Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
BMC Genomics
2006 Jan 27;7:17. doi: 10.1186/1471-2164-7-17.
Show Gene links
Show Anatomy links
Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus.
Yasuda N
,
Hamaguchi M
,
Sasaki M
,
Nagai S
,
Saba M
,
Nadaoka K
.
???displayArticle.abstract???
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.
Figure 1. Alignment of the twenty-two tRNA form mitochondrial genome of A. planci, A. brevispinus and Asterina pectinifera. * Data from Asakawa et al. 199510. A. planci: Acanthaster planci; A. brevis: Acanthaster brevispinus; Asterina: Asterina pectinifera, Each anticodon is located at the middle of anticodon loop (+++). Bars above alignments indicate unambiguously aligned stem regions. Asterisks indicate deletions and dots indicate the same nucleotides as A. planci. The last one letter is one nucleotide protrusion of 3' amino-acid accepter stem.
Figure 2. The molecular phylogeny of asteroid species based on the CO1 sequence data. Cucumaria miniata (Cucumariidae) and Paracentrotus lividus (Echinidae) were used as the out-groups. The ML tree was reconstructed with the TrN + I + G model using PAUP 4.0b10. Only bootstrap values of 50% or higher are shown to the left of internal nodes. The first numbers are from neighbor-joining analyses (1000 replications), the second numbers are from maximum likelihood analyses (100 replications) and the last numbers are from Parsimony analyses (1000 replications; characters were unweighted).
Anderson,
Sequence and organization of the human mitochondrial genome.
1981, Pubmed
Anderson,
Sequence and organization of the human mitochondrial genome.
1981,
Pubmed
Asakawa,
Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes.
1991,
Pubmed
,
Echinobase
Asakawa,
Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome.
1995,
Pubmed
,
Echinobase
Bendezu,
Identification of Mytilus spp. and Pecten maximus in Irish waters by standard PCR of the 18S rDNA gene and multiplex PCR of the 16S rDNA gene.
2005,
Pubmed
Boore,
Animal mitochondrial genomes.
1999,
Pubmed
Cantatore,
The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus.
1989,
Pubmed
,
Echinobase
De Giorgi,
Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome.
1996,
Pubmed
,
Echinobase
De Giorgi,
Lineage-specific evolution of echinoderm mitochondrial ATP synthase subunit 8.
1997,
Pubmed
,
Echinobase
Dreyer,
The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca).
2004,
Pubmed
Folmer,
DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.
1994,
Pubmed
,
Echinobase
Hebert,
Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species.
2003,
Pubmed
Jacobs,
Nucleotide sequence and gene organization of sea urchin mitochondrial DNA.
1988,
Pubmed
,
Echinobase
Johns,
A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene.
1998,
Pubmed
Lavrov,
The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus.
2000,
Pubmed
Le,
Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes.
2004,
Pubmed
Lucas,
Hybrid crown-of-thorns starfish (Acanthaster planci xA. brevispinus) reared to maturity in the laboratory.
1976,
Pubmed
,
Echinobase
Matsubara,
Close relationship between Asterina and Solasteridae (Asteroidea) supported by both nuclear and mitochondrial gene molecular phylogenies.
2004,
Pubmed
,
Echinobase
Oberst,
PCR-based DNA amplification and presumptive detection of Escherichia coli O157:H7 with an internal fluorogenic probe and the 5' nuclease (TaqMan) assay.
1998,
Pubmed
Perna,
Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes.
1995,
Pubmed
Posada,
MODELTEST: testing the model of DNA substitution.
1998,
Pubmed
Scouras,
Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny.
2004,
Pubmed
,
Echinobase
Shin,
Rapid identification of up to three Candida species in a single reaction tube by a 5' exonuclease assay using fluorescent DNA probes.
1999,
Pubmed
Tamura,
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
1993,
Pubmed
Thompson,
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
1997,
Pubmed
Wada,
Mitochondrial rDNA phylogeny of the asteroidea suggests the primitiveness of the paxillosida.
1996,
Pubmed
,
Echinobase
Wolstenholme,
Animal mitochondrial DNA: structure and evolution.
1992,
Pubmed
Yasuda,
Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus.
2006,
Pubmed
