Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functiona...

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Autores principales:	Tiange Lang, Kangquan Yin, Jinyu Liu, Kunfang Cao, Charles H Cannon, Fang K Du
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a304137a657f46acb5714719873a1b62
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spelling	oai:doaj.org-article:a304137a657f46acb5714719873a1b622021-11-25T05:58:27ZProtein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.1932-620310.1371/journal.pone.0108719https://doaj.org/article/a304137a657f46acb5714719873a1b622014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0108719https://doaj.org/toc/1932-6203Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.Tiange LangKangquan YinJinyu LiuKunfang CaoCharles H CannonFang K DuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 9, p e108719 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tiange Lang Kangquan Yin Jinyu Liu Kunfang Cao Charles H Cannon Fang K Du Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.
description	Predicting protein domains is essential for understanding a protein's function at the molecular level. However, up till now, there has been no direct and straightforward method for predicting protein domains in species without a reference genome sequence. In this study, we developed a functionality with a set of programs that can predict protein domains directly from genomic sequence data without a reference genome. Using whole genome sequence data, the programming functionality mainly comprised DNA assembly in combination with next-generation sequencing (NGS) assembly methods and traditional methods, peptide prediction and protein domain prediction. The proposed new functionality avoids problems associated with de novo assembly due to micro reads and small single repeats. Furthermore, we applied our functionality for the prediction of leucine rich repeat (LRR) domains in four species of Ficus with no reference genome, based on NGS genomic data. We found that the LRRNT_2 and LRR_8 domains are related to plant transpiration efficiency, as indicated by the stomata index, in the four species of Ficus. The programming functionality established in this study provides new insights for protein domain prediction, which is particularly timely in the current age of NGS data expansion.
format	article
author	Tiange Lang Kangquan Yin Jinyu Liu Kunfang Cao Charles H Cannon Fang K Du
author_facet	Tiange Lang Kangquan Yin Jinyu Liu Kunfang Cao Charles H Cannon Fang K Du
author_sort	Tiange Lang
title	Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.
title_short	Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.
title_full	Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.
title_fullStr	Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.
title_full_unstemmed	Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.
title_sort	protein domain analysis of genomic sequence data reveals regulation of lrr related domains in plant transpiration in ficus.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/a304137a657f46acb5714719873a1b62
work_keys_str_mv	AT tiangelang proteindomainanalysisofgenomicsequencedatarevealsregulationoflrrrelateddomainsinplanttranspirationinficus AT kangquanyin proteindomainanalysisofgenomicsequencedatarevealsregulationoflrrrelateddomainsinplanttranspirationinficus AT jinyuliu proteindomainanalysisofgenomicsequencedatarevealsregulationoflrrrelateddomainsinplanttranspirationinficus AT kunfangcao proteindomainanalysisofgenomicsequencedatarevealsregulationoflrrrelateddomainsinplanttranspirationinficus AT charleshcannon proteindomainanalysisofgenomicsequencedatarevealsregulationoflrrrelateddomainsinplanttranspirationinficus AT fangkdu proteindomainanalysisofgenomicsequencedatarevealsregulationoflrrrelateddomainsinplanttranspirationinficus
_version_	1718414357734359040

Protein domain analysis of genomic sequence data reveals regulation of LRR related domains in plant transpiration in Ficus.

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