Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

Abstract

Coconut, Cocos nucifera L. is a major plantation crop, which ensures income for millions of people in the tropical region. Detailed molecular studies on zygotic embryo development would provide valuable clues for the identification of molecular markers to improve somatic embryogenesis. Since there is no ongoing genome project for this species, coconut expressed sequence tags (EST) would be an interesting technique to identify important coconut embryo specific genes as well as other functional genes in different biochemical pathways. The goal of this study was to analyse the ESTs by examining the transcriptome data of the different embryo tissue types together with one somatic tissue. Here, four cDNA libraries from immature embryo, mature embryo, microspore derived embryo and mature leaves were constructed. cDNA was sequenced by the Roche-454 GS-FLX system and assembled into 32621 putative unigenes and 155017 singletons. Of these unigenes, 18651 had significant sequence similarities to non-redundant protein database, from which 16153 were assigned to one or more gene ontology categories. Homologue genes, which are responsible for embryo development such as chitinase, beta-1,3-glucanase, ATP synthase CF0 subunit, thaumatin-like protein and metallothionein-like protein were identified among the embryo EST collection. Of the unigenes, 6694 were mapped into 139 KEGG pathways including carbohydrate metabolism, energy metabolism, lipid metabolism, amino acid metabolism and nucleotide metabolism. This collection of 454-derived EST data generated from different tissue types provides a significant resource for genome wide studies and gene discovery of coconut, a non-model species.

Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut

“…These findings show that short RNA-mediated epigenetic control plays a significant role in coconut seed development, particularly in the mature endosperm [124]. Bandupriya and Dunwell (2015) classified key embryo-specific genes using transcriptome data from four EST libraries from early and late embryos, microspore-derived embryos, and adult leaves. The four libraries yielded 32,621 putative unigenes, 18,651 of which matched the non-redundant protein database.…”

“…The four libraries yielded 32,621 putative unigenes, 18,651 of which matched the non-redundant protein database. Comparing embryo-specific transcriptomes to leaf transcriptomes revealed significant differentially expressed genes such as chitinase, β-1,3-glucanase, ATP synthase CF0 component, thaumatin-like protein, and metallothionein-like protein [125]. Punzalan et al (2019a) isolated total RNA from Laguna Tall (LAGT) nuts, leaves, and flowers at the mature stage.…”