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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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Related in: MedlinePlus

Species distribution of coconut transcripts (FPKM >1.00) resulting from de novo assembly. Sections <2% are not labeled.
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fig3: Species distribution of coconut transcripts (FPKM >1.00) resulting from de novo assembly. Sections <2% are not labeled.

Mentions: Our blast search showed that a significant number of unigenes in the embryo transcriptome (57%) and leaf transcriptome (22%) do not have any match in GenBank (Figure 3). Matches between coconut unigenes and entries of nr protein database showed that species of monocots have the best match (highest total score), particularly from the Poaceae (true grass) family, which includes 16%, 38%, and 28% of the best matches in embryo, endosperm, and leaf transcriptomes (Figure 3). Somewhat surprisingly, the species with the second-best match was Vitis vinifera (common grape vine), which contains 11%, 30%, and 23% of the best matching sequences in embryo, endosperm, and leaf transcriptomes. The significance of these similarities in protein sequence between two rather distantly related plants (monocot coconut and dicot grape) is not yet clear, but a relatively high percentages of matches to Vitis were also found for other monocots such as date palm (Al-Dous et al. 2011), pineapple (Ong et al. 2012), and banana (Passos et al. 2013). Other eudicots combined together to comprise 10%–25% of the best matches. A small proportion of unigenes matched to members of basal angiosperms, gymnosperms, and ferns. Very few unigenes matched to sequences of nonvascular plants (bryophytes) or green algae.


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)

Species distribution of coconut transcripts (FPKM >1.00) resulting from de novo assembly. Sections <2% are not labeled.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Species distribution of coconut transcripts (FPKM >1.00) resulting from de novo assembly. Sections <2% are not labeled.
Mentions: Our blast search showed that a significant number of unigenes in the embryo transcriptome (57%) and leaf transcriptome (22%) do not have any match in GenBank (Figure 3). Matches between coconut unigenes and entries of nr protein database showed that species of monocots have the best match (highest total score), particularly from the Poaceae (true grass) family, which includes 16%, 38%, and 28% of the best matches in embryo, endosperm, and leaf transcriptomes (Figure 3). Somewhat surprisingly, the species with the second-best match was Vitis vinifera (common grape vine), which contains 11%, 30%, and 23% of the best matching sequences in embryo, endosperm, and leaf transcriptomes. The significance of these similarities in protein sequence between two rather distantly related plants (monocot coconut and dicot grape) is not yet clear, but a relatively high percentages of matches to Vitis were also found for other monocots such as date palm (Al-Dous et al. 2011), pineapple (Ong et al. 2012), and banana (Passos et al. 2013). Other eudicots combined together to comprise 10%–25% of the best matches. A small proportion of unigenes matched to members of basal angiosperms, gymnosperms, and ferns. Very few unigenes matched to sequences of nonvascular plants (bryophytes) or green algae.

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