De Novo Transcriptome Sequence Assembly from Coconut Leaves and Seeds with a Focus on Factors Involved in RNA-Directed DNA Methylation
Identifieur interne : 000C38 ( Main/Curation ); précédent : 000C37; suivant : 000C39De Novo Transcriptome Sequence Assembly from Coconut Leaves and Seeds with a Focus on Factors Involved in RNA-Directed DNA Methylation
Auteurs : Ya-Yi Huang [Taïwan] ; Chueh-Pai Lee [Taïwan] ; Jason L. Fu [Taïwan] ; Bill Chia-Han Chang [Taïwan] ; Antonius J. M. Matzke [Taïwan] ; Marjori Matzke [Taïwan]Source :
- G3: Genes|Genomes|Genetics [ 2160-1836 ] ; 2014.
Abstract
Coconut palm (
Url:
DOI: 10.1534/g3.114.013409
PubMed: 25193496
PubMed Central: 4232540
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PMC:4232540Le document en format XML
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Transcriptome Sequence Assembly from Coconut Leaves and Seeds with a Focus on Factors Involved in RNA-Directed DNA Methylation</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>De Novo</italic>
Transcriptome Sequence Assembly from Coconut Leaves and Seeds with a Focus on Factors Involved in RNA-Directed DNA Methylation</title>
<author><name sortKey="Huang, Ya Yi" sort="Huang, Ya Yi" uniqKey="Huang Y" first="Ya-Yi" last="Huang">Ya-Yi Huang</name>
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<author><name sortKey="Lee, Chueh Pai" sort="Lee, Chueh Pai" uniqKey="Lee C" first="Chueh-Pai" last="Lee">Chueh-Pai Lee</name>
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<author><name sortKey="Fu, Jason L" sort="Fu, Jason L" uniqKey="Fu J" first="Jason L." last="Fu">Jason L. Fu</name>
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<front><div type="abstract" xml:lang="en"><p>Coconut palm (<italic>Cocos nucifera</italic>
) is a symbol of the tropics and a source of numerous edible and nonedible products of economic value. Despite its nutritional and industrial significance, coconut remains under-represented in public repositories for genomic and transcriptomic data. We report <italic>de novo</italic>
transcript assembly from RNA-seq data and analysis of gene expression in seed tissues (embryo and endosperm) and leaves of a dwarf coconut variety. Assembly of 10 GB sequencing data for each tissue resulted in 58,211 total unigenes in embryo, 61,152 in endosperm, and 33,446 in leaf. Within each unigene pool, 24,857 could be annotated in embryo, 29,731 could be annotated in endosperm, and 26,064 could be annotated in leaf. A KEGG analysis identified 138, 138, and 139 pathways, respectively, in transcriptomes of embryo, endosperm, and leaf tissues. Given the extraordinarily large size of coconut seeds and the importance of small RNA-mediated epigenetic regulation during seed development in model plants, we used homology searches to identify putative homologs of factors required for RNA-directed DNA methylation in coconut. The findings suggest that RNA-directed DNA methylation is important during coconut seed development, particularly in maturing endosperm. This dataset will expand the genomics resources available for coconut and provide a foundation for more detailed analyses that may assist molecular breeding strategies aimed at improving this major tropical crop.</p>
</div>
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