Complete Mitochondrial Genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura, Arthropoda) and Implications for Chelicerate Phylogenetic Studies

Abstract

Horseshoe crabs (order Xiphosura) are often referred to as an ancient order of marine chelicerates and have been considered as keystone taxa for the understanding of chelicerate evolution. However, the mitochondrial genome of this order is only available from a single species, Limulus polyphemus. In the present study, we analyzed the complete mitochondrial genomes from two Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus tridentatus to offer novel data for the evolutionary relationship within Xiphosura and their position in the chelicerate phylogeny. The mitochondrial genomes of C. rotundicauda (15,033 bp) and T. tridentatus (15,006 bp) encode 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Overall sequences and genome structure of two Asian species were highly similar to that of Limulus polyphemus, though clear differences among three were found in the stem-loop structure of the putative control region. In the phylogenetic analysis with complete mitochondrial genomes of 43 chelicerate species, C. rotundicauda and T. tridentatus were recovered as a monophyly, while L. polyphemus solely formed an independent clade. Xiphosuran species were placed at the basal root of the tree, and major other chelicerate taxa were clustered in a single monophyly, clearly confirming that horseshoe crabs composed an ancestral taxon among chelicerates. By contrast, the phylogenetic tree without the information of Asian horseshoe crabs did not support monophyletic clustering of other chelicerates. In conclusion, our analyses may provide more robust and reliable perspective on the study of evolutionary history for chelicerates than earlier analyses with a single Atlantic species.

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

“…Different gene rearrangements in the mitochondrial genome is relatively common in crustacean species (Shen et al, 2007), and are probably caused by slipped-strand mispair and gene deletions (Yamauchi et al, 2003). Nine 1-to 7-bp overlaps and 13 intergenic spacers that were between 1 and 30 bp in length were found, which in general is similar to that reported in other species' mitochondrial genomes (Ma et al, 2013;Baek et al, 2014;Wang et al, 2014). The A + T contents of the different regions ranged from 66.79% (protein-coding region) to 76.22% (control region), and the overall A + T content was 68.72%, which is similar to that in C. japonica, Scylla olivacea, and S. serrata (Table 2).…”

“…Complete mitochondrial genome sequence information is useful in studying genome-level characteristics and phylogenetic relationships (Knudsen et al, 2006), because of its high mutation rate, simple structure, abundant distribution, and maternal inheritance (Yu et al, 2012;Ma et al, 2013;Baek et al, 2014). With the development of molecular techniques, it has become easier to obtain complete mitochondrial genome sequences (Wang et al, 2015), and they have been reported in many crustacean species (Shen et al, 2007;Liu and Cui, 2010;Jondeung et al, 2012;Ma et al, 2013).…”

First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics

“…Ten gene overlaps and ten intergenic spacers were found in mitochondrial genome of C. feriata , most of them have been reported in many other species mitochondrial genomes 23 24 47 . The total length of overlaps and intergenic spacers were 24 and 105 bp, with ranges from 1 to 7 and from 2 to 27 bp, respectively.…”

“…Mitochondrial genome is a typically closed-circular molecule ranging approximately from 14 to 18 kb in size, and it consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 rRNA genes, and a control region. It is thought to be an ideal marker for studies on population genetic diversity, molecular phylogeny, and species identification because of its high mutation rate, simple structure, abundant distribution, and maternal inheritance 22 23 24 . Thus far, complete mitochondrial genomes have been reported in many crustacean species, such as Litopenaeus vannamei 25 , C. japonica 21 , Scylla serrata 26 , and S. paramamosain 23 .…”

Phylogenetic analysis and identification of Charybdis natator (Herbst, 1794) from the Egyptian Coast of the Red Sea

“…Recently, molecular techniques are considered the most precise and quick methods for identification (Marshall, 2005). A mitochondrial genome is a common tool in studying species identification, molecular phylogeny and population genetic diversity (Ma et al, 2013;Baek et al, 2014). One of the most important mitochondrial genomes is the Cytochrome Oxidase subunit I (COI) gene due to its effort in various genetic studies (Buhay, 2009).…”