Shedding new light on old algae

The existence of massive cryptic diversity in algae makes linking DNA-based lineages to existing taxa exceedingly difficult. A better integration of historical collections into modern taxonomic research is therefore highly desirable. Using the brown algal genus Lobophora as a test case, we explore the feasibility of linking taxonomic names to clades in modern phylogenies.

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Phylogeny of Lobophora with holotypes indicated in red and epitypes and a neotype in green

Despite Lobophora being a pantropical genus with probably more than 100 species, traditionally only a handful of species have been recognized. In this study we reevaluated the identity of 17 historical taxa thought to belong to Lobophora by attempting DNA amplification of herbarium material as well as specimens recently collected from the type localities (epitypes). In an attempt to assign them to Molecular Operational Taxonomic Units, the obtained sequences were integrated in a global Lobophora phylogeny based upon data derived from more than 650 specimens. Our results indicate that although five sequences were obtained from type specimens, exclusive reliance on information preserved in type specimens is problematic. Epitype material proved a more successful way forward, but this route often comes with a considerable degree of uncertainty, especially in tropical regions where the extent of sympatry among Lobophora lineages is often considerable. More problematic from a broader perspective is the fact that for 35% of historical taxa, either the type could not be traced or permission was not granted to extract DNA from the types. Such a low accessibility rate may reduce our reliance on type material and jeopardize future efforts to integrate historical taxa into a framework of a modern DNA-based taxonomy.

Vieira C, Camacho O, Wynne MJ, Mattio L, Anderson RJ, Bolton JJ, Sansón M, D’Hondt S, Leliaert F, Fredericq S, Payri C, De Clerck O. 2016. Shedding new light on old algae: Matching names and sequences in the brown algal genus Lobophora (Dictyotales, Phaeophyceae). Taxon 65:689-707.

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A new class of green algae: Palmophyllophyceae class. nov.

In a recent study, published in Scientific Reports, we provide solid phylogenetic evidence that the enigmatic green seaweed order Palmophyllales together with the unicellular planktonic Prasinococcales (= prasinophyte clade VI) form the deepest-branching clade of the Chlorophyta. Our analyses are based on chloroplast genomic, and nuclear rDNA data.

 

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Phylogeny of the green plants inferred from 71 concatenated plastid genes showing the position of the new class Palmophyllophyceae.

Species of Palmophyllales typically grow in deep marine waters and other shady habitats. The group is characterized by a unique form of multicellularity, forming macroscopic plants that are composed of isolated and undifferentiated spherical cells embedded in an amorphous gelatinous matrix. In 2010, we showed that the Palmophyllales formed an early-diverging lineage of green plants, but the exact phylogenetic position could not be determined with certainty.

Our phylogenetic results improve our understanding of morphological evolution in the green algae. Until present, the early-diverging lineages of the Chlorophyta (the prasinophytes) were only known to comprise unicellular planktonic algae. Our results point to an independent origin of macroscopic growth and multicellularity outside of the core Chlorophyta.

Our study also contributes to a better understanding of plastid genome evolution in green plants. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants.

The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov.

 

Leliaert F, Tronholm A, Lemieux C, Turmel M, et al. 2016. Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. Scientific Reports 6:25367. article

Leliaert F, Verbruggen H, Zechman FW. 2011. Into the deep: New discoveries at the base of the green plant phylogeny. BioEssays 33:683-692. article

Zechman FW, Verbruggen H, Leliaert F, Ashworth M, et al. 2010. An unrecognized ancient lineage of green plants persists in deep marine waters. Journal of Phycology 46:1288-1295. article

New book

Hot off the press: Part 2/1 of Engler’s Syllabus of Plant Families – Photoautotrophic eukaryotic Algae provides a thorough treatise of the world-wide morphological and molecular diversity of the Glaucocystophyta, Cryptophyta, Dinophyta/Dinozoa, Haptophyta, Heterokontophyta/Ochrophyta, Chlorarachniophyta/Cercozoa, Euglenophyta/Euglenozoa, Chlorophyta, and Streptophyta (p.p.) (The red algae will be treated in Part 2/2).

Part 2/1 of Engler's Syllabus of Plant Families - Photoautotrophic eukaryotic Algae
Part 2/1 of Engler’s Syllabus of Plant Families – Photoautotrophic eukaryotic Algae

Engler’s Syllabus of Plant Families has since its first publication in 1887 aimed to provide a concise survey of the plant kingdom as a whole, presenting all higher systematic units right down to families and genera of plants and fungi. In 1954, more than 60 years ago, the 12th edition of the well-known “Syllabus der Pflanzenfamilien” (“Syllabus of Plant Families”) was published.

Now, the completely restructured and revised 13th edition of Engler’s Syllabus published in 5 parts and in English language for the first time also considers molecular data, which have only recently become available in order to provide an up-to-date evolutionary and systematic overview of the plant groups treated.

Horizontal transfer of bacterial gene regions to chloroplast genomes of green algae

Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. In a paper we recently published in BMC Genomics, we report on the complete cpDNAs of Bryopsis plumosa and Tydemania expeditionis, as well as a re-annotated cpDNA of B. hypnoides (which was shown to contain a higher number of genes than originally published).

Gene maps of the chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones. The red arcs indicate gene regions of putative bacterial origin.
Gene maps of the chloroplast genomes of Bryopsis plumosa and Tydemania expeditionis. The red arcs indicate gene regions of bacterial origin.

The cpDNAs of B. plumosa and T. expeditionis are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta, and both lack a large inverted repeat.

Both chloroplast genomes contain DNA regions with genes of bacterial origin, including rhs-family genes, and several genes involved in mobile functions, such as transposases, integrases, DNA polymerases, and phage/plasmid DNA primases. Another unexpected finding was the presence of two genes in T. expeditionis showing close similarity to bacterial DNA methyltransferases, a family of genes that have up till now not been found in any plastid genome.

The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae. Our data adds to the scarce knowledge of horizontal transfer of bacterial DNA to plastid genomes.

In addition, chloroplast genomic data were used to evaluate phylogenetic hypotheses in the Chlorophyta. These analyses, however, were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.

Phylogenetic trees of Chlorophyta inferred from a 50-gene dataset.  (A) Bayesian majority rule tree showing all compatible partitions, inference from the protein alignment of 51 concatenated chloroplast genes (9,300 amino acid positions and 44 terminal taxa). Node support is given as Bayesian posterior probabilities and maximum-likelihood (ML) bootstrap values of the protein analyses (above branches), and the nucleotide analyses (below branches); values <0.9 and 50, respectively, are not shown; asterisks indicated full support in both the Bayesian and ML analyses. (B) Bayesian tree inference from the nucleotide alignment (first two codon positions) of 51 concatenated chloroplast genes (18,600 nucleotide positions and 44 terminal taxa). Prasinophytes are not shown. Node support is given as Bayesian posterior probabilities and maximum-likelihood (ML) bootstrap values, and asterisks indicate full support in both analyses.
Phylogenetic trees of Chlorophyta inferred from a 50-gene dataset (A: protein dataset, B: nucleotide dataset).

Read more: www.biomedcentral.com/1471-2164/16/204 (i)

Diversity and Evolution of Algae