Open Access Research article

Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae)

Nataliya Rybalka12, Matthias Wolf3, Robert A Andersen4 and Thomas Friedl1*

Author affiliations

1 Experimental Phycology and Culture Collection of Algae (SAG), Georg August University Göttingen, Untere Karspüle 2a, Göttingen, 37073, Germany

2 Plant Cell Physiology and Biotechnology, Botanical Institute, Christian Albrechts University of Kiel, Am Botanischen Garten 1-9, Kiel, 24118, Germany

3 Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, 97074, Germany

4 Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, 98250, USA

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Citation and License

BMC Evolutionary Biology 2013, 13:39  doi:10.1186/1471-2148-13-39

Published: 13 February 2013



Heterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium. Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity.


Two independent types of molecular data, the chloroplast-encoded psbA/rbcL spacer complemented by rbcL gene and the internal transcribed spacer 2 of the nuclear rDNA cistron (ITS2), congruently recovered a robust phylogenetic structure. With ITS2 considerable sequence and secondary structure divergence existed among the eight species, but a combined sequence and secondary structure phylogenetic analysis confined to helix II of ITS2 corroborated relationships as inferred from the rbcL gene phylogeny. Intra-genomic divergence of ITS2 sequences was revealed in many strains. The ‘monophyletic species concept’, appropriate for microalgae without known sexual reproduction, revealed eight different species. Species boundaries established using the molecular-based monophyletic species concept were more conservative than the traditional morphological species concept. Within a species, almost identical chloroplast marker sequences (genotypes) were repeatedly recovered from strains of different origins. At least two species had widespread geographical distributions; however, within a given species, genotypes recovered from Antarctic strains were distinct from those in temperate habitats. Furthermore, the sequence diversity may correspond to adaptation to different types of habitats or climates.


We established a method and a reference data base for the unambiguous identification of species of the common soil microalgal genus Heterococcus which uses DNA sequence variation in markers from plastid and nuclear genomes. The molecular data were more reliable and more conservative than morphological data.

Soil algae; Heterococcus; Xanthophyceae; psbA/rbcL spacer; ITS2; Systematics; Molecular phylogeny; Species concept