Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura)

Abstract

We determined the complete mitochondrial DNA sequence for a swimming crab Portunus trituberculatus (Miers, 1876) (Crustacea: Decapoda: Brachyura). The entire genome was amplified using a long PCR technique, and the products were subsequently used as templates for direct sequencing using a primer walking strategy. The genome (16,026 bp) contained the same 37 genes (two rRNAs, 22 tRNAs, and 13 proteins) plus the putative control region as found in other arthropods. The gene order of P. trituberculatus was largely identical to those so far obtained for other arthropods such as Drosophila yakuba, although the relative position of the tRNA^His gene differed from all other arthropods studied so far. While the tRNA^His gene in other arthropod mitochondrial genomes is located between the ND4 and ND5 genes, that of P. trituberculatus was found between the tRNA^Glu and the tRNA^Phe genes, which were located downstream of the ND5 gene. The present gene order could have resulted from tandem duplication occurring in the tRNA^Phe-ND5-tRNA^His region (typical gene order in other arthropods) and following deletions of redundant genes. This is the first report of a mitochondrial genome of a brachyuran crab, one of the most diversified and economically important groups of crustaceans.

Introduction

The mitochondrial DNA (mtDNA), which is typically a single circular duplex molecule ranging in size from approximately 15–17 kilobases and encoding genes of 13 proteins, 22 tRNAs, and two rRNAs (Wolstenholme, 1992), has been studied in detail in numerous metazoan species, and an increasing number of the complete sequences have become available (Boore, 1999; NCBI at http://www.ncbi.nlm.nih.gov/). In crustaceans, complete or nearly complete mtDNA sequences for six species have been reported: two branchiopods, Artemia franciscana (see Valverde et al., 1994) and Daphnia pulex (see Crease, 1999); a copepod, Tigriopus japonicus (see Machida et al., 2002); three decapods, Penaeus monodon (giant tiger prawn; Wilson et al., 2000), Pagurus longicarpus (hermit crab; Hickerson and Cunningham, 2000), and Panulirus japonicus (Japanese spiny lobster; Yamauchi et al., 2002).

Because of maternal inheritance, a fast evolutionary rate compared to that of the nuclear DNA, and a lack of intermolecular genetic recombination, mtDNAs have been extensively used for studying population structure, phylogeography, and phylogenetic relationships at various taxonomic levels (Avise, 2000). Much more mitochondrial genomic information from various species is required in order to advance these researches effectively, and in particular its uses in crustacean biology have been restricted to few genes, such as the COI and lrRNA genes. It appears that this result from the early availability of ‘universal’ primers for those genes (Folmer et al., 1994, Simon et al., 1994). There is a critical paucity of information on crustacean mitochondrial genome.

The brachyuran species (belonging to Decapoda) are generally called crabs, and are known as one of the most typical crustaceans to many people. In terms of numbers of species, they are one of the biggest groups of the crustaceans (Warner, 1977), comprising about 6000 species placed in 47 families (Bowman and Abele, 1982). These species are found worldwide, largely in marine habitats, being distributed from tropical mountains to deep-sea hydrothermal vents. Life-styles are also diverse, ranging from benthic to free living and planktonic or parasitic. Their adult sizes range from <5.0 mm width in clam crabs (Pinnotheridae) to >3.0 m width in a giant spider crab (Majidae) including the legs. Furthermore, this group includes a lot of commercially important species, such as swimming crabs, giant crabs, and queen crabs. Crabs have been widely used in zoological research, because of their diversity, easy availability, and convenient size (Warner, 1977).

A swimming crab, Portunus trituberculatus (Crustacea: Decapoda: Brachyura), inhabits the seafloor habitats with sand or pebbles, being widely distributed in the coastal waters of Japan, Korea, China, and Taiwan (Sakai, 1976). This species is one of the most common edible crabs in Japanese waters, and has been artificially propagated and stocked. Because of its commercial importance, the genetic structure of P. trituberculatus has been investigated by analysis of the restriction fragment length polymorphisms (RFLPs) of mtDNA (Imai et al., 1999) with respect to stock identification, management, and conservation. These analyses, however, have failed to reveal unambiguous geographic structure of the local populations, partly because of paucity of the information contained in the RFLPs.

In this study, we report the first example of a complete nucleotide sequence of the mitochondrial genome for a crab, P. trituberculatus, determined by using a long PCR technique (Cheng et al., 1994, Miya and Nishida, 1999) and primer walking strategy (Machida et al., 2002, Yamauchi et al., 2002). The new sequence data from this crab may be of importance not only for macroevolutionary studies, such as crustacean phylogenies, but also for microevolutionary studies, such as population structure and stock identifications.