New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data

Fučíková, Karolina; Leliaert, Frédérik; Cooper, Endymion D.; Škaloud, Pavel; D’hondt, Sofie; Clerck, Olivier De; Gurgel, Carlos Frederico D.; Lewis, Louise A.; Lewis, Paul O.; Lopez-Bautista, Juan; Delwiche, Charles F.; Verbruggen, Heroen

doi:10.3389/fevo.2014.00063

Cited by 24 publications

(29 citation statements)

References 64 publications

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“…In this study, we follow the traditional circumscription of the class Trebouxiophyceae (Friedl et al 2012, Leliaert et al 2012 considering it as a coherent group, although the monophyly of this class is not yet unequivocally demonstrated (Turmel et al 2009, Fu c ıkov a et al 2014a. We refer to the main lineages in the class as delineated by molecular phylogenetic studies carried out in recent years (Darienko et al 2010, Th€ us et al 2011, Neustupa et al 2013a,b, Moniz et al 2014.…”

Section: Methodsmentioning

confidence: 95%

Meiotic genes and sexual reproduction in the green algal class Trebouxiophyceae (Chlorophyta)

Fučíková

Pažoutová

Rindi

2015

Journal of Phycology

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Sexual reproduction is widespread in eukaryotes and is well documented in chlorophytan green algae. In this lineage, however, the Trebouxiophyceae represent a striking exception: in contrast to its relatives Chlorophyceae and Ulvophyceae this group appears to be mostly asexual, as fertilization has been rarely observed. Assessments of sexual reproduction in the Trebouxiophyceae have been based on microscopic observation of gametes fusing. New genomic data offer now the opportunity to check for the presence of meiotic genes, which represent an indirect evidence of a sexual life cycle. Using genomic and transcriptomic data for 12 taxa spanning the phylogenetic breadth of the class, we tried to clarify whether genuine asexuality or cryptic sexuality is the most likely case for the numerous putatively asexual trebouxiophytes. On the basis of these data and a bibliographic review, we conclude that the view of trebouxiophytes as primarily asexual is incorrect. In contrast to the limited number of reports of fertilization, meiotic genes were found in all genomes and transcriptomes examined, even in species presumed asexual. In the taxa examined the totality or majority of the genes were present, Helicosporidium and Auxenochlorella being the only partial exceptions (only four genes present). The evidence of sex provided by the meiotic genes is phylogenetically widespread in the class and indicates that sexual reproduction is not associated with any particular morphological or ecological trait. On the basis of the results, we expect that the existence of the meiotic genes will be documented in all trebouxiophycean genomes that will become available in the future.

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Section: Methodsmentioning

confidence: 95%

Meiotic genes and sexual reproduction in the green algal class Trebouxiophyceae (Chlorophyta)

Fučíková

Pažoutová

Rindi

2015

Journal of Phycology

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“…(formerly included in Ulvophyceae), Micromonas Manton & Parke, Pseudoscourfieldia Manton and Pyramimonas Schmarda were placed in the Prasinophyceae. Partial resolution of the phylogenetic relationships of these genera was provided by Marin &Melkonian (2009) andFučíková et al (2014) leading to the adoption of the 'prasinophytes' group concept, coined by Leliaert et al (2012).…”

Section: Methodsmentioning

confidence: 99%

Update of the Brazilian floristic list of Algae and Cyanobacteria

Menezes¹,

Bicudo²,

Moura³

et al. 2015

Rodriguésia

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An updated synthesis of cyanobacteria and algae information is presented for Brazil aiming to refine the data gathered to date and evaluate the progress of the biodiversity knowledge about these organisms in the country since the publication of the Catálogo de Plantas e Fungos do Brasil. The results of 2015 showed an increase of 1,250 species (35.7%) when compared to 2010, reaching a total of 4,747 species. The most diverse classes in species number were the Bacillariophyceae, Conjugatophyceae, Florideophyceae, Cyanophyceae, Dinophyceae and Euglenophyceae. Bacillariophyceae and Cyanophyceae had the highest increase in species number in the five-year interval. The Southeast and South regions were the most diverse, however, the Northeast, with the states of Piauí and Sergipe, and the Central-west region, with Mato Grosso, Goiás and Distrito Federal, also stood out in the national algal biodiversity scenario. Despite the shortage of taxonomists and limited infrastructure, the results showed a significant improvement in the knowledge regarding the diversity of cyanobacteria and algae in the country during the study period, starting to even out regional geographical differences caused by subsampling. Key words: Biodiversity, phycology. ResumoApresenta-se uma síntese atualizada de informações sobre algas no Brasil objetivando refinar os dados reunidos até o presente, bem como avaliar os avanços sobre o conhecimento da diversidade de algas no país desde a publicação do Catálogo de Plantas e Fungos do Brasil. Os resultados de 2015 mostraram um acréscimo de 1.250 espécies (35.7%) a um total de 4.747 em relação a 2010. As classes mais diversas em número de espécies foram Bacillariophyceae, Conjugatophyceae, Florideophyceae, Cyanophyceae, Dinophyceae e Euglenophyceae. Bacillariophyceae e Cyanophyceae tiveram o maior acréscimo de espécies no intervalo de cinco anos. A região Sudeste e Sul foram as mais diversas, porém, as regiões Nordeste com os estados do Piauí e Sergipe e Centro-Oeste com os estados de Mato Grosso, Goiás e Distrito Federal destacaram--se no cenário da biodiversidade nacional. Apesar da escassez de taxonomistas e da infraestrutura limitada, os resultados obtidos evidenciaram um avanço significativo no conhecimento da diversidade de algas no país nesse período de cinco anos, iniciando uma mudança quanto as diferenças geográficas regionais. Palavras-chave: Biodiversidade, ficologia.

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“…Like the Chlorodendrophyceae, Pedinophyceae, Ulvophyceae and Trebouxiophyceae, this class is part of the core Chlorophyta, i.e., the rapid radiation of lineages that took place following the diversification of the prasinophyte algae. The precise relationships of the Chlorophyceae with the other core chlorophyte classes are still uncertain (Fucikova et al, 2014; Lemieux, Otis & Turmel, 2014; Leliaert & Lopez-Bautista, 2015; Sun et al, 2016; Turmel et al, 2016a). Five orders are currently recognized in the Chlorophyceae and as revealed by phylogenetic analyses of multiple chloroplast-encoded proteins/genes from representative taxa, they form two distinct clades: the CS clade consisting of the Chlamydomonadales (or Volvocales) and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales (Turmel et al, 2008; Brouard et al, 2010; Lemieux et al, 2015; Watanabe et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

Brouard

Turmel

Otis

et al. 2016

PeerJ

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BackgroundThe 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.MethodsThe 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.ResultsThe 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.DiscussionOur 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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New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data

Cited by 24 publications

References 64 publications

Meiotic genes and sexual reproduction in the green algal class Trebouxiophyceae (Chlorophyta)

Meiotic genes and sexual reproduction in the green algal class Trebouxiophyceae (Chlorophyta)

Update of the Brazilian floristic list of Algae and Cyanobacteria

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

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