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Charles F. Delwiche - One of the best experts on this subject based on the ideXlab platform.
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uncovering the evolutionary origin of plant molecular processes comparison of coleochaete Coleochaetales and spirogyra zygnematales transcriptomes
BMC Plant Biology, 2010Co-Authors: Ruth E. Timme, Charles F. DelwicheAbstract:Background The large and diverse land plant lineage is nested within a clade of fresh water green algae, the charophytes. Collection of genome-scale data for land plants and other organisms over the past decade has invigorated the field of evolutionary biology. One of the core questions in the field asks: how did a colonization event by a green algae over 450 mya lead to one of the most successful lineages on the tree of life? This question can best be answered using the comparative method, the first step of which is to gather genome-scale data across closely related lineages to land plants. Before sequencing an entire genome it is useful to first gather transcriptome data: it is less expensive, it targets the protein coding regions of the genome, and provides support for gene models for future genome sequencing. We built Expressed Sequence Tag (EST) libraries for two charophyte species, Coleochaete orbicularis (Coleochaetales) and Spirogyra pratensis (Zygnematales). We used both Sanger sequencing and next generation 454 sequencing to cover as much of the transcriptome as possible.
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uncovering the evolutionary origin of plant molecular processes comparison of coleochaete Coleochaetales and spirogyra zygnematales transcriptomes
BMC Plant Biology, 2010Co-Authors: Ruth E. Timme, Charles F. DelwicheAbstract:Background The large and diverse land plant lineage is nested within a clade of fresh water green algae, the charophytes. Collection of genome-scale data for land plants and other organisms over the past decade has invigorated the field of evolutionary biology. One of the core questions in the field asks: how did a colonization event by a green algae over 450 mya lead to one of the most successful lineages on the tree of life? This question can best be answered using the comparative method, the first step of which is to gather genome-scale data across closely related lineages to land plants. Before sequencing an entire genome it is useful to first gather transcriptome data: it is less expensive, it targets the protein coding regions of the genome, and provides support for gene models for future genome sequencing. We built Expressed Sequence Tag (EST) libraries for two charophyte species, Coleochaete orbicularis (Coleochaetales) and Spirogyra pratensis (Zygnematales). We used both Sanger sequencing and next generation 454 sequencing to cover as much of the transcriptome as possible.
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Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants
Current Biology, 2010Co-Authors: Cédric Finet, Charles F. Delwiche, Ruth Timme, Ferdinand MarlétazAbstract:Summary The Viridiplantae (green plants) include land plants as well as the two distinct lineages of green algae, chlorophytes and charophytes. Despite their critical importance for identifying the closest living relatives of land plants, phylogenetic studies of charophytes have provided equivocal results [1–5]. In addition, many relationships remain unresolved among the land plants, such as the position of mosses, liverworts, and the enigmatic Gnetales. Phylogenomics has proven to be an insightful approach for resolving challenging phylogenetic issues, particularly concerning deep nodes [6–8]. Here we extend this approach to the green lineage by assembling a multilocus data set of 77 nuclear genes (12,149 unambiguously aligned amino acid positions) from 77 taxa of plants. We therefore provide the first multigene phylogenetic evidence that Coleochaetales represent the closest living relatives of land plants. Moreover, our data reinforce the early divergence of liverworts and the close relationship between Gnetales and Pinaceae. These results provide a new phylogenetic framework and represent a key step in the evolutionary interpretation of developmental and genomic characters in green plants.
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(1569-1570) Proposals to conserve the name Coleochaete soluta against C. prostrata and the name C. orbicularis against Phyllactidium pulchellum with a note on the name C. nitellarum (Coleochaetaceae, Chlorophyceae)
TAXON, 2003Co-Authors: Matthew T. Cimino, James L. Reveal, Charles F. DelwicheAbstract:The genus Coleochaete Breb. (in Ann. Sci. Nat., ser. 3, 1: 29. 1844), nom. cons., comprising roughly 15 species, is found in clean freshwater lakes and ponds worldwide. The genus is becoming the subject of many studies, particularly because this and other members of the Coleochaetales and Charales are considered key elements in the evolution of early land plants (Karol & al. in Science 294: 2351-2353. 2001). Members of both orders have been investigated by a number of researchers, all of whom have used a consistent nomenclature based to a significant degree on their exchange of cultures and genetic material. Though effort has been made to clarify the nomenclature of many of the earliest names in Coleochaete (Szymanska in Taxon 39: 572-575. 1990; Szymanska & Spalik in Arch. Hydrobiol. 98 (Suppl.): 29-37. 1993), the names applied to two widely studied species remain particularly at risk while that of a third has been questioned. Given the body of literature containing the names Coleochaete soluta (Rabenhorst, Fl. Eur. Alg. 3(2): 389. 1868; Wolle, Fresh-water Alg.: 64. 1887; Wildeman, Fl. Alg.: 22. 1896; G. S. West, Algae: 315. 1916; Graham in Amer. J. Bot. 69: 447-454. 1982; Graham & Wilcox in Amer. J. Bot. 70: 113-120. 1983; Graham & Wilcox, Algae: 525. 2000), C. orbicularis (e.g., Rabenhorst, I.c.: 390. 1868; Wolle, l.c.: 64. 1887; Wildeman, l.c.: 20. 1896; G. S. West, l.c.: 315. 1916; Islam in Bangladesh J. Bot. 3: 35-43. 1974; Graham in Amer. J. Bot. 69: 447-454. 1982; Graham & Wilcox in Amer. J. Bot. 70: 113-120. 1983; Delwiche, Graham, & Thompson in Science 245: 399-401. 1989; Graham, Delwiche & Mishler in Adv. Bryol. 4: 213-244. 1991; Kenrick & Crane, Origin Diversif. Land PI.: 30. 1997; Graham & Wilcox, Algae: 535. 2000), and C. nitellarum (G. M. Smith, Fresh-waterAlg. U.S.: 410. 1933; Chapman & al., Molec. Syst. P1. 2: 530. 1998; Nishiyama & Kato in Molec. Biol. Evol. 16: 1027-1036. 1999; Graham & Wilcox, Algae: 535. 2000; Cimino & Delwiche in J. Phycol. 38: 1213-1221. 2002), changes in the application of these names would only result in unnecessary nomenclatural confusion. Therefore, our effort here is to ensure the maintenance of these three names in current
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MOLECULAR AND MORPHOLOGICAL DATA IDENTIFY A CRYPTIC SPECIES COMPLEX IN ENDOPHYTIC MEMBERS OF THE GENUS COLEOCHAETE BRÉB. (CHAROPHYTA: COLEOCHAETACEAE) 1
Journal of Phycology, 2002Co-Authors: Matthew T. Cimino, Charles F. DelwicheAbstract:The genus Coleochaete Breb. is a relatively small group of freshwater microscopic green algae with about 15 recognized species. Although Coleochaete has long been considered to be a close relative of embryophytes, a comprehensive study of the genus has not been published since Pringsheim's 1860 monograph. As part of a systematic study of Coleochaete, we investigated four accessions of the genus that are morphologically similar to the endophytic species C. nitellarum Jost. Each of the four cultures was determined to be capable of endophytic growth in Nitella C. A. Agardh, a member of the closely related order Charales. Maximum likelihood and maximum parsimony analyses were performed on nucleotide data from the chloroplast genes atpB and rbcL that were sequenced from 16 members of the Coleochaetales and from other members of the Charophyceae, embryophytes, and outgroup taxa. These analyses indicate that the Coleochaetales are monophyletic and that the endophytic accessions are members of the scutata group of species. In addition, cell size and nucleotide data suggest that at least three different endophytic species may be represented. Herbivory, nutritional benefits, and substrate competition are three hypotheses that could explain the evolution and maintenance of the endophytic habit in Coleochaete. These data also imply that diversity in the genus may be markedly underestimated.
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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phylogeny of the conjugating green algae zygnematales and desmidiales based on plastid and mitochondrial gene sequences
Journal of Phycology, 2002Co-Authors: Richard M. Mccourt, D A Hewitt, J. Park, Kenneth G. KarolAbstract:The conjugating green algae (Order Zygnematales and Desmidiales) are charophyceans, that is, they are among the green algae most closely related to land plants. Compared to the five other groups of charophyceans (Mesostigma, Klebsormidiales, Chlorokybales, Coleochaetales, Charales), the conjugating greens are by far the most diverse taxonomically (6 families, about 55 genera, 3–4000 species) and very widespread in distribution (including common species such as Spirogyra, Zygnema, Cosmarium, and Staurastrum). Thallus shape ranges from simple, oblong unicells (saccoderm desmids, or Mesotaeniaceae), to unbranched filaments of cells with smooth walls (Zygnemataceae), to elaborately ornate and deeply incised unicells or filaments made of such cells (placoderm desmids, in four families). Prior analyses of sequences of the chloroplast-encoded gene rbcL (1354 bp, or 95% of the gene) sampled from all six families showed that two of the traditional families (saccoderms and filamentous forms) are paraphyletic, i.e. they do not form two independent clades, although the component genera may together constitute a monophyletic group. In contrast, three families of placoderm desmids formed three monophyletic groups within a larger clade. New analyses using partial sequences from the mitochondrial gene coxIII (608 bp, or 76% of the gene) for 21 species of conjugating green algae from all six families supported the conclusions of the rbcL analysis, although bootstrap support for each gene along was weak for many branches. The coxIII sequences are more variable than rbcL and have proportionately more parsimony-informative sites (43% vs. 34%, respectively). Combining the two genes improved the resolution of the resulting tree: (1) bootstrap support increased for all branches, particularly in regards relationships of placoderm desmids; and (2) monophyly of a clade containing filamentous and saccoderm desmids was strongly supported. We conclude that phylogeny of conjugating green algae will be much improved by sampling from additional genes.
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One Small Step: Why Did the Charophytes Have the Right Stuff?
Journal of Phycology, 2002Co-Authors: Charles F. Delwiche, Kenneth G. Karol, Richard M. MccourtAbstract:The origin and evolution of land plants (i.e. embryophytes) represents one of the seminal events in the history of life on earth. When the land plant lineage took hold upon the continents, there were profound changes in the global environment including dramatic modification of the erosion regime, correlated changes in marine nutrient inputs, and striking fluctuations in atmospheric chemistry. These changes took place not only because of the ability of land plants to survive on land, but also because their structure and physiology permitted them to make efficient use of resources, anchor themselves effectively and in so doing stabilize the substrate and permit the formation of modern soils, and maintain metabolic activity for long periods of time even in the absence of rainfall and surface moisture. Molecular phylogenetic analyses show the order Charales is the sister group to all land plants, with the Coleochaetales sister to the land plant/Charales lineage. Thus, in a very real sense, the embryophytes are ‘drier algae.’ Many groups of green algae live in the terrestrial environment, but only one of these – the land plants – has radiated into a wide range of habitats. It is not known why the land plant lineage has been so successful. Traits that are likely to have played a role in their success include cell wall biochemistry, desiccation resistance and tolerance, structural complexity, and various reproductive strategies. In all probability, the success of the land plant lineage was not the result of a single ‘key innovation’, but an emergent property resulting from complex interactions among these and other features of the lineage. Comparative study of the properties of diverse aquatic and terrestrial algae can be used to identify properties that were important in the colonization of the land and how they interact.
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The Roots of Land Plants: Recent Research on Early Diverging Lineages in the Evolution of Higher Drier Algae
Journal of Phycology, 2002Co-Authors: Richard M. Mccourt, Kenneth G. Karol, Charles F. DelwicheAbstract:Recent multigene phylogenetic analyses of charophycean algae sensu Mattox and Stewart have advanced our understanding of the relationships of the green algae that are most closely related to land plants. Several clades of green algae are monophyletic with land plants (i.e. liverworts, mosses, nonvascular and vascular plants that arose from an aquatic ancestor) to the exclusion of other green algae: Mesostigma (a flagellate unicell); the Chlorokybales (small packets of cells); Klebsormidiales (unbranched filaments); Zygnematales (conjugating unicells, filaments, and colonies); Coleochaetales (filamentous and parenchymatous thalli); and Charales (branched filamentous thalli with complex nodal structure). The morphological and molecular diversity of the extant members of this nearly exclusively freshwater clade is remarkable. Moreover, the taxon diversity within clades is highly asymmetric, having yielded several distinctive albeit small groups of green algae, as well as one of the major evolutionary success stories on earth, viz. land plants. The most recent analysis (Karol et al. (2001) Science 294 : 2351–2353) of four genes from plastid, mitochondrial, and nuclear compartments strongly support the sister relationships of Charales (stoneworts) to the most primitive land plants. The analysis also shows that within this clade there has been a trend toward increasing complexity of thallus form (from unicells, to filaments, to branching and parenchymatous thalli) and reproduction (absence of sexual reproduction to iso- or anisogamy, to oogamy). Although the major clades mentioned above are well supported by molecular analyses, relationships among these groups are less well-resolved, especially for the Klebsormidiales, Chlorokybales, and Mesostigma. This paper reviews the morphological and molecular evidence for the relationships among and within these groups. More sequence data from a broader sampling of taxa at the base of the charophyceans (including perhaps some algae not now known to be charophytes) should provide a clearer picture of the evolution of this group and the reasons for its success.
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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.
Claude Lemieux - One of the best experts on this subject based on the ideXlab platform.
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Tracing the evolution of streptophyte algae and their mitochondrial genome.
Genome Biology and Evolution, 2013Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Six monophyletic groups of charophycean green algae are recognized within the Streptophyta. Although incongruent with earlier studies based on genes from three cellular compartments, chloroplast and nuclear phylogenomic analyses have resolved identical relationships among these groups, placing the Zygnematales or the Zygnematales+ Coleochaetales as sister to land plants. The present investigation aimed at determining whether this consensus view is supported by the mitochondrial genome and at gaining insight into mitochondrial DNA (mtDNA) evolution within and across streptophyte algal lineages and during the transition toward the first land plants. We present here the newly sequenced mtDNAs of representatives of the Klebsormidiales (Entransia fimbriata and Klebsormidium spec.) and Zygnematales (Closterium baillyanum and Roya obtusa) and compare them with their homologs in other charophycean lineages as well as in selected embryophyte and chlorophyte lineages. Our results indicate that important changes occurred at the levels of genome size, gene order, and intron content within the Zygnematales. Although the representatives of the Klebsormidiales display more similarity in genome size and intron content, gene order seems more fluid and gene losses more frequent than in other charophycean lineages. In contrast, the two members of the Charales display an extremely conservative pattern of mtDNA evolution. Collectively, our analyses of gene order and gene content and the phylogenies we inferred from 40 mtDNAencoded proteins failed to resolve the relationships among the Zygnematales, Coleochaetales, and Charales; however, they are consistent with previous phylogenomic studies in favoring that the morphologically complex Charales are not sister to land plants.
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THE GREEN ALGAL ANCESTRY OF LAND PLANTS AS REVEALED BY THE CHLOROPLAST GENOME
International Journal of Plant Sciences, 2007Co-Authors: Monique Turmel, Jean-françois Pombert, Patrick Charlebois, Christian Otis, Claude LemieuxAbstract:The phylum Streptophyta comprises all land plants and six monophyletic groups of charophycean green algae. Which of these charophycean groups is the most closely related to land plants has long been debated. In 2001, a phylogenetic analysis of four genes encoded by three cellular compartments was inferred that robustly supports the placement of the Charales as sister to land plants as well as the notion that charophycean green algae evolved progressively toward an increasing cellular complexity. This view on the origin of land plants is now being challenged by recent analyses of chloroplast genome sequences from six charophyceans. Phylogenies inferred from multiple chloroplast genes and proteins support the hypothesis that the Charales are sister to a clade composed of the Coleochaetales, the Zygnematales, and land plants, thus implying a more complex evolutionary history for charophycean green algae. Analyses of four sets of genomic features (gene content, intron content, gene order, and insertions/delet...
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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.
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the complete chloroplast dna sequences of the charophycean green algae staurastrum and zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the zygnematales
BMC Biology, 2005Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The Streptophyta comprise all land plants and six monophyletic groups of charophycean green algae. Phylogenetic analyses of four genes from three cellular compartments support the following branching order for these algal lineages: Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales and Charales, with the last lineage being sister to land plants. Comparative analyses of the Mesostigma viride (Mesostigmatales) and land plant chloroplast genome sequences revealed that this genome experienced many gene losses, intron insertions and gene rearrangements during the evolution of charophyceans. On the other hand, the chloroplast genome of Chaetosphaeridium globosum (Coleochaetales) is highly similar to its land plant counterparts in terms of gene content, intron composition and gene order, indicating that most of the features characteristic of land plant chloroplast DNA (cpDNA) were acquired from charophycean green algae. To gain further insight into when the highly conservative pattern displayed by land plant cpDNAs originated in the Streptophyta, we have determined the cpDNA sequences of the distantly related zygnematalean algae Staurastrum punctulatum and Zygnema circumcarinatum.
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The Mitochondrial Genome of Chara vulgaris: Insights into the Mitochondrial DNA Architecture of the Last Common Ancestor of Green Algae and Land Plants
The Plant Cell, 2003Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Mitochondrial DNA (mtDNA) has undergone radical changes during the evolution of green plants, yet little is known about the dynamics of mtDNA evolution in this phylum. Land plant mtDNAs differ from the few green algal mtDNAs that have been analyzed to date by their expanded size, long spacers, and diversity of introns. We have determined the mtDNA sequence of Chara vulgaris (Charophyceae), a green alga belonging to the charophycean order (Charales) that is thought to be the most closely related alga to land plants. This 67,737-bp mtDNA sequence, displaying 68 conserved genes and 27 introns, was compared with those of three angiosperms, the bryophyte Marchantia polymorpha, the charophycean alga Chaetosphaeridium globosum (Coleochaetales), and the green alga Mesostigma viride. Despite important differences in size and intron composition, Chara mtDNA strikingly resembles Marchantia mtDNA; for instance, all except 9 of 68 conserved genes lie within blocks of colinear sequences. Overall, our genome comparisons and phylogenetic analyses provide unequivocal support for a sister-group relationship between the Charales and the land plants. Only four introns in land plant mtDNAs appear to have been inherited vertically from a charalean algar ancestor. We infer that the common ancestor of green algae and land plants harbored a tightly packed, gene-rich, and relatively intron-poor mitochondrial genome. The group II introns in this ancestral genome appear to have spread to new mtDNA sites during the evolution of bryophytes and charalean green algae, accounting for part of the intron diversity found in Chara and land plant mitochondria.
Richard M. Mccourt - One of the best experts on this subject based on the ideXlab platform.
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phylogeny of the conjugating green algae zygnematales and desmidiales based on plastid and mitochondrial gene sequences
Journal of Phycology, 2002Co-Authors: Richard M. Mccourt, D A Hewitt, J. Park, Kenneth G. KarolAbstract:The conjugating green algae (Order Zygnematales and Desmidiales) are charophyceans, that is, they are among the green algae most closely related to land plants. Compared to the five other groups of charophyceans (Mesostigma, Klebsormidiales, Chlorokybales, Coleochaetales, Charales), the conjugating greens are by far the most diverse taxonomically (6 families, about 55 genera, 3–4000 species) and very widespread in distribution (including common species such as Spirogyra, Zygnema, Cosmarium, and Staurastrum). Thallus shape ranges from simple, oblong unicells (saccoderm desmids, or Mesotaeniaceae), to unbranched filaments of cells with smooth walls (Zygnemataceae), to elaborately ornate and deeply incised unicells or filaments made of such cells (placoderm desmids, in four families). Prior analyses of sequences of the chloroplast-encoded gene rbcL (1354 bp, or 95% of the gene) sampled from all six families showed that two of the traditional families (saccoderms and filamentous forms) are paraphyletic, i.e. they do not form two independent clades, although the component genera may together constitute a monophyletic group. In contrast, three families of placoderm desmids formed three monophyletic groups within a larger clade. New analyses using partial sequences from the mitochondrial gene coxIII (608 bp, or 76% of the gene) for 21 species of conjugating green algae from all six families supported the conclusions of the rbcL analysis, although bootstrap support for each gene along was weak for many branches. The coxIII sequences are more variable than rbcL and have proportionately more parsimony-informative sites (43% vs. 34%, respectively). Combining the two genes improved the resolution of the resulting tree: (1) bootstrap support increased for all branches, particularly in regards relationships of placoderm desmids; and (2) monophyly of a clade containing filamentous and saccoderm desmids was strongly supported. We conclude that phylogeny of conjugating green algae will be much improved by sampling from additional genes.
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One Small Step: Why Did the Charophytes Have the Right Stuff?
Journal of Phycology, 2002Co-Authors: Charles F. Delwiche, Kenneth G. Karol, Richard M. MccourtAbstract:The origin and evolution of land plants (i.e. embryophytes) represents one of the seminal events in the history of life on earth. When the land plant lineage took hold upon the continents, there were profound changes in the global environment including dramatic modification of the erosion regime, correlated changes in marine nutrient inputs, and striking fluctuations in atmospheric chemistry. These changes took place not only because of the ability of land plants to survive on land, but also because their structure and physiology permitted them to make efficient use of resources, anchor themselves effectively and in so doing stabilize the substrate and permit the formation of modern soils, and maintain metabolic activity for long periods of time even in the absence of rainfall and surface moisture. Molecular phylogenetic analyses show the order Charales is the sister group to all land plants, with the Coleochaetales sister to the land plant/Charales lineage. Thus, in a very real sense, the embryophytes are ‘drier algae.’ Many groups of green algae live in the terrestrial environment, but only one of these – the land plants – has radiated into a wide range of habitats. It is not known why the land plant lineage has been so successful. Traits that are likely to have played a role in their success include cell wall biochemistry, desiccation resistance and tolerance, structural complexity, and various reproductive strategies. In all probability, the success of the land plant lineage was not the result of a single ‘key innovation’, but an emergent property resulting from complex interactions among these and other features of the lineage. Comparative study of the properties of diverse aquatic and terrestrial algae can be used to identify properties that were important in the colonization of the land and how they interact.
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The Roots of Land Plants: Recent Research on Early Diverging Lineages in the Evolution of Higher Drier Algae
Journal of Phycology, 2002Co-Authors: Richard M. Mccourt, Kenneth G. Karol, Charles F. DelwicheAbstract:Recent multigene phylogenetic analyses of charophycean algae sensu Mattox and Stewart have advanced our understanding of the relationships of the green algae that are most closely related to land plants. Several clades of green algae are monophyletic with land plants (i.e. liverworts, mosses, nonvascular and vascular plants that arose from an aquatic ancestor) to the exclusion of other green algae: Mesostigma (a flagellate unicell); the Chlorokybales (small packets of cells); Klebsormidiales (unbranched filaments); Zygnematales (conjugating unicells, filaments, and colonies); Coleochaetales (filamentous and parenchymatous thalli); and Charales (branched filamentous thalli with complex nodal structure). The morphological and molecular diversity of the extant members of this nearly exclusively freshwater clade is remarkable. Moreover, the taxon diversity within clades is highly asymmetric, having yielded several distinctive albeit small groups of green algae, as well as one of the major evolutionary success stories on earth, viz. land plants. The most recent analysis (Karol et al. (2001) Science 294 : 2351–2353) of four genes from plastid, mitochondrial, and nuclear compartments strongly support the sister relationships of Charales (stoneworts) to the most primitive land plants. The analysis also shows that within this clade there has been a trend toward increasing complexity of thallus form (from unicells, to filaments, to branching and parenchymatous thalli) and reproduction (absence of sexual reproduction to iso- or anisogamy, to oogamy). Although the major clades mentioned above are well supported by molecular analyses, relationships among these groups are less well-resolved, especially for the Klebsormidiales, Chlorokybales, and Mesostigma. This paper reviews the morphological and molecular evidence for the relationships among and within these groups. More sequence data from a broader sampling of taxa at the base of the charophyceans (including perhaps some algae not now known to be charophytes) should provide a clearer picture of the evolution of this group and the reasons for its success.
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PHYLOGENY OF THE CONJUGATING GREEN ALGAE (ZYGNEMOPHYCEAE) BASED ON rbc L SEQUENCES
Journal of Phycology, 2000Co-Authors: Richard M. Mccourt, Jeremy Bell, Kathleen Helm-bychowski, Anna Grajewska, Kenneth G. Karol, Martin F Wojciechowski, Robert W HoshawAbstract:Sequences of the gene encoding the large subunit of RUBISCO (rbcL) for 30 genera in the six currently recognized families of conjugating green algae (Desmidiaceae, Gonatozygaceae, Mesotaeniaceae, Peniaceae, and Zygnemataceae) were analyzed using maximum parsimony and maximum likelihood; bootstrap replications were performed as a measure of support for clades. Other Charophyceae sensu Mattox and Stewart and representative land plants were used as outgroups. All analyses supported the monophyly of the conjugating green algae. The Desmidiales, or placoderm desmids, constitute a monophyletic group, with moderate to strong support for the four component families of this assemblage (Closteriaceae, Desmidiaceae, Gonatozygaceae, and Peniaceae). The analyses showed that the two families of Zygnematales (Mesotaeniaceae, Zygnemataceae), which have plesiomorphic, unornamented and unsegmented cell walls, are not monophyletic. However, combined taxa of these two traditional families may constitute a monophyletic group. Partitioning the data by codon position revealed no significant differences across all positions or between partitions of positions one and two versus position three. The trees resulting from parsimony analyses using first plus second positions versus third position differed only in topology of branches with poor bootstrap support. The tree derived from third positions only was more resolved than the tree derived from first and second positions. The rbcL-based phylogeny is largely congruent with published analyses of small subunit rDNA sequences for the Zygnematales. The molecular data do not support hypotheses of monophyly for groups of extant unicellular and filamentous or colonial desmid genera exhibiting a common cell shape. A trend is evident from simple omniradiate cell shapes to taxa with lobed cell and plastid shapes, which supports the hypothesis that chloroplast shape evolved generally from simple to complex. The data imply that multicellular placoderm desmids are monophyletic. Several anomalous placements of genera were found, including the saccoderm desmid Roya in the Gonatozygaceae and the zygnematacean Entransia in the Coleochaetales. The former is strongly supported, although the latter is not, and Entransia's phylogenetic position warrants further study.
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PHYLOGENY OF THE BASAL LINEAGES OF STREPTOPHYTA BASED ON RBCL AND ATPB GENE SEQUENCE DATA
Journal of Phycology, 2000Co-Authors: Kenneth G. Karol, Charles F. Delwiche, Richard M. MccourtAbstract:The streptophytes comprise the Charophyceae sensu Mattox and Stewart (a morphologically diverse group of fresh-water green algae) and the embryophytes (land plants). Several charophycean groups are currently recognized. These include the Charales, Coleochaetales, Chlorokybales, Klebsormidiales and Zygnemophyceae (Desmidiales and Zygnematales). Recently, SSU rRNA gene sequence data allied Mesostigma viride (Prasinophyceae) with the Streptophyta. Complete chloroplast sequence data, however, placed Mesostigma sister to all green algae, not with the streptophytes. Several morphological, ultrastructural and biochemical features unite these lineages into a monophyletic group including embryophytes, but evolutionary relationships among the basal streptophytes remain ambiguous. To date, numerous studies using SSU rRNA gene sequences have yielded differing phylogenies with varying degrees of support dependent upon taxon sampling and choice of phylogenetic method. Like SSU data, chloroplast DNA sequence data have been used to examine relationships within the Charales, Coleochaetales, Zygnemophyceae and embryophytes. Representatives of all basal streptophyte lineages have not been examined using chloroplast data in a single analysis. Phylogenetic analyses were performed using DNA sequences of rbcL (the genes encoding the large subunit of rubisco) and atpB (the beta-subunit of ATPase) to examine relationships of basal streptophyte lineages. Preliminary analyses placed the branch leading to Mesostigma as the basal lineage in the Streptophyta with Chlorokybus, the sole representative of the Chlorokybales, branching next. Klebsormidiales and the enigmatic genus Entransia were sister taxa. Sister to these, the Charales, Coleochaetales, embryophytes and Zygnemophyceae formed a monophyletic group with Charales and Coleochaetales sister to each other and this clade sister to the embryophytes.
Monique Turmel - One of the best experts on this subject based on the ideXlab platform.
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Tracing the evolution of streptophyte algae and their mitochondrial genome.
Genome Biology and Evolution, 2013Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Six monophyletic groups of charophycean green algae are recognized within the Streptophyta. Although incongruent with earlier studies based on genes from three cellular compartments, chloroplast and nuclear phylogenomic analyses have resolved identical relationships among these groups, placing the Zygnematales or the Zygnematales+ Coleochaetales as sister to land plants. The present investigation aimed at determining whether this consensus view is supported by the mitochondrial genome and at gaining insight into mitochondrial DNA (mtDNA) evolution within and across streptophyte algal lineages and during the transition toward the first land plants. We present here the newly sequenced mtDNAs of representatives of the Klebsormidiales (Entransia fimbriata and Klebsormidium spec.) and Zygnematales (Closterium baillyanum and Roya obtusa) and compare them with their homologs in other charophycean lineages as well as in selected embryophyte and chlorophyte lineages. Our results indicate that important changes occurred at the levels of genome size, gene order, and intron content within the Zygnematales. Although the representatives of the Klebsormidiales display more similarity in genome size and intron content, gene order seems more fluid and gene losses more frequent than in other charophycean lineages. In contrast, the two members of the Charales display an extremely conservative pattern of mtDNA evolution. Collectively, our analyses of gene order and gene content and the phylogenies we inferred from 40 mtDNAencoded proteins failed to resolve the relationships among the Zygnematales, Coleochaetales, and Charales; however, they are consistent with previous phylogenomic studies in favoring that the morphologically complex Charales are not sister to land plants.
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THE GREEN ALGAL ANCESTRY OF LAND PLANTS AS REVEALED BY THE CHLOROPLAST GENOME
International Journal of Plant Sciences, 2007Co-Authors: Monique Turmel, Jean-françois Pombert, Patrick Charlebois, Christian Otis, Claude LemieuxAbstract:The phylum Streptophyta comprises all land plants and six monophyletic groups of charophycean green algae. Which of these charophycean groups is the most closely related to land plants has long been debated. In 2001, a phylogenetic analysis of four genes encoded by three cellular compartments was inferred that robustly supports the placement of the Charales as sister to land plants as well as the notion that charophycean green algae evolved progressively toward an increasing cellular complexity. This view on the origin of land plants is now being challenged by recent analyses of chloroplast genome sequences from six charophyceans. Phylogenies inferred from multiple chloroplast genes and proteins support the hypothesis that the Charales are sister to a clade composed of the Coleochaetales, the Zygnematales, and land plants, thus implying a more complex evolutionary history for charophycean green algae. Analyses of four sets of genomic features (gene content, intron content, gene order, and insertions/delet...
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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.
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the complete chloroplast dna sequences of the charophycean green algae staurastrum and zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the zygnematales
BMC Biology, 2005Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Background The Streptophyta comprise all land plants and six monophyletic groups of charophycean green algae. Phylogenetic analyses of four genes from three cellular compartments support the following branching order for these algal lineages: Mesostigmatales, Chlorokybales, Klebsormidiales, Zygnematales, Coleochaetales and Charales, with the last lineage being sister to land plants. Comparative analyses of the Mesostigma viride (Mesostigmatales) and land plant chloroplast genome sequences revealed that this genome experienced many gene losses, intron insertions and gene rearrangements during the evolution of charophyceans. On the other hand, the chloroplast genome of Chaetosphaeridium globosum (Coleochaetales) is highly similar to its land plant counterparts in terms of gene content, intron composition and gene order, indicating that most of the features characteristic of land plant chloroplast DNA (cpDNA) were acquired from charophycean green algae. To gain further insight into when the highly conservative pattern displayed by land plant cpDNAs originated in the Streptophyta, we have determined the cpDNA sequences of the distantly related zygnematalean algae Staurastrum punctulatum and Zygnema circumcarinatum.
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The Mitochondrial Genome of Chara vulgaris: Insights into the Mitochondrial DNA Architecture of the Last Common Ancestor of Green Algae and Land Plants
The Plant Cell, 2003Co-Authors: Monique Turmel, Christian Otis, Claude LemieuxAbstract:Mitochondrial DNA (mtDNA) has undergone radical changes during the evolution of green plants, yet little is known about the dynamics of mtDNA evolution in this phylum. Land plant mtDNAs differ from the few green algal mtDNAs that have been analyzed to date by their expanded size, long spacers, and diversity of introns. We have determined the mtDNA sequence of Chara vulgaris (Charophyceae), a green alga belonging to the charophycean order (Charales) that is thought to be the most closely related alga to land plants. This 67,737-bp mtDNA sequence, displaying 68 conserved genes and 27 introns, was compared with those of three angiosperms, the bryophyte Marchantia polymorpha, the charophycean alga Chaetosphaeridium globosum (Coleochaetales), and the green alga Mesostigma viride. Despite important differences in size and intron composition, Chara mtDNA strikingly resembles Marchantia mtDNA; for instance, all except 9 of 68 conserved genes lie within blocks of colinear sequences. Overall, our genome comparisons and phylogenetic analyses provide unequivocal support for a sister-group relationship between the Charales and the land plants. Only four introns in land plant mtDNAs appear to have been inherited vertically from a charalean algar ancestor. We infer that the common ancestor of green algae and land plants harbored a tightly packed, gene-rich, and relatively intron-poor mitochondrial genome. The group II introns in this ancestral genome appear to have spread to new mtDNA sites during the evolution of bryophytes and charalean green algae, accounting for part of the intron diversity found in Chara and land plant mitochondria.