The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

Abstract

Background: Animal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome evolution. Within the phylum Arthropoda the subphylum Crustacea includes over 50,000 named species with immense variation in body plans and habitats, yet only 23 complete mitochondrial genomes are available from this subphylum.

Results: I describe here the complete mitochondrial genome of the crustacean Squilla mantis (Crustacea: Malacostraca: Stomatopoda). This 15994-nucleotide genome, the first described from a hoplocarid, contains the standard complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region that is found in most other metazoans. The gene order is identical to that considered ancestral for hexapods and crustaceans. The 70% AT base composition is within the range described for other arthropods. A single unusual feature of the genome is a 230 nucleotide non-coding region between a serine transfer RNA and the nad1 gene, which has no apparent function. I also compare gene order, nucleotide composition, and codon usage of the S. mantis genome and eight other malacostracan crustaceans. A translocation of the histidine transfer RNA gene is shared by three taxa in the order Decapoda, infraorder Brachyura; Callinectes sapidus, Portunus trituberculatus and Pseudocarcinus gigas. This translocation may be diagnostic for the Brachyura. For all nine taxa nucleotide composition is biased towards AT-richness, as expected for arthropods, and is within the range reported for other arthropods. Codon usage is biased, and much of this bias is probably due to the skew in nucleotide composition towards AT-richness.

Conclusion: The mitochondrial genome of Squilla mantis contains one unusual feature, a 230 base pair non-coding region has so far not been described in any other malacostracan. Comparisons with other Malacostraca show that all nine genomes, like most other mitochondrial genomes, share a bias toward AT-richness and a related bias in codon usage. The nine malacostracans included in this analysis are not representative of the diversity of the class Malacostraca, and additional malacostracan sequences would surely reveal other unusual genomic features that could be useful in understanding mitochondrial evolution in this taxon.

Figure 1

Squilla mantis mitochondrial tRNA genes folded into inferred cloverleaf structures.

Figure 2

Mitochondrial gene orders for nine malacostracan crustaceans. The style of the figure is adapted from Figure 1 of Lavrov et al. [25]. Protein and ribosomal RNA genes (large boxes) are abbreviated as in the text. Transfer RNA genes are abbreviated with single letter codes (see Figure 1). The striped box represents the AT-rich region. The ancestral pancrustacean gene order is found for five of the nine taxa, including Squilla mantis. The position of AT-rich region 1 in the S. mantis genome is noted with an arrow. Genes are transcribed from right to left except when underlined. Shaded boxes indicate genes whose positions differ from their positions in the ancestral pancrustacean sequence. The number in parentheses next to taxa names represents the minimum number of rearrangement events that separates that gene arrangement from the ancestral pancrustacean gene order (see Miller et al. [20] for a fuller discussion of the rearrangements in C. destructor).

Figure 3

Relationship between GC content and effective number of codons for mitochondrial protein-coding genes. The line represents the least squares linear regression calculated for the all genes data set. This equation is shown in Table 4.