Characterization of the cork oak transcriptome dynamics during acorn development

Abstract

BackgroundCork oak (Quercus suber L.) has a natural distribution across western Mediterranean regions and is a keystone forest tree species in these ecosystems. The fruiting phase is especially critical for its regeneration but the molecular mechanisms underlying the biochemical and physiological changes during cork oak acorn development are poorly understood. In this study, the transcriptome of the cork oak acorn, including the seed, was characterized in five stages of development, from early development to acorn maturation, to identify the dominant processes in each stage and reveal transcripts with important functions in gene expression regulation and response to water.ResultsA total of 80,357 expressed sequence tags (ESTs) were de novo assembled from RNA-Seq libraries representative of the several acorn developmental stages. Approximately 7.6 % of the total number of transcripts present in Q. suber transcriptome was identified as acorn specific. The analysis of expression profiles during development returned 2,285 differentially expressed (DE) transcripts, which were clustered into six groups. The stage of development corresponding to the mature acorn exhibited an expression profile markedly different from other stages. Approximately 22 % of the DE transcripts putatively code for transcription factors (TF) or transcriptional regulators, and were found almost equally distributed among the several expression profile clusters, highlighting their major roles in controlling the whole developmental process. On the other hand, carbohydrate metabolism, the biological pathway most represented during acorn development, was especially prevalent in mid to late stages as evidenced by enrichment analysis. We further show that genes related to response to water, water deprivation and transport were mostly represented during the early (S2) and the last stage (S8) of acorn development, when tolerance to water desiccation is possibly critical for acorn viability.ConclusionsTo our knowledge this work represents the first report of acorn development transcriptomics in oaks. The obtained results provide novel insights into the developmental biology of cork oak acorns, highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for adaptation. It is expected that this knowledge can be transferred to other oak species of great ecological value.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0534-1) contains supplementary material, which is available to authorized users.

Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting

“…Several studies have reported differentially expressed transcripts in different stages of development, such as acorn development [12].…”

Roles of metabolic regulation in developing Quercus variabilis acorns at contrasting geologically-derived phosphorus sites in subtropical China

“…Although the most active genes in seeds were shared throughout development, each developmental stage utilized a set of genes that was up-regulated compared with other stages, or special at the GeneChip level [46]. Similarly, the transcriptome research of developing acorns by Miguel et al [47] revealed that, carbohydrate metabolism, including sugar metabolism, the TCA cycle, and amino acid metabolism, was most represented during acorn development, but every stage had special up-regulated metabolisms, such as carbohydrates and energy metabolism for the middle stage. Similarly, even though some special metabolisms appeared in July, sugar metabolism, the TCA cycle, and amino acid metabolism comprised the core metabolic pathways in developing acorns (Figure 2; Additional le 5: Table S2), with the size and dry mass increasing signi cantly from July to September at both P-rich and P-de cient sites (p < 0.05) (Figure 1).…”

“…As the reproductive organ of Q. variabilis trees, acorns were characterized by the enrichment of starch during the development process [49]. Carbohydrate metabolism, including glycolysis, gluconeogenesis, amino sugar and nucleotide sugar metabolism, served as the essential biochemical process (Figure 2) [47]. As two vital forms of metabolites, sugars and organic acids hold a larger percentage in plants than other metabolites, and sugars (e.g., fructose, sucrose, glucose) and organic acids (e.g., shikimate, glycine, glutamate) were the primary intermediates that participated in the carbon and nitrogen metabolism of plant seeds (Figure 2) [38].…”

Genome-Wide Identification of Epigenetic Regulators inQuercus suber

“…RNA sequencing data was acquired from the Sequencing Read Archive of NCBI (https://www.ncbi.nlm.nih.gov/sra/) using the experiments provided by the high-throughput sequencing of the Q. suber transcriptome [24]. The Q. suber transcriptome was obtained using tissues at different stages/conditions of development such as: acorns from developmental stage 2 (ERR490202), 3 and 4 (ERR490203) and 5 (ERR490204) [25]; a pool of embryos collected from the acorns of stage 1 to 8 (ERR490207) [25]; cork of bad (SRR1009171) and good (SRR1009172) quality [26]; male (SRR1609152) and female (SRR1609153) flowers [27]; roots of plants with different degrees of watering: medium (SRR1812375), low (SRR1812376) and abundant (SRR1812377) [28]; red and opened buds (SRR5345606) and dormant and swollen buds (SRR5345607) [29]. The libraries where first trimmed to remove SMART adapters, present in the 454 libraries, using AlienTrimmer [30] and then filtered by QTRIM [31] using default quality parameters.…”

“…To infer the putative function of the identified enzymes under study, their transcript levels were analyzed in RNAseq experiments representing five Q. suber tissues in different developmental stages/conditions: acorns from developmental stage 2, 3/4 and 5 [25]; a pool of embryos collected from the acorns of stage 1 to [25]; cork of bad and good quality [24]; male and female flowers [27]; well-watered roots and roots with medium and severe drought [28];…”