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
expressedsequence tags (EST) would be aninterestingtechnique
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.