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

Abstract

ABSTRACT. This study determined the mitochondrial genome structure of the blue swimming crab (Portunus pelagicus), and elucidated its phylogenetic relationships among the species within the order Decapoda. The complete mitochondrial genome was 16,155 bp long, and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 DNA control region. The gene order of the genome was the same as that found within the family Portunidae. Twenty-three genes were on the heavy strand and 14 were on the light strand. Almost all of the protein-coding genes were initiated by an ATG codon, except for three genes (ATP6, ND1, and ND3) that started with a rare ATT codon. Of the 13 protein-coding genes, 10 ended with complete TAA or TAG stop codons and three ended with an incomplete T codon. Thirteen non-coding regions were identified that ranged from 1 to 30 bp in length. Nine overlaps were found, which ranged from 1 to 7 bp in length. Phylogenetic analyses based on 12 concatenated protein-coding genes revealed that P. pelagicus formed a monophyletic group with Portunus trituberculatus, which were in a larger group with Callinectes sapidus, while the genera Charybdis and Thalamita formed another group. These two groups clustered together and grouped with the genus Scylla. The phylogenetic analysis supported the inclusion of Charybdis in subfamily Portuninae of the family Portunidae, and revealed a close relationship between Charybdis and Thalamita. We suggest that Thalamita should also be classified into the subfamily Portuninae. The results can be used in the study of phylogenetic, population genetic and conservation genetics of P. pelagicus.

Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae)

“…Furthermore, several repeated motifs were identified at the 3’ end of the central domain for three Sinopotamon species, including TA (TC), TA (T), CA (TA) and AT ( AA ). Similar motifs were found in other brachyurans ( Pie et al 2008 ; Jondeung et al 2012 ; Shi et al 2015 ; Ma et al 2016a , 2016b ). These results indicate that mNCR could be used as a genetic marker for studies regarding population structure and phylogeographic patterns of related species ( Diniz et al 2005 ).…”

“…The largest non-coding region between rrnS and trnI was predicted to be the putative mNCR in the two Sinopotamon crab species ranging from 1194 bp ( S. yangtsekiense ) to 1231 bp ( S. yaanense ), where the position is similar to that found in Geothelphusa dehaani and other brachyurans (see Segawa and Aotsuka 2005 ; Bai et al 2016 ; Ma et al 2016a , 2016b ). The comparisons of mNCR of the two Sinopotamon species revealed a highly conserved structure, including a central domain and ETAS (Supporting information, Suppl.…”