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chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the sphaeropleales Chlorophyceae
BMC Evolutionary Biology, 2015Co-Authors: Claude Lemieux, Christian Otis, Antony T Vincent, Aurelie Labarre, Monique TurmelAbstract:The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis and the Crucicarteria, and was followed by the Radicarteria and then by the Chloromonadinia. The latter lineage was sister to two superclades, one consisting of the Oogamochlamydinia and Reinhardtinia and the other of the Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the two spine-bearing green algae belonging to the Golenkinia and Treubaria genera were recovered in a highly supported monophyletic group that also included three taxa representing distinct families of the Sphaeropleales (Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae). Our phylogenomic study advances our knowledge regarding the circumscription and internal structure of the Chlamydomonadales, suggesting that a previously unrecognized lineage is sister to the Sphaeropleales. In addition, it offers new insights into the flagellar structures of the founding members of both the Chlamydomonadales and Sphaeropleales.
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The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae
Genome Biology and Evolution, 2010Co-Authors: Jean-simon Brouard, Christian Otis, Claude Lemieux, Monique TurmelAbstract:The Chlorophyceae, an advanced class of chlorophyte green algae, comprises five lineages that form two major clades (Chlamydomonadales + Sphaeropleales and Oedogoniales + Chaetopeltidales + Chaetophorales). The four complete chloroplast DNA (cpDNA) sequences currently available for chlorophyceans uncovered an extraordinarily fluid genome architecture as well as many structural features distinguishing this group from other green algae. We report here the 521,168-bp cpDNA sequence from a member of the Chaetopeltidales (Floydiella terrestris), the sole chlorophycean lineage not previously sampled for chloroplast genome analysis. This genome, which contains 97 conserved genes and 26 introns (19 group I and 7 group II introns), is the largest chloroplast genome ever sequenced. Intergenic regions account for 77.8% of the genome size and are populated by short repeats. Numerous genomic features are shared with the cpDNA of the chaetophoralean Stigeoclonium helveticum, notably the absence of a large inverted repeat and the presence of unique gene clusters and trans-spliced group II introns. Although only one of the Floydiella group I introns encodes a homing endonuclease gene, our finding of five free-standing reading frames having similarity with such genes suggests that chloroplast group I introns endowed with mobility were once more abundant in the Floydiella lineage. Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. An evolutionary scenario of the molecular events that shaped the chloroplast genome in the Chlorophyceae is presented.
Christian Otis - One of the best experts on this subject based on the ideXlab platform.
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Complete mitogenomes of the chlorophycean green algae Bulbochaete rectangularis var. hiloensis (Oedogoniales) and Stigeoclonium helveticum (Chaetophorales) provide insight into the sequence of events that led to the acquisition of a reduced-derived p
Mitochondrial DNA. Part B Resources, 2020Co-Authors: Monique Turmel, Anne-sophie Bélanger, Christian Otis, Claude LemieuxAbstract:Mitogenome evolution in the Chlorophyceae is characterized by the acquisition of a reduced-derived pattern by the Chlamydomonadales + Sphaeropleales clade. Because no mitogenomes are available for ...
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complete mitogenomes of the chlorophycean green algae bulbochaete rectangularis var hiloensis oedogoniales and stigeoclonium helveticum chaetophorales provide insight into the sequence of events that led to the acquisition of a reduced derived patter
Mitochondrial DNA Part B, 2020Co-Authors: Monique Turmel, Anne-sophie Bélanger, Christian Otis, Claude LemieuxAbstract:AbstractMitogenome evolution in the Chlorophyceae is characterized by the acquisition of a reduced-derived pattern by the Chlamydomonadales + Sphaeropleales clade. Because no mitogenomes are availa...
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Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)
PeerJ Inc., 2016Co-Authors: Jean-simon Brouard, Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site. Discussion Our results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites
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chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the sphaeropleales Chlorophyceae
BMC Evolutionary Biology, 2015Co-Authors: Claude Lemieux, Christian Otis, Antony T Vincent, Aurelie Labarre, Monique TurmelAbstract:The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis and the Crucicarteria, and was followed by the Radicarteria and then by the Chloromonadinia. The latter lineage was sister to two superclades, one consisting of the Oogamochlamydinia and Reinhardtinia and the other of the Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the two spine-bearing green algae belonging to the Golenkinia and Treubaria genera were recovered in a highly supported monophyletic group that also included three taxa representing distinct families of the Sphaeropleales (Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae). Our phylogenomic study advances our knowledge regarding the circumscription and internal structure of the Chlamydomonadales, suggesting that a previously unrecognized lineage is sister to the Sphaeropleales. In addition, it offers new insights into the flagellar structures of the founding members of both the Chlamydomonadales and Sphaeropleales.
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The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae
Genome Biology and Evolution, 2010Co-Authors: Jean-simon Brouard, Christian Otis, Claude Lemieux, Monique TurmelAbstract:The Chlorophyceae, an advanced class of chlorophyte green algae, comprises five lineages that form two major clades (Chlamydomonadales + Sphaeropleales and Oedogoniales + Chaetopeltidales + Chaetophorales). The four complete chloroplast DNA (cpDNA) sequences currently available for chlorophyceans uncovered an extraordinarily fluid genome architecture as well as many structural features distinguishing this group from other green algae. We report here the 521,168-bp cpDNA sequence from a member of the Chaetopeltidales (Floydiella terrestris), the sole chlorophycean lineage not previously sampled for chloroplast genome analysis. This genome, which contains 97 conserved genes and 26 introns (19 group I and 7 group II introns), is the largest chloroplast genome ever sequenced. Intergenic regions account for 77.8% of the genome size and are populated by short repeats. Numerous genomic features are shared with the cpDNA of the chaetophoralean Stigeoclonium helveticum, notably the absence of a large inverted repeat and the presence of unique gene clusters and trans-spliced group II introns. Although only one of the Floydiella group I introns encodes a homing endonuclease gene, our finding of five free-standing reading frames having similarity with such genes suggests that chloroplast group I introns endowed with mobility were once more abundant in the Floydiella lineage. Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. An evolutionary scenario of the molecular events that shaped the chloroplast genome in the Chlorophyceae is presented.
Kamilia Hasna - One of the best experts on this subject based on the ideXlab platform.
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Analisa Biodiversitas Fitoplankton dan Keterkaitannya dengan Produktivitas Udang Vaname (Litopenaeus vannamei) Sistem Intensif di Desa Alasbulu, Kecamatan Wongsorejo, Banyuwangi
2020Co-Authors: Kamilia HasnaAbstract:Budidaya udang vaname sistem intensif tidak terlepas dari aspek-aspek lingkungannya, seperti keberadaan fitoplankton sebagai produktivitas primer dan kualitas air. Fitoplankton erat kaitannya dengan kualitas air, dimana efektivitas dan besarnya serapan nutrien oleh fitoplankton di perairan tambak sangat dipengaruhi oleh ketersedian bahan organik serta unsur-unsur hara lainnya yang dipengaruhi oleh oksigen terlarut, kecerahan, salinitas, suhu, nitrit dan amonia. Selain berfungsi sebagai pakan alami, fitoplankton juga berfungsi untuk menjaga kestabilan ekosistem tambak. Kestabilan lingkungan perairan tambak ditandai dengan keragaman fitoplankton yang tinggi, kepadatan fitoplankton menguntungkan yang tinggi, serta parameter kualitas air yang sesuai untuk mendukung pertumbuhan udang vaname. Tujuan dari penelitian ini adalah untuk mengetahui komposisi fitoplankton yang diperoleh, kepadatan fitoplankton, keragaman fitoplankton, nilai-nilai parameter kualitas air dan kaitannya terhadap produktivitas budidaya udang vaname (Litopenaeus vannamei) di lokasi penelitian. Penelitian ini dilaksanakan di tambak udang vaname (Litopenaeus vannamei) sistem intensif Desa Alasbulu, Kecamatan Wongsorejo, Kabupaten Banyuwangi, Jawa Timur pada tanggal 16 Februari 2020 hingga 14 Maret 2020. Metode yang digunakan dalam penelitian ini adalah menggunakan metode deskriptif dengan mendeskripsikan fakta-fakta yang ada di lapangan, yaitu dengan cara mengumpulkan data fitoplankton, data kualitas air fisika maupun kimia, dan data hasil produksi di akhir periode budidaya. Selanjutnya dilakukan analisa untuk melihat keterkaitan antara seluruh parameter yang didapatkan. Hasil yang didapatkan pada penelitian yaitu kelas fitoplankton yang ditemukan pada kolam 1 dan 2 yaitu Chlorophyceae, Cyanophyceae, Bacillariophyceae, Dinophyceae, Euglenophyceae dan Cryptophyceae. Fitoplankton kelompok Chlorophyceae mendominasi dengan persentase 51% dan 44% masing-masing pada kolam 1 dan 2. Kondisi lingkungan perairan tambak penelitian tergolong stabil ditinjau dari indeks diversitas fitoplankton moderat yang didapatkan. Hasil produksi kolam 1 lebih besar dibandingkan kolam 2, dengan tonase panen kolam 1 sebesar 1,8 kg/m2 dan kolam 2 sebesar 1,4 kg/m2. Besarnya hasil produksi berkaitan dengan dominansi Chlorophyceae, dimana kolam 1 memiliki persentase dan total kepadatan Chlorophyceae yang lebih tinggi dibandingkan dengan kolam 2. Parameter kualitas air suhu, salinitas, DO, kecerahan dan pH dapat dikatakan optimal. Parameter kualitas air nitrit, nitrat, TAN dan fosfat meningkat seiring dengan penambahan masa budidaya dan berada di atas ambang batas yang optimal bagi perairan budidaya.Kesimpulan yang didapatkan pada penelitian yaitu kepadatan dan biodiversitas fitoplankton serta parameter kualitas air fisika maupun kimia memiliki keterkaitan terhadap produktivitas budidaya udang vaname (Litopenaeus vannamei). Kondisi perairan kolam pada lokasi penelitian dikatakan cukup stabil karena memiliki nilai H’ yang termasuk dalam kategori perairan sedang atau moderat. Perbedaan hasil produksi pada kedua kolam diduga dipengaruhi oleh kepadatan fitoplankton kelompok tertentu yang bersifat merugikan bagi budidaya udang vaname dan kepadatan Chlorophyceae sebagai fitoplankton yang bersifat menguntungkan
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Analisa Biodiversitas Fitoplankton dan Keterkaitannya dengan Produktivitas Udang Vaname (Litopenaeus vannamei) Sistem Intensif di Desa Alasbulu, Kecamatan Wongsorejo, Banyuwangi.
2020Co-Authors: Kamilia HasnaAbstract:Budidaya udang vaname sistem intensif tidak terlepas dari aspek-aspek lingkungannya, seperti keberadaan fitoplankton sebagai produktivitas primer dan kualitas air. Fitoplankton erat kaitannya dengan kualitas air, dimana efektivitas dan besarnya serapan nutrien oleh fitoplankton di perairan tambak sangat dipengaruhi oleh ketersedian bahan organik serta unsur-unsur hara lainnya yang dipengaruhi oleh oksigen terlarut, kecerahan, salinitas, suhu, nitrit dan amonia. Selain berfungsi sebagai pakan alami, fitoplankton juga berfungsi untuk menjaga kestabilan ekosistem tambak. Kestabilan lingkungan perairan tambak ditandai dengan keragaman fitoplankton yang tinggi, kepadatan fitoplankton menguntungkan yang tinggi, serta parameter kualitas air yang sesuai untuk mendukung pertumbuhan udang vaname. Tujuan dari penelitian ini adalah untuk mengetahui komposisi fitoplankton yang diperoleh, kepadatan fitoplankton, keragaman fitoplankton, nilai-nilai parameter kualitas air dan kaitannya terhadap produktivitas budidaya udang vaname (Litopenaeus vannamei) di lokasi penelitian. Penelitian ini dilaksanakan di tambak udang vaname (Litopenaeus vannamei) sistem intensif Desa Alasbulu, Kecamatan Wongsorejo, Kabupaten Banyuwangi, Jawa Timur pada tanggal 16 Februari 2020 hingga 14 Maret 2020. Metode yang digunakan dalam penelitian ini adalah menggunakan metode deskriptif dengan mendeskripsikan fakta-fakta yang ada di lapangan, yaitu dengan cara mengumpulkan data fitoplankton, data kualitas air fisika maupun kimia, dan data hasil produksi di akhir periode budidaya. Selanjutnya dilakukan analisa untuk melihat keterkaitan antara seluruh parameter yang didapatkan. Hasil yang didapatkan pada penelitian yaitu kelas fitoplankton yang ditemukan pada kolam 1 dan 2 yaitu Chlorophyceae, Cyanophyceae, Bacillariophyceae, Dinophyceae, Euglenophyceae dan Cryptophyceae. Fitoplankton kelompok Chlorophyceae mendominasi dengan persentase 51% dan 44% masing-masing pada kolam 1 dan 2. Kondisi lingkungan perairan tambak penelitian tergolong stabil ditinjau dari indeks diversitas fitoplankton moderat yang didapatkan. Hasil produksi kolam 1 lebih besar dibandingkan kolam 2, dengan tonase panen kolam 1 sebesar 1,8 kg/m2 dan kolam 2 sebesar 1,4 kg/m2. Besarnya hasil produksi berkaitan dengan dominansi Chlorophyceae, dimana kolam 1 memiliki persentase dan total kepadatan Chlorophyceae yang lebih tinggi dibandingkan dengan kolam 2. Parameter kualitas air suhu, salinitas, DO, kecerahan dan pH dapat dikatakan optimal. Parameter kualitas air nitrit, nitrat, TAN dan fosfat meningkat seiring dengan penambahan masa budidaya dan berada di atas ambang batas yang optimal bagi perairan budidaya. Kesimpulan yang didapatkan pada penelitian yaitu kepadatan dan biodiversitas fitoplankton serta parameter kualitas air fisika maupun kimia memiliki keterkaitan terhadap produktivitas budidaya udang vaname (Litopenaeus vannamei). Kondisi perairan kolam pada lokasi penelitian dikatakan cukup stabil karena memiliki nilai H’ yang termasuk dalam kategori perairan sedang atau moderat. Perbedaan hasil produksi pada kedua kolam diduga dipengaruhi oleh kepadatan fitoplankton kelompok tertentu yang bersifat merugikan bagi budidaya udang vaname dan kepadatan Chlorophyceae sebagai fitoplankton yang bersifat menguntungkan
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Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)
PeerJ Inc., 2016Co-Authors: Jean-simon Brouard, Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site. Discussion Our results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites
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The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae
Genome Biology and Evolution, 2010Co-Authors: Jean-simon Brouard, Christian Otis, Claude Lemieux, Monique TurmelAbstract:The Chlorophyceae, an advanced class of chlorophyte green algae, comprises five lineages that form two major clades (Chlamydomonadales + Sphaeropleales and Oedogoniales + Chaetopeltidales + Chaetophorales). The four complete chloroplast DNA (cpDNA) sequences currently available for chlorophyceans uncovered an extraordinarily fluid genome architecture as well as many structural features distinguishing this group from other green algae. We report here the 521,168-bp cpDNA sequence from a member of the Chaetopeltidales (Floydiella terrestris), the sole chlorophycean lineage not previously sampled for chloroplast genome analysis. This genome, which contains 97 conserved genes and 26 introns (19 group I and 7 group II introns), is the largest chloroplast genome ever sequenced. Intergenic regions account for 77.8% of the genome size and are populated by short repeats. Numerous genomic features are shared with the cpDNA of the chaetophoralean Stigeoclonium helveticum, notably the absence of a large inverted repeat and the presence of unique gene clusters and trans-spliced group II introns. Although only one of the Floydiella group I introns encodes a homing endonuclease gene, our finding of five free-standing reading frames having similarity with such genes suggests that chloroplast group I introns endowed with mobility were once more abundant in the Floydiella lineage. Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. An evolutionary scenario of the molecular events that shaped the chloroplast genome in the Chlorophyceae is presented.
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chloroplast dna sequence of the green alga oedogonium cardiacum Chlorophyceae unique genome architecture derived characters shared with the chaetophorales and novel genes acquired through horizontal transfer
BMC Genomics, 2008Co-Authors: Jean-simon Brouard, Christian Otis, Claude Lemieux, Monique TurmelAbstract:Background To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA) from representative taxa. The complete cpDNA sequences previously reported for Chlamydomonas (Chlamydomonadales), Scenedesmus (Sphaeropleales), and Stigeoclonium (Chaetophorales) revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus. Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade) and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade). Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales).
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Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer
BMC Genomics, 2008Co-Authors: Jean-simon Brouard, Christian Otis, Claude Lemieux, Monique TurmelAbstract:Background To gain insight into the branching order of the five main lineages currently recognized in the green algal class Chlorophyceae and to expand our understanding of chloroplast genome evolution, we have undertaken the sequencing of chloroplast DNA (cpDNA) from representative taxa. The complete cpDNA sequences previously reported for Chlamydomonas (Chlamydomonadales), Scenedesmus (Sphaeropleales), and Stigeoclonium (Chaetophorales) revealed tremendous variability in their architecture, the retention of only few ancestral gene clusters, and derived clusters shared by Chlamydomonas and Scenedesmus . Unexpectedly, our recent phylogenies inferred from these cpDNAs and the partial sequences of three other chlorophycean cpDNAs disclosed two major clades, one uniting the Chlamydomonadales and Sphaeropleales (CS clade) and the other uniting the Oedogoniales, Chaetophorales and Chaetopeltidales (OCC clade). Although molecular signatures provided strong support for this dichotomy and for the branching of the Oedogoniales as the earliest-diverging lineage of the OCC clade, more data are required to validate these phylogenies. We describe here the complete cpDNA sequence of Oedogonium cardiacum (Oedogoniales). Results Like its three chlorophycean homologues, the 196,547-bp Oedogonium chloroplast genome displays a distinctive architecture. This genome is one of the most compact among photosynthetic chlorophytes. It has an atypical quadripartite structure, is intron-rich (17 group I and 4 group II introns), and displays 99 different conserved genes and four long open reading frames (ORFs), three of which are clustered in the spacious inverted repeat of 35,493 bp. Intriguingly, two of these ORFs ( int and dpoB ) revealed high similarities to genes not usually found in cpDNA. At the gene content and gene order levels, the Oedogonium genome most closely resembles its Stigeoclonium counterpart. Characters shared by these chlorophyceans but missing in members of the CS clade include the retention of psaM , rpl32 and trnL (caa), the loss of petA , the disruption of three ancestral clusters and the presence of five derived gene clusters. Conclusion The Oedogonium chloroplast genome disclosed additional characters that bolster the evidence for a close alliance between the Oedogoniales and Chaetophorales. Our unprecedented finding of int and dpoB in this cpDNA provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor.
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DEEP DIVISION IN THE Chlorophyceae (CHLOROPHYTA) REVEALED BY CHLOROPLAST PHYLOGENOMIC ANALYSES(1).
Journal of Phycology, 2008Co-Authors: Monique Turmel, Jean-simon Brouard, Cédric Gagnon, Christian Otis, Claude LemieuxAbstract:The Chlorophyceae (sensu Mattox and Stewart) is a morphologically diverse class of the Chlorophyta displaying biflagellate and quadriflagellate motile cells with varying configurations of the flagellar apparatus. Phylogenetic analyses of 18S rDNA data and combined 18S and 26S rDNA data from a broad range of chlorophycean taxa uncovered five major monophyletic groups (Chlamydomonadales, Sphaeropleales, Oedogoniales, Chaetophorales, and Chaetopeltidales) but could not resolve their branching order. To gain insight into the interrelationships of these groups, we analyzed multiple genes encoded by the chloroplast genomes of Chlamydomonas reinhardtii P. A. Dang. and Chlamydomonas moewusii Gerloff (Chlamydomonadales), Scenedesmus obliquus (Turpin) Kutz. (Sphaeropleales), Oedogonium cardiacum Wittr. (Oedogoniales), Stigeoclonium helveticum Vischer (Chaetophorales), and Floydiella terrestris (Groover et Hofstetter) Friedl et O’Kelly (Chaetopeltidales). The C. moewusii, Oedogonium, and Floydiella chloroplast DNAs were partly sequenced using a random strategy. Trees were reconstructed from nucleotide and amino acid data sets derived from 44 protein-coding genes of 11 chlorophytes and nine streptophytes as well as from 57 protein-coding genes of the six chlorophycean taxa. All best trees identified two robustly supported major lineages within the Chlorophyceae: a clade uniting the Chlamydomonadales and Sphaeropleales, and a clade uniting the Oedogoniales, Chaetophorales, and Chaetopeltidales (OCC clade). This dichotomy is independently supported by molecular signatures in chloroplast genes, such as insertions/deletions and the distribution of trans-spliced group II introns. Within the OCC clade, the sister relationship observed for the Chaetophorales and Chaetopeltidales is also strengthened by independent data. Character state reconstruction of basal body orientation allowed us to refine hypotheses regarding the evolution of the flagellar apparatus.