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Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis

Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild c...

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Main Authors: Chang, Wendy, EE-ULI, J., NG, W. L., Rovie-Ryan, Jeffrine J., Tan, S. G., Yong, Christina S. Y.
Format: Article
Language:English
Published: Springer Nature Limited 2019
Subjects:
QL Zoology
Online Access:http://ir.unimas.my/id/eprint/36068/1/genic1.pdf
http://ir.unimas.my/id/eprint/36068/
https://www.nature.com/articles/s41598-019-44870-4
https://doi.org/10.1038/s41598-019-44870-4
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spelling my.unimas.ir.360682021-09-13T04:14:42Z http://ir.unimas.my/id/eprint/36068/ Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis Chang, Wendy EE-ULI, J. NG, W. L. Rovie-Ryan, Jeffrine J. Tan, S. G. Yong, Christina S. Y. QL Zoology Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species. Springer Nature Limited 2019-06-11 Article PeerReviewed text en http://ir.unimas.my/id/eprint/36068/1/genic1.pdf Chang, Wendy and EE-ULI, J. and NG, W. L. and Rovie-Ryan, Jeffrine J. and Tan, S. G. and Yong, Christina S. Y. (2019) Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis. Scientific Reports, 9 (8504). pp. 1-8. ISSN 2045-2322 https://www.nature.com/articles/s41598-019-44870-4 https://doi.org/10.1038/s41598-019-44870-4
institution Universiti Malaysia Sarawak
building Centre for Academic Information Services (CAIS)
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaysia Sarawak
content_source UNIMAS Institutional Repository
url_provider http://ir.unimas.my/
language English
topic QL Zoology
spellingShingle QL Zoology
Chang, Wendy
EE-ULI, J.
NG, W. L.
Rovie-Ryan, Jeffrine J.
Tan, S. G.
Yong, Christina S. Y.
Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
description Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.
format Article
author Chang, Wendy
EE-ULI, J.
NG, W. L.
Rovie-Ryan, Jeffrine J.
Tan, S. G.
Yong, Christina S. Y.
author_facet Chang, Wendy
EE-ULI, J.
NG, W. L.
Rovie-Ryan, Jeffrine J.
Tan, S. G.
Yong, Christina S. Y.
author_sort Chang, Wendy
title Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
title_short Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
title_full Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
title_fullStr Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
title_full_unstemmed Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
title_sort discovery of novel genic-ssr markers from transcriptome dataset of an important non-human primate, macaca fascicularis
publisher Springer Nature Limited
publishDate 2019
url http://ir.unimas.my/id/eprint/36068/1/genic1.pdf
http://ir.unimas.my/id/eprint/36068/
https://www.nature.com/articles/s41598-019-44870-4
https://doi.org/10.1038/s41598-019-44870-4
_version_ 1712289125200035840
score 13.244745

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