Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis

MADS-box genes encode a group of transcription factor family, well known as key regulators of plant vegetative and development processes, including flowering. Here, we aimed at analysing MADS-box genes in African oil palm (Elaeis guineensis) genome, the pre-dominant source of worldwide production...

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Main Authors:	Suhaila Sulaiman, Lee, Yang Ping, Kwan, Yen Yen, Sharifah Shahrul Rabiah Syed Alwee
Format:	Article
Language:	English
Published:	Penerbit Universiti Kebangsaan Malaysia 2017
Online Access:	http://journalarticle.ukm.my/12316/ http://journalarticle.ukm.my/12316/ http://journalarticle.ukm.my/12316/1/46_01_23.pdf

id	ukm-12316
recordtype	eprints
spelling	ukm-123162018-11-16T12:31:24Z http://journalarticle.ukm.my/12316/ Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis Suhaila Sulaiman, Lee, Yang Ping Kwan, Yen Yen Sharifah Shahrul Rabiah Syed Alwee, MADS-box genes encode a group of transcription factor family, well known as key regulators of plant vegetative and development processes, including flowering. Here, we aimed at analysing MADS-box genes in African oil palm (Elaeis guineensis) genome, the pre-dominant source of worldwide production of vegetable oils. A total of 209 potential MADSbox genes are identified in the published 1.8 Gb E. guineensis draft genome. A de novo assembly of RNA-seq data from inflorescence tissues was constructed using Trinity software. The analysed transcriptome data has validated 36 full-length genes, inclusive of seven transcripts that were previously annotated to encode unknown proteins. Of the 36 genes discovered, 21 genes were characterised as Type I MADS-box genes and phylogenetic analysis using maximum likelihood approach further classified them into three sub-groups of Mα, Mβ and Mγ. Based on in silico analyses, we have successfully identified one gene annotated as unknown protein to contain a domain of “MADS-box transcription factor”. Its differential expression data, comparison between normal and mantled inflorescence of oil palm, suggested the involvement of the gene in the mantling related process. The findings contribute to updated oil palm genome information which may potentially lead to future understanding of the association of MADS-box genes in mantled oil palm. This may also lead to a resource for biomarker discovery. Penerbit Universiti Kebangsaan Malaysia 2017-03 Article PeerReviewed application/pdf en http://journalarticle.ukm.my/12316/1/46_01_23.pdf Suhaila Sulaiman, and Lee, Yang Ping and Kwan, Yen Yen and Sharifah Shahrul Rabiah Syed Alwee, (2017) Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis. Malaysian Applied Biology, 46 (1). pp. 159-163. ISSN 0126-8643 http://www.mabjournal.com/index.php?option=com_content&view=article&id=623&catid=59:current-view&Itemid=56
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Kebangasaan Malaysia
building	UKM Institutional Repository
collection	Online Access
language	English
description	MADS-box genes encode a group of transcription factor family, well known as key regulators of plant vegetative and development processes, including flowering. Here, we aimed at analysing MADS-box genes in African oil palm (Elaeis guineensis) genome, the pre-dominant source of worldwide production of vegetable oils. A total of 209 potential MADSbox genes are identified in the published 1.8 Gb E. guineensis draft genome. A de novo assembly of RNA-seq data from inflorescence tissues was constructed using Trinity software. The analysed transcriptome data has validated 36 full-length genes, inclusive of seven transcripts that were previously annotated to encode unknown proteins. Of the 36 genes discovered, 21 genes were characterised as Type I MADS-box genes and phylogenetic analysis using maximum likelihood approach further classified them into three sub-groups of Mα, Mβ and Mγ. Based on in silico analyses, we have successfully identified one gene annotated as unknown protein to contain a domain of “MADS-box transcription factor”. Its differential expression data, comparison between normal and mantled inflorescence of oil palm, suggested the involvement of the gene in the mantling related process. The findings contribute to updated oil palm genome information which may potentially lead to future understanding of the association of MADS-box genes in mantled oil palm. This may also lead to a resource for biomarker discovery.
format	Article
author	Suhaila Sulaiman, Lee, Yang Ping Kwan, Yen Yen Sharifah Shahrul Rabiah Syed Alwee,
spellingShingle	Suhaila Sulaiman, Lee, Yang Ping Kwan, Yen Yen Sharifah Shahrul Rabiah Syed Alwee, Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis
author_facet	Suhaila Sulaiman, Lee, Yang Ping Kwan, Yen Yen Sharifah Shahrul Rabiah Syed Alwee,
author_sort	Suhaila Sulaiman,
title	Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis
title_short	Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis
title_full	Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis
title_fullStr	Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis
title_full_unstemmed	Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis
title_sort	analyses using genomic and transcriptomic data of mads-box genes in elaeis guineensis
publisher	Penerbit Universiti Kebangsaan Malaysia
publishDate	2017
url	http://journalarticle.ukm.my/12316/ http://journalarticle.ukm.my/12316/ http://journalarticle.ukm.my/12316/1/46_01_23.pdf
first_indexed	2023-09-18T20:02:20Z
last_indexed	2023-09-18T20:02:20Z
_version_	1777406931324895232

Analyses using genomic and transcriptomic data of mads-box genes in Elaeis guineensis

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