Comparison and analysis of <em>Alpheus japonicus</em> and <em>A. distinguendus</em> complete mitochondrial genome sequences

SHEN Xin; LI Xiao; XU Qihua

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SHEN Xin, LI Xiao, XU Qihua. Comparison and analysis of Alpheus japonicus and A. distinguendus complete mitochondrial genome sequences[J]. Haiyang Xuebao, 2012, 34(5): 147-153.

Citation:

SHEN Xin, LI Xiao, XU Qihua. Comparison and analysis of Alpheus japonicus and A. distinguendus complete mitochondrial genome sequences[J]. Haiyang Xuebao, 2012, 34(5): 147-153.

SHEN Xin, LI Xiao, XU Qihua. Comparison and analysis of Alpheus japonicus and A. distinguendus complete mitochondrial genome sequences[J]. Haiyang Xuebao, 2012, 34(5): 147-153.

Citation:

SHEN Xin, LI Xiao, XU Qihua. Comparison and analysis of Alpheus japonicus and A. distinguendus complete mitochondrial genome sequences[J]. Haiyang Xuebao, 2012, 34(5): 147-153.

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Comparison and analysis of Alpheus japonicus and A. distinguendus complete mitochondrial genome sequences

1.
College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, China;Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
2.
Shandong Peanut Research Institute, Qingdao 266100, China
3.
College of Electronic Engineering, Huaihai Institute of Technology, Lianyungang 222005, China

Received Date: 2011-07-06
Rev Recd Date: 2011-09-11

Abstract

Abstract

The mitochondrial genomic DNA of Alpheus japonicus was obtained by genomic DNA extraction combined with universal primers PCR and long PCR amplification. The complete mitochondrial genome sequence was sequenced using shotgun and primer-walking strategies. Comparative analyses were done combined with A. distinguendus mitochondrial genome, including the basic characteristics, gene order, protein-coding genes, selection pressure, and different sites and so on. The results show that overlapping is found in nine pairs genes of A. japonicus mitochondrial genome. The A. japonicus mitochondrial genome is 16 487 bp in length and is longer than A. distinguendus mitochondrial genome (15 700 bp), mainly due to the length difference of the largest non-coding region. The mitochondrial genomes of A. japonicus and A. distinguendus both contain 37 genes. Gene order of the A. japonicus and A. distinguendus mitochondrial genomes is identical. The translocation of one transfer RNA gene (trnE) involving inversion is found in 2 Alpheus mitochondrial genomes when compared with the pancrustacean ground pattern. There are differences in the usage of start codon and stop codon in protein-coding genes of 2 Alpheus mitochondrial genomes. Except for the cob gene, the numbers of amino acids encoded by the remaining 12 protein-coding genes are identical. The Ka/Ks ratio of all 13 mitochondrial protein coding genes is much lower than 1, indicating a strong negative selection. In 15 major coding genes, nad5 has the largest number of different loci, followed by nad4 and lrRNA genes, can be used as alternative molecular markers to analyze biodiversity among Alpheus species and populations.
- Alpheus,
- mitochondrial genome,
- selection pressure,
- gene order,
- molecular marker

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References(16)

References

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