New book: Freshwater Flora of Central Europe, Vol 13: Chlorophyta: Ulvophyceae

This volume of the “Süßwasserflora von Mitteleuropa” covers the freshwater, aerophytic, and terrestrial species of Ulvophyceae, one of the main classes of green algae. Although most of the species diversity of Ulvophyceae is found in the marine environment, a substantial number of species also occurs in brackish, freshwater, and aero-terrestrial habitats. These species are found in nine orders: Ulvales and Ulotrichales, which contain most freshwater species, the Trentepohliales which is exclusively aero-terrestrial, the smaller orders Chlorocystidales, Oltmannsiellopsidales, Scotinosphaerales, and Ignatiales, and the large but mainly marine orders Cladophorales and Bryopsidales. One other order, Dasycladales, only includes marine species and is thus not included in the present volume.

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Current view of phylogenetic relationships of the core Chlorophyta

Freshwater ulvophycean algae display a wide variety of thallus morphologies, ranging from microscopic unicellular organisms to larger, filamentous or parenchymatic algae.

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Species are also found in a wide diversity of habitats, generally attached, or sometimes free-floating. Several marine species occur over a broad salinity range, and are found in brackish to freshwater and semi-terrestrial habitats. Other species are restricted to freshwater or aero-terrestrial habitats. Several species are found in highly specialized habitats such as epizoic on freshwater snails or on carapaces of freshwater turtles, epiphytic on aquatic lichens or as lichen phycobionts, or endophytic in filamentous algae or mesophyll of vascular plants. This volume serves as a reference work for identifying these ulvophyte green algae by providing keys, detailed descriptions, and illustrations of the more than 100 European species. As in other volumes of this series, this treatment is not restricted to European taxa, and includes descriptions and illustrations of more than other 100 taxa found on other continents. The present study incorporates the latest findings in molecular phylogeny, ultrastructure and morphology for the classification, delimitation and identification of the species. In addition, it significantly revises the taxonomy of ulvophytes, in particular the orders Ulvales and Ulotrichales, based on new molecular phylogenetic data, combined with morphological data.

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Phylogeny of the Ulvales
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Phylogeny of the Ulotrichales

We propose to resurrect one order and family (Chlorocystidales and Chlorocystidaceae), and describe five new families (Binucleariaceae, Planophilaceae, Hazeniaceae, Sarcinofilaceae, and Tupiellaceae). In addition, we formally describe the order Ignatiales and family Ignatiaceae based on published molecular and ultrastructural data. This book is one of the first comprehensive treatments of species diversity of nonmarine Ulvophyceae, and we hope that it will be a useful tool in green algal research worldwide.

Škaloud, P., Rindi, F., Boedeker, C. & Leliaert, F. (2018) Freshwater Flora of Central Europe, Vol 13: Chlorophyta: Ulvophyceae (Süßwasserflora von Mitteleuropa, Bd. 13: Chlorophyta: Ulvophyceae). Springer Spektrum, Berlin, Heidelberg.
http://www.springer.com/gp/book/9783662554944

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The prodigious chloroplast genome of Cladophorales green algae

After more than 10 years of research, and sequencing millions of reads, we were finally able to uncover secrets of the chloroplast genome of Cladophorales green algae. In stark contrast to other algae, little was known about the gene content and structure of the chloroplast genome in this ecologically important group of marine and freshwater green algae. Most previous attempts to amplify common chloroplast genes have failed, and an atypical plastid genome has been suggested by the presence of abundant plasmid-like DNA in the chloroplasts of several species. Pioneering work of John La Claire and colleagues in the 1990-ies revealed that these structures are single-stranded DNA molecules of 1.5-3.0 kb that fold in a hairpin configuration, and contain putatively transcribed sequences with similarity to chloroplast genes.

In a recent study, we describe intriguing features of the plastid genome of Cladophorales. Through the integration of different DNA sequencing methods, combined with RNA sequencing, we found that chloroplast protein-coding genes are highly expressed and encoded on 1-7 kb linear single-stranded DNA molecules. Due to the wide-spread presence of inverted repeats, these molecules fold into a hairpin configuration. The chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes and highlights unexpected variation in plastid genome architecture.

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Schematic representation of Boodlea chloroplast genome

Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. 2017. The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes. Current Biology 24:3771–3782 doi:10.1016/j.cub.2017.11.004.

Smith DR. 2017. Evolution: In Chloroplast Genomes, Anything Goes. Current Biology 27:R1305-R1307 doi:10.1016/j.cub.2017.10.049.

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.

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

Diversity and Evolution of Algae