Sains Malaysiana 40(5)(2011): 497–502

Characterisation of Simple Sequence Repeats in the Asian Seabass, Lates calcarifer by Random Sequencing

(Pencirian Ulangan Jujukan Ringkas dalam Ikan Siakap, Lates calcarifer melalui Penjujukan Rawak)

Pan-Pan Chong, AduraMohd. Adnan & Kiew-Lian Wan*

School of Biosciences and Biotechnology, Faculty of Science and Technology

Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor D.E., Malaysia

Malaysia Genome Institute, Heliks Emas Block, UKM-MTDC Technology Centre

Unversiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor D.E., Malaysia

Received: 1 June 2010 / Accepted: 27 July 2010

ABSTRACT

In recent years, there has been considerable interest in simple sequence repeats (SSRs) particularly as molecular markers with applications in many different fields. We have carried out an effort to identify and analyse SSRs in the genome of the Asian seabass, Lates calcarifer by random sequencing. Genomic DNA was isolated from the muscle tissue of L. calcarifer, sheared by nebulisation and ligated into plasmid vector. Recombinant clones were selected randomly from the genomic libraries constructed. Subsequently, plasmid DNA was extracted and subjected to one-pass sequencing. A total of 4175 random sequences, also known as genome survey sequences (GSSs), with a total length of 1.7 Mb was generated. Screening of the whole L. calcarifer GSS data set allowed for the identification of a total of 151 perfect (100% similarity) SSRs. These SSR consensus patterns spread over a wide range of size (1 to 226 bp). The most frequent consensus pattern is dinucleotide, which represents 60% of all SSRs identified. The dinucleotides (AC)n, (AT)n and (AG)n were also found to occur frequently in the L. calcarifer genome. Sequence comparison between L. calcarifer and other fish species showed variation in repeat content, indicating the different ways in which repeats may evolve in the genome of these species. Data generated from this random sequencing of the L. calcarifer genome should serve as a valuable resource for further studies of this organism.

Keywords: Genome survey sequence; GSS; molecular marker; SSR

ABSTRAK

Sejak kebelakangan ini, terdapat minat yang mendalam mengenai ulangan jujukan ringkas (SSR), terutamanya sebagai penanda molekul dengan kegunaan dalam pelbagai bidang. Kami telah melaksanakan usaha untuk mengenal pasti dan menganalisis SSR dalam genom ikan siakap, Lates calcarifer melalui penjujukan rawak. DNA genom telah dipencilkan daripada tisu otot L. calcarifer, diserpihkan dengan nebulisasi dan diligasikan ke dalam vektor plasmid. Klon rekombinan telah dipilih secara rawak daripada perpustakaan genom yang telah dibina. Seterusnya, DNA plasmid telah diekstrak dan diperlakukan penjujukan sekali lalu. Sejumlah 4175 jujukan rawak, yang juga dikenali sebagai jujukan tinjauan genom (GSS), dengan jumlah panjang 1.7 Mb telah dijana. Penabiran keseluruhan set data GSS L. calcarifer telah membolehkan pengenalpastian sejumlah 151 SSR sempurna (persamaan 100%). Corak konsensus SSR ini tersebar merentasi julat saiz yang luas (1 hingga 226 pb). Corak konsensus yang paling sering ditemui adalah dinukleotida, yang mewakili 60% daripada kesemua SSR yang dikenal pasti. Dinukleotida (AC)n, (AT)n dan (AG)n juga dijumpai hadir dengan banyak dalam genom L. calcarifer. Perbandingan jujukan di antara L. calcarifer dengan spesies ikan lain mempamerkan variasi dalam kandungan ulangan, dan ini menunjukkan cara berbeza bagaimana ulangan berupaya berevolusi dalam genom spesies ini. Data yang terjana daripada penjujukan rawak genom L. calcarifer ini merupakan sumber yang berharga untuk kajian lanjut tentang organisma ini.

Kata kunci: GSS; jujukan tinjauan genom; penanda molekul; SSR

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*Corresponding author: email: klwan@ukm.my