Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.)

Abstract

Background: Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.

Growth and physiological responses to water and nutrient stress in oil palm

“…The fruit pulp and nut that provide palm and kernel oil, respectively, made oil palm a high yielding oil-producing crop (Henderson and Osborne, 2000;Corley and Tinker, 2003). At present, palm oil production is second only to that of soybean oil in terms of world vegetable oil production and the demand for palm oil is expected to increase in future (Ho et al, 2007;Yusof, 2007;Corley, 2009;Bateman et al, 2010). In order to meet the increasing demand for palm oil, an improvement in yield is required despite the large body of literature on water and nutrient stress, as the important stress of oil palm in most tropical or subtropical area.…”

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

“…In this study, EST data were used to compare and identify the genes, which are expressed abundantly in different libraries, assuming that a higher number of reads in a particular unigene represent higher a number of mRNA molecules encoding that gene in a given EST library as described in previous studies (Ho et al, 2007;Costa et al, 2010). The ESTs identified in different libraries showed that all four libraries are informative.…”

“…Beta-1,3-glucanase, ATP synthase CF0 subunit (Ho et al, 2007), thaumatin like protein and metallothionein-like protein (Ho et al, 2007) are some of the genes previously characterised during oil palm embryogenesis. Since the oil palm whole genome sequencing project has come to an end (Singh et al, 2013), the data gathered from this study will have substantial value for the comparative studies between coconut and oil palm in the future.…”

“…Chitinases affect the early phases of embryo development and it could rescue somatic embryo development in mutant lines (De Jong et al, 1992), play a crucial role in embryogenesis by exhibiting higher expression mainly in transcriptome analysis in different species [e.g. Cyclamen persicum (Rensing et al, 2005); oil palm (Ho et al, 2007) . The abundance levels of chitinase in the embryo libraries were suggestive of its involvement in embryo development and should be considered as a candidate gene for further studies.…”

“…Since non-coding and repetitive DNA, which is normally a major portion of a genome are avoided and only expressed genes are sequenced EST analysis is a rapid and cost effective way to generate important genetic information. High-throughput sequencing technologies have been used widely in gene expression studies in various tissue types, developmental stages or under different environmental conditions (Ho et al, 2007;Kyndt et al, 2012;Firon et al, 2013). Transcriptomic approaches have been successfully used to catalogue genes that are expressed during embryogenesis in economically important species such as potato (Sharma et al, 2008) and rice (Xu et al, 2012).…”