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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

Expression profile of top 50 expressed genes in the three tissues. The colors denote absence (white) and presence (red) of a particular gene transcript. Photosynthetic genes are almost exclusively found in the leaf transcriptome. Seed storage (7S globulin) and heat shock proteins are prominent in the embryo. Translational and cytoskeleton proteins are abundant in embryo and in endosperm, but rarely found in leaf. Cell wall–associated hydrolase and major intrinsic proteins are evenly distributed in three tissues. Uncharacterized proteins exist in all three tissues, but unigenes without matched sequences in GenBank are found only in embryo and in leaf, not in endosperm.
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fig2: Expression profile of top 50 expressed genes in the three tissues. The colors denote absence (white) and presence (red) of a particular gene transcript. Photosynthetic genes are almost exclusively found in the leaf transcriptome. Seed storage (7S globulin) and heat shock proteins are prominent in the embryo. Translational and cytoskeleton proteins are abundant in embryo and in endosperm, but rarely found in leaf. Cell wall–associated hydrolase and major intrinsic proteins are evenly distributed in three tissues. Uncharacterized proteins exist in all three tissues, but unigenes without matched sequences in GenBank are found only in embryo and in leaf, not in endosperm.

Mentions: Complete gene expression lists (FPKM > 1) from the embryo, endosperm, and leaf transcriptomes are provided as Table S2, Table S3, and Table S4. Expression profiling of the top 50 expressed genes (Figure 2) reflects the physiological characteristics and/or function of the different tissues. As expected, photosynthetic genes are found almost exclusively in the leaf transcriptome, with the most abundant transcript encoding the small subunit of ribulose-1,5-bisphosphate carboxylase (Table 2). In endosperm, which has been sampled at the gelatinous stage undergoing active cell division (Abraham and Mathew 1963), transcripts for cytoskeletal and translational proteins are abundant. Alpha-tubulin, which forms microtubules in the mitotic spindle, is the most highly transcribed gene in endosperm and translationally controlled tumor protein (Amson et al. 2013), which binds to microtubules (Santa Brigida et al. 2014) and regulates cell division (Brioudes et al. 2010), is in the top 10 (Table 2). Other highly expressed genes in coconut endosperm (Table 2), including annexin, enolase, and metallothionein type 2A (MT2A), are also among those expressed at a high level in endosperm of castor bean (Lu et al. 2007) and Brassica napus (Huang et al. 2009).


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)

Expression profile of top 50 expressed genes in the three tissues. The colors denote absence (white) and presence (red) of a particular gene transcript. Photosynthetic genes are almost exclusively found in the leaf transcriptome. Seed storage (7S globulin) and heat shock proteins are prominent in the embryo. Translational and cytoskeleton proteins are abundant in embryo and in endosperm, but rarely found in leaf. Cell wall–associated hydrolase and major intrinsic proteins are evenly distributed in three tissues. Uncharacterized proteins exist in all three tissues, but unigenes without matched sequences in GenBank are found only in embryo and in leaf, not in endosperm.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Expression profile of top 50 expressed genes in the three tissues. The colors denote absence (white) and presence (red) of a particular gene transcript. Photosynthetic genes are almost exclusively found in the leaf transcriptome. Seed storage (7S globulin) and heat shock proteins are prominent in the embryo. Translational and cytoskeleton proteins are abundant in embryo and in endosperm, but rarely found in leaf. Cell wall–associated hydrolase and major intrinsic proteins are evenly distributed in three tissues. Uncharacterized proteins exist in all three tissues, but unigenes without matched sequences in GenBank are found only in embryo and in leaf, not in endosperm.
Mentions: Complete gene expression lists (FPKM > 1) from the embryo, endosperm, and leaf transcriptomes are provided as Table S2, Table S3, and Table S4. Expression profiling of the top 50 expressed genes (Figure 2) reflects the physiological characteristics and/or function of the different tissues. As expected, photosynthetic genes are found almost exclusively in the leaf transcriptome, with the most abundant transcript encoding the small subunit of ribulose-1,5-bisphosphate carboxylase (Table 2). In endosperm, which has been sampled at the gelatinous stage undergoing active cell division (Abraham and Mathew 1963), transcripts for cytoskeletal and translational proteins are abundant. Alpha-tubulin, which forms microtubules in the mitotic spindle, is the most highly transcribed gene in endosperm and translationally controlled tumor protein (Amson et al. 2013), which binds to microtubules (Santa Brigida et al. 2014) and regulates cell division (Brioudes et al. 2010), is in the top 10 (Table 2). Other highly expressed genes in coconut endosperm (Table 2), including annexin, enolase, and metallothionein type 2A (MT2A), are also among those expressed at a high level in endosperm of castor bean (Lu et al. 2007) and Brassica napus (Huang et al. 2009).

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