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

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....

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Main Authors:	Pan, Pan Chong, Adura Mohd. Adnan, Kiew, Lian Wan
Format:	Article
Language:	English
Published:	Universiti Kebangsaan Malaysia 2011
Online Access:	http://journalarticle.ukm.my/2489/ http://journalarticle.ukm.my/2489/ http://journalarticle.ukm.my/2489/1/13_Pan_Chong.pdf

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recordtype	eprints
spelling	ukm-24892016-12-14T06:31:46Z http://journalarticle.ukm.my/2489/ Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing Pan, Pan Chong Adura Mohd. Adnan, Kiew, Lian Wan 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 Universiti Kebangsaan Malaysia 2011-05 Article PeerReviewed application/pdf en http://journalarticle.ukm.my/2489/1/13_Pan_Chong.pdf Pan, Pan Chong and Adura Mohd. Adnan, and Kiew, Lian Wan (2011) Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing. Sains Malaysiana, 40 (5). pp. 497-502. ISSN 0126-6039 http://www.ukm.my/jsm/
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Kebangasaan Malaysia
building	UKM Institutional Repository
collection	Online Access
language	English
description	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
format	Article
author	Pan, Pan Chong Adura Mohd. Adnan, Kiew, Lian Wan
spellingShingle	Pan, Pan Chong Adura Mohd. Adnan, Kiew, Lian Wan Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing
author_facet	Pan, Pan Chong Adura Mohd. Adnan, Kiew, Lian Wan
author_sort	Pan, Pan Chong
title	Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing
title_short	Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing
title_full	Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing
title_fullStr	Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing
title_full_unstemmed	Characterisation of simple sequence repeats in the Asian Seabass,Lates calcarifer by random sequencing
title_sort	characterisation of simple sequence repeats in the asian seabass,lates calcarifer by random sequencing
publisher	Universiti Kebangsaan Malaysia
publishDate	2011
url	http://journalarticle.ukm.my/2489/ http://journalarticle.ukm.my/2489/ http://journalarticle.ukm.my/2489/1/13_Pan_Chong.pdf
first_indexed	2023-09-18T19:36:14Z
last_indexed	2023-09-18T19:36:14Z
_version_	1777405289449914368

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

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