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De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation.

Huang YY, Lee CP, Fu JL, Chang BC, Matzke AJ, Matzke M - G3 (Bethesda) (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.

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Relative abundance of RdDM-associated gene transcripts found in three tissues of coconut.
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fig5: Relative abundance of RdDM-associated gene transcripts found in three tissues of coconut.

Mentions: We identified partial or nearly full-length transcripts for a number of factors involved in RdDM, including the largest subunits of Pol IV and Pol V (NRPD1 and NRPE1, respectively), as well as AGO4, DRD1, and the three major DNA methyltransferases, MET1, DRM, and CMT3 (Table 3). Notably, the relative abundance of most of these factors is highest in endosperm tissue compared with leaves and embryos (Figure 5). In particular, the relative abundance of the largest subunits of Pol IV and Pol V are higher in endosperm than in embryos or leaves. By contrast, the largest subunits of Pol I (RPA1) and Pol II (RPB1) have similar relative abundances in the three tissues. Although RDR2 is expressed in endosperm, the relative abundance is not overly high compared with the other tissues (Figure 5). Interestingly, a gene encoding a protein similar to the repressor of silencing-1/Demeter (ROS1/DME) family of DNA glycosylase/lyases involved in active DNA demethylation is highly expressed in endosperm. This finding is significant in view of the requirement for DME in establishing parental imprints in Arabidopsis and rice endosperm (Gehring 2013).


De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation.

Huang YY, Lee CP, Fu JL, Chang BC, Matzke AJ, Matzke M - G3 (Bethesda) (2014)

Relative abundance of RdDM-associated gene transcripts found in three tissues of coconut.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232540&req=5

fig5: Relative abundance of RdDM-associated gene transcripts found in three tissues of coconut.
Mentions: We identified partial or nearly full-length transcripts for a number of factors involved in RdDM, including the largest subunits of Pol IV and Pol V (NRPD1 and NRPE1, respectively), as well as AGO4, DRD1, and the three major DNA methyltransferases, MET1, DRM, and CMT3 (Table 3). Notably, the relative abundance of most of these factors is highest in endosperm tissue compared with leaves and embryos (Figure 5). In particular, the relative abundance of the largest subunits of Pol IV and Pol V are higher in endosperm than in embryos or leaves. By contrast, the largest subunits of Pol I (RPA1) and Pol II (RPB1) have similar relative abundances in the three tissues. Although RDR2 is expressed in endosperm, the relative abundance is not overly high compared with the other tissues (Figure 5). Interestingly, a gene encoding a protein similar to the repressor of silencing-1/Demeter (ROS1/DME) family of DNA glycosylase/lyases involved in active DNA demethylation is highly expressed in endosperm. This finding is significant in view of the requirement for DME in establishing parental imprints in Arabidopsis and rice endosperm (Gehring 2013).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.

Show MeSH
Related in: MedlinePlus