Characterisation of simple sequence repeats in the Asian seabass, Lates calcarifer by random sequencing

Pan Pan Chong, Adura Mohd. Adnan, Kiew Lian Wan

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish
Pages (from-to)497-502
Number of pages6
JournalSains Malaysiana
Volume40
Issue number5
Publication statusPublished - May 2011

Fingerprint

Lates calcarifer
microsatellite repeats
genome
atomization
plasmid vectors
genomic libraries
muscle tissues
plasmids
clones
screening
genomics
genetic markers
organisms
DNA
fish

Keywords

  • Genome survey sequence
  • GSS
  • Molecular marker
  • SSR

ASJC Scopus subject areas

  • General

Cite this

Characterisation of simple sequence repeats in the Asian seabass, Lates calcarifer by random sequencing. / Chong, Pan Pan; Mohd. Adnan, Adura; Wan, Kiew Lian.

In: Sains Malaysiana, Vol. 40, No. 5, 05.2011, p. 497-502.

Research output: Contribution to journalArticle

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