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Background  The crown-of-thorns starfish,  Acanthaster planci  (L.), has been blamed for coral mortality in a large number of coral reef systems situated in the Indo-Pacific region. Because of its high fecundity and the long duration of the pelagic larval stage, the mechanism of outbreaks may be related to its meta-population dynamics, which should be examined by larval sampling and population genetic analysis. However,  A. planci  larvae have undistinguished morphological features compared with other asteroid larvae, hence it has been difficult to discriminate  A. planci  larvae in plankton samples without species-specific markers. Also, no tools are available to reveal the dispersal pathway of  A. planci  larvae. Therefore the development of highly polymorphic genetic markers has the potential to overcome these difficulties. To obtain genomic information for these purposes, the complete nucleotide sequences of the mitochondrial genome of  A. planci  and its putative sibling species,  A. brevispinus  were determined and their characteristics discussed.    Results  The complete mtDNA of  A. planci  and  A. brevispinus  are 16,234 bp and 16,254 bp in size, respectively. These values fall within the length variation range reported for other metazoan mitochondrial genomes. They contain 13 proteins, 2 rRNA, and 22 tRNA genes and the putative control region in the same order as the asteroid,  Asterina pectinifera . The A + T contents of  A. planci  and  A. brevispinus  on their L strands that encode the majority of protein-coding genes are 56.3% and 56.4% respectively and are lower than that of  A. pectinifera  (61.2%). The percent similarity of nucleotide sequences between  A. planci  and  A. brevispinus  is found to be highest in the  CO2  and  CO3  regions (both 90.6%) and lowest in  ND2  gene (84.2%) among the 13 protein-coding genes. In the deduced putative amino acid sequences,  CO1  is highly conserved (99.2%), and  ATP8  apparently evolves faster any of the other protein-coding gene (85.2%).    Conclusion  The gene arrangement, base composition, codon usage and tRNA structure of  A. planci  are similar to those of  A. brevispinus . However, there are significant variations between  A. planci  and  A. brevispinus . Complete mtDNA sequences are useful for the study of phylogeny, larval detection and population genetics.

Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus