De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation.
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.
Affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.Show MeSH
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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).
Affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.