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New haplotype of the complete mitochondrial genome of Crocodylus siamensis and its species-specific DNA markers: distinguishing C. siamensis from C. porosus in Thailand

Molecular Biology Reports volume 39, pages 4709–4717 (2012)Cite this article

Abstract

Based on molecular phylogeny of available complete mitochondrial DNA (mtDNA) genome sequences reveals that Crocodylus siamensis and C. porosus are closely related species. Yet, the sequence divergence of their mtDNA showed only a few values under conspecific level. In this study, a new haplotype (haplotype2, EF581859) of the complete mtDNA genome of Siamese crocodile (C. siamensis) was determined. The genome organization, which appeared to be highly similar to haplotype1 (DQ353946) mtDNA genome of C. siamensis, was 16,814 bp in length. However, the sequence divergence between the two genomes differed by around 7–10 and 0.7–2.1% for the haplotype1 between C. siamensis and C. porosus (AJ810453). These results were consistent with the phylogenetic relationship among the three genomes, suggesting that C. siamensis haplotype1 mtDNA genome might be the hybrid or the intraspecific variation of C. porosus. On the other hand, our specimen was found to be a true C. siamensis. Simultaneously, the seven species-specific DNA markers designed based on the distinctive site between haplotype2 mtDNA sequences of C. siamensis and haplotype1 mtDNA sequence of C. siamensis–C. porosus were successfully used to distinguish C. siamensis from C. porosus. These effective markers could be used primarily for rapid and accurate species identification in population, ecology and conservation studies.

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Abbreviations

mtDNA:

Mitochondrial DNA

MYA:

Million year ago

NCBI:

National Center for Biotechnology Information

PCR:

Polymerase chain reaction

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Acknowledgement

This study was financially supported by Kasetsart University Research and Development Institute (KURDI), Kasetsart University, Thailand. The authors would like to acknowledge Sriracha Moda Co., Ltd., Chonburi, Thailand, for providing all crocodile specimens.

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Affiliations

  1. Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand

    Kornsorn Srikulnath

  2. Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand

    Kornsorn Srikulnath, Amara Thongpan, Saowanee Suputtitada & Somsak Apisitwanich

  3. Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU), Bangkok, Thailand

    Kornsorn Srikulnath & Somsak Apisitwanich

  4. Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen, Nakorn-Pathom, 73140, Thailand

    Somsak Apisitwanich

Authors
  1. Kornsorn Srikulnath
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  2. Amara Thongpan
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  3. Saowanee Suputtitada
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  4. Somsak Apisitwanich
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Corresponding author

Correspondence to Somsak Apisitwanich.

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Srikulnath, K., Thongpan, A., Suputtitada, S. et al. New haplotype of the complete mitochondrial genome of Crocodylus siamensis and its species-specific DNA markers: distinguishing C. siamensis from C. porosus in Thailand. Mol Biol Rep 39, 4709–4717 (2012). https://doi.org/10.1007/s11033-011-1263-7

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  • DOI: https://doi.org/10.1007/s11033-011-1263-7

Keywords

  • mtDNA genome
  • Crocodile
  • Sequence divergence
  • DNA marker