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

Abstract

Coconut palm (Cocos nucifera) 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 de novo 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.

Keywords: RNA-seq; coconut; endosperm; epigenetics; monocot.

Figure 1

Venn chart showing unique and shared unigenes found in three coconut transcriptomes.

Figure 2

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.

Figure 3

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

Figure 4

Analysis of GO enrichment at level eight.

Figure 5

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

Figure 6

(A) Relative quantity of four RdDM-related genes (DRM, NRPD1, NRPE1, and MET1) in three different developmental stages of endosperm. (B) Relative quantity of the same four genes in two different developmental stages of embryo.