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Genetic diversity, morphological uniformity and polyketide production in dinoflagellates (Amphidinium, Dinoflagellata).

Murray SA, Garby T, Hoppenrath M, Neilan BA - PLoS ONE (2012)

Bottom Line: We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families.Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species.We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, University of New South Wales, New South Wales, Sydney, Australia. s.murray@unsw.edu.au

ABSTRACT
Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a 'model' dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the diversity of 'cryptic' species of Amphidinium that are morphologically similar to A. carterae, including the very similar species Amphidinium massartii, based on light and electron microscopy, two nuclear gene regions (LSU rDNA and ITS rDNA) and one mitochondrial gene region (cytochrome b). We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families. Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species. We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them.

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Partial alignment of β-ketosynthase protein sequence from bacteria and alveolates, including three conserved active site residues, and showing conserved regions against which degenerate primers were designed.
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pone-0038253-g006: Partial alignment of β-ketosynthase protein sequence from bacteria and alveolates, including three conserved active site residues, and showing conserved regions against which degenerate primers were designed.

Mentions: Partial KS sequences from Amphidinium strain CS-740 (A. carterae) and from CS-259 (A. massartii) were amplified and sequenced (Table 3, Fig. 6). We attempted to amplify KS sequences from all 6 strains examined in this study (Table 1). The lack of recovery of a KS sequence from a strain is not necessarily indicative of its absence, as even the KS sequences that we did recover varied considerably in DNA sequence, and so the primer sets we used may not have been specific enough to amplify KS genes from every strain. The recovered sequences were included in an alignment of KS sequences from dinoflagellates and several unrelated organisms (Fig. 6). Translated protein sequences were found to align well to sequences from other dinoflagellates, over several key conserved regions (Fig. 6). The Amphidinium CS-740 KS sequence was 47% similar to the Karenia brevis and Alexandrium catenella sequences based on a 233 amino acid alignment; and was found to be most similar to a Type I PKS, which included a dinoflagellate specific spliced leader sequence on the 5′ end (Table 3). The Amphidinium CS-259 KS sequence was 32% similar to the K. brevis and A. catenella sequences based on a 149 amino acid alignment. This sequence was most similar to a PKS sequence from Karenia brevis, which had a spliced leader sequence on the 5′ end (Table 3). Two histidine active sites were found to be conserved in the Amphidinium CS-740 sequence (Fig. 6).


Genetic diversity, morphological uniformity and polyketide production in dinoflagellates (Amphidinium, Dinoflagellata).

Murray SA, Garby T, Hoppenrath M, Neilan BA - PLoS ONE (2012)

Partial alignment of β-ketosynthase protein sequence from bacteria and alveolates, including three conserved active site residues, and showing conserved regions against which degenerate primers were designed.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3366924&req=5

pone-0038253-g006: Partial alignment of β-ketosynthase protein sequence from bacteria and alveolates, including three conserved active site residues, and showing conserved regions against which degenerate primers were designed.
Mentions: Partial KS sequences from Amphidinium strain CS-740 (A. carterae) and from CS-259 (A. massartii) were amplified and sequenced (Table 3, Fig. 6). We attempted to amplify KS sequences from all 6 strains examined in this study (Table 1). The lack of recovery of a KS sequence from a strain is not necessarily indicative of its absence, as even the KS sequences that we did recover varied considerably in DNA sequence, and so the primer sets we used may not have been specific enough to amplify KS genes from every strain. The recovered sequences were included in an alignment of KS sequences from dinoflagellates and several unrelated organisms (Fig. 6). Translated protein sequences were found to align well to sequences from other dinoflagellates, over several key conserved regions (Fig. 6). The Amphidinium CS-740 KS sequence was 47% similar to the Karenia brevis and Alexandrium catenella sequences based on a 233 amino acid alignment; and was found to be most similar to a Type I PKS, which included a dinoflagellate specific spliced leader sequence on the 5′ end (Table 3). The Amphidinium CS-259 KS sequence was 32% similar to the K. brevis and A. catenella sequences based on a 149 amino acid alignment. This sequence was most similar to a PKS sequence from Karenia brevis, which had a spliced leader sequence on the 5′ end (Table 3). Two histidine active sites were found to be conserved in the Amphidinium CS-740 sequence (Fig. 6).

Bottom Line: We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families.Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species.We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, University of New South Wales, New South Wales, Sydney, Australia. s.murray@unsw.edu.au

ABSTRACT
Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a 'model' dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the diversity of 'cryptic' species of Amphidinium that are morphologically similar to A. carterae, including the very similar species Amphidinium massartii, based on light and electron microscopy, two nuclear gene regions (LSU rDNA and ITS rDNA) and one mitochondrial gene region (cytochrome b). We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families. Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species. We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them.

Show MeSH