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Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

¹ School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
² Centre for Marine Sciences, University of Queensland, Qld 4072, Australia

Correspondence
Dee A. Carter
d.carter{at}mmb.usyd.edu.au

The chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium. DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or ‘twin’ formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium.

This paper was presented at the XIVth meeting of the International Society for Evolutionary Protistology in Vancouver, Canada, 19–24 June 2002.

The GenBank accession numbers for the full non-coding DNA sequences of psbA minicircles from Sym-Gt1, -Gt2, -Ha, -Lp and -Pd are AY160085–AY160089, respectively. The GenBank accession number for the complete psbA ORF sequence from culture Tm8.2 is AY160084.

Phylogenetic information on relatedness of selected OTI zooxanthellae is available as supplementary material in IJSEM Online.

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