Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We se...

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Autores principales:	Yong Xiao, Wei Xia, Yaodong Yang, Annaliese S Mason, Xintao Lei, Zilong Ma
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9616477d4e014d7996885ba79ccf57b7
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spelling	oai:doaj.org-article:9616477d4e014d7996885ba79ccf57b72021-11-18T09:00:34ZCharacterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).1932-620310.1371/journal.pone.0071435https://doaj.org/article/9616477d4e014d7996885ba79ccf57b72013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23951162/?tool=EBIhttps://doaj.org/toc/1932-6203MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.Yong XiaoWei XiaYaodong YangAnnaliese S MasonXintao LeiZilong MaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 8, p e71435 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yong Xiao Wei Xia Yaodong Yang Annaliese S Mason Xintao Lei Zilong Ma Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
description	MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.
format	article
author	Yong Xiao Wei Xia Yaodong Yang Annaliese S Mason Xintao Lei Zilong Ma
author_facet	Yong Xiao Wei Xia Yaodong Yang Annaliese S Mason Xintao Lei Zilong Ma
author_sort	Yong Xiao
title	Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
title_short	Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
title_full	Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
title_fullStr	Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
title_full_unstemmed	Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).
title_sort	characterization and evolution of conserved microrna through duplication events in date palm (phoenix dactylifera).
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/9616477d4e014d7996885ba79ccf57b7
work_keys_str_mv	AT yongxiao characterizationandevolutionofconservedmicrornathroughduplicationeventsindatepalmphoenixdactylifera AT weixia characterizationandevolutionofconservedmicrornathroughduplicationeventsindatepalmphoenixdactylifera AT yaodongyang characterizationandevolutionofconservedmicrornathroughduplicationeventsindatepalmphoenixdactylifera AT annaliesesmason characterizationandevolutionofconservedmicrornathroughduplicationeventsindatepalmphoenixdactylifera AT xintaolei characterizationandevolutionofconservedmicrornathroughduplicationeventsindatepalmphoenixdactylifera AT zilongma characterizationandevolutionofconservedmicrornathroughduplicationeventsindatepalmphoenixdactylifera
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Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).

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