Transcriptomic analysis of developing embryos of apricot (Prunus armeniaca L.)

Abstract

Apricot (Prunus armeniaca L.) is an important, nutritionally valuable agricultural crop. A scarcity of transcriptomic and genomic data hinders progress toward understanding the molecular events of apricot embryogenesis, which is the primary determinant of fruit yield and kernel quality. In this study, three cDNA libraries were sequenced using an Illumina/Solexa platform. We obtained 35,928,496, 40,656,940, and 35,970,214 clean reads from endosperm formation (LT-A), embryo development (LT-B), and mature embryo (LT-C) cDNA libraries, respectively. De novo assembly of cDNA sequence data generated 35,614 unigenes with an average length of 973 bp. A total of 29,971 unigenes were matched in Nr, Nt, Swiss-Prot, KEGG, GO, and COG databases. The top matching species in the Nr database was P. persica (88.3% of matched Nr database accessions). A total of 8,327 differentially expressed genes (DEGs) were detected between LT-A and LT-B, of which 3,663 were upregulated and 4,664 were downregulated. Between LT-B and LT-C, 12,673 DEGs were detected, while 13,892 DEGs were uncovered between LT-A and LT-C. This work is the first reported application of next-generation sequencing techniques for transcriptome analysis of apricot embryo development. Besides providing valuable information on apricot embryo development, the comprehensive set of transcript sequences generated in this study may serve as additional molecular resources for the development of apricot functional genomics.

De novo transcriptome assembly and SSR markerdevelopment in apricot (Prunus armeniaca)

“…In this study, we have performed transcriptome analysis of leaves from 7 apricot accessions and obtained an average of 43,023 transcripts (N50: 1762 nt) for all accessions with a mean length 1095 nt. The results are compatible with recently published transcriptome analysis of apricots: Bai et al (2016) obtained 59,851, 57,163, and 54,792 contigs from three embryo samples of apricot with average contigs size exceeding 427 nt (N50 of 908 nt). Niu et al (2015) generated 124,070 contigs (N50: 1603 bp) with the mean length of 829.62 bp in Siberian apricot.…”

“…The present findings are in agreement with previous results; Dong et al (2014) reported the highest assignments of transcripts of embryos of Siberian apricot to biological processes (54,667, 40.72%), followed by cellular components (51,551, 38.40%) and molecular functions (28,039, 20.88%). Similarly, GO assignment of transcripts sequenced from buds, leaves, stems, flowers, fruit pulp, and seeds of commercial apricot resulted in maximum hits to biological processes, followed by cellular components and molecular function (Bai et al, 2016). The highest hits were related to the biological process GO category, which may indicate that the analyzed tissues were undergoing extensive metabolic activities.…”

“…The potential of NGS in apricot science was reviewed by Martínez-Gómez et al (2011). NGS technologies have been applied in apricot species to facilitate the transcriptome analysis of several biological and agronomical aspects: seasonal bud dormancy (Zhong et al, 2013) and self-and cross-pollinated pistils (Habu et al, 2014) in Japanese apricot, global gene profiling and the search for potential SSR markers (Dong et al, 2014), oil dynamic accumulation in developing seed kernels for the development of woody biodiesel (Niu et al, 2015) in Siberian apricot (Prunus sibirica L.), Plum Pox Virus (PPV) (Sharka) susceptibility/ resistance (Rubio et al, 2015), single nucleotide polymorphism (SNP) discovery (Salazar et al, 2015), the study of the development of embryos (Bai et al, 2016), and SNP discovery and genetic characterization via genotyping by sequencing in common apricot (Gürcan et al, 2016).…”

Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening

“…This technology has been used to examine gene function in many fruit crops; however, to date there are only a few published transcriptome studies of apricot fruit. These have focused on pericarp tissue development [6], mining of simple sequence repeat (SSR) markers [7], the identification of genes associated with pistil abortion [8], comparative analysis of fruit development in interspecific and intraspecific hybrids [9], developing embryos [10], oil accumulation in seed kernels [11], and endocarp cleaving [12]. At present, the apricot genome sequence is not publicly available and related genomic resources, including information to enhance molecular breeding of apricot fruit, are somewhat limited.…”