The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration |
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Authors: | Hongyu Ma Chunyan MaXincang Li Zhen XuNana Feng Lingbo Ma |
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Affiliation: | Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China |
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Abstract: | The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNAHis differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy. |
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Keywords: | PCR, polymerase chain reaction tRNA, transfer RNA rRNA, ribosomal RNA CR, control region ATP6 and ATP8, ATPase subunits 6 and 8 ND1&ndash ND6 and ND4L, NADH dehydrogenase subunits 1&ndash 6 and 4L COI&ndash COIII, cytochrome c oxidase subunits I&ndash III 16S and 12S, large and small subunits ribosomal RNA Cyt b, cytochrome b bp, base pair H-strand, heavy strand L-strand, light strand SNP, single nucleotide polymorphism |
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