Sains Malaysiana 41(12)(2012): 1527–1533

 

Limit of DNA Barcode in Delineating Penaeus monodon and in its Developing Stages

(Had Penggunaan Barkod DNA untuk Menentukan Penaeus monodon dan Peringkat Tumbesarannya)

 

 

C. Prasanna Kumar, S. Ajmal Khan & P.S. Lyla

Centre for Advanced Study in Marine Biology, Faculty of Marine Biology

Annamalai University, Parangipettai – 608502, Tamil Nadu, India

 

B. Akbar John* & K.C.A. Jalal

Department of Biotechnology, Kulliyyah of Science

International Islamic University Malaysia, Jalan Sultan Ahmad Shah

Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia

 

Diserahkan: 23 Mac 2011 / Diterima: 2Ogos 2012

 

ABSTRACT

Mysis, post larvae and adult specimens of Penaeus monodon were sequenced for Cyctochrome C Oxidase subunit I (COI) gene (DNA barcode) to check the efficiency of DNA barcode in delineating species irrespective of its different life stages. COI gene sequences of different life stages of P. monodon were subjected to pair-wise distance analysis, nucleotide sequence diversity estimation, phylogenetic and BOLD analysis. The pair-wise distance estimation revealed that intra-specific variations within the barcode sequences of P. monodon were low when compared with other species of genus Penaeus spp. The average pair-wise distance within the sequences of different stages of P. monodon was two times lesser than the pair-wise distance of the out-group used. The nucleotide diversity within the barcodes were low (π = 0.324). The constructed phylogram clearly showed that the DNA barcoding using partial COI gene would provide an accurate delineation of species irrespective of their different life stages. The BOLD analysis accurately identified all sequences as belonging to P. monodon.

 

Keywords: COI; DNA barcoding; nucleotide diversity; pair-wise distance; Penaeus monodon

 

ABSTRAK

Sampel mysis, anak pra-matang dan dewasa Peneaus monodon telah dianalisis mengggunakan gen subunit I sitokrom C oksidase (COI) untuk menentukan keupayaan barkod DNA untuk mengenal pasti peringkat tumbesaran Peneaus monodon. Jujukan COI Peneaus monodon pada peringkat yang berbeza telah dianalisis menggunakan kaedah jarak pasangan demi pasangan, kepelbagaian jujukan nukleofida, filogenetik dan BOLD. Analisis jarak pasangan demi pasangan menunjukkan variasi intra-spesifik dalam jujukan barkod Peneaus monodon adalah lebih rendah berbanding spesies Peneaus yang lain. Purata jarak pasangan demi pasangan pada peringkat berbeza Peneaus monodon adalah dua kali lebih rendah berbanding kumpulan luar. Kepelbagaian nukleotida dalam barkod adalah rendah (π= 0.324). Filogram yang dihasilkan menunjukkan barkod DNA yang menggunakan gen COI mampu menentukan tumbesaran spesies mengikut peringkatnya. Analisis BOLD pula menunjukkan bahawa kesemua jujukan yang dihasilkan adalah Peneaus monodon.

 

Kata kunci: Barkod DNA; COI; jarak pasangan demi pasangan;  kepelbagaian jujukan nukleofida; Peneaus monodon

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*Pengarang untuk surat-menyurat; email: akbarjohn50@gmail.com