Parra Ruben, Paredes Miguel A, Sanchez-Calle Isabel M, Gomez-Jimenez Maria C
Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz 06006, Spain.
BMC Genomics. 2013 Dec 9;14(1):866. doi: 10.1186/1471-2164-14-866.
In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (Olea europaea L. cv. Picual), there is a coupling of the full ripening and the activation of the abscission-zone (AZ). Although fully ripe fruit have marked physiological differences with respect to their AZs, dissimilarities in gene expression have not been thoroughly investigated. The present study examines the transcriptome of olive fruit and their AZ tissues at the last stage of ripening, monitored using mRNA-Seq.
Roche-454 massive parallel pyrosequencing enabled us to generate 397,457 high-quality EST sequences, among which 199,075 were from ripe-fruit pericarp and 198,382 from AZ tissues. We assembled these sequences into 19,062 contigs, grouped as 17,048 isotigs. Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts. A comparative analysis of the transcription profiles conducted in ripe-fruit pericarp and AZ evidenced that 4,391 genes were differentially expressed genes (DEGs) in fruit and AZ. Functional categorization of the DEGs revealed that AZ tissue has an apparently higher response to external stimuli than does that of ripe fruit, revealing a higher expression of auxin-signaling genes, as well as lignin catabolic and biosynthetic pathway, aromatic amino acid biosynthetic pathway, isoprenoid biosynthetic pathway, protein amino acid dephosphorylation, amino acid transport, and photosynthesis. By contrast, fruit-enriched transcripts are involved in ATP synthesis coupled proton transport, glycolysis, and cell-wall organization. Furthermore, over 150 transcripts encoding putative transcription-factors (TFs) were identified (37 fruit TFs and 113 AZ TFs), of which we randomly selected eight genes and we confirmed their expression patterns using quantitative RT-PCR.
We generated a set of EST sequences from olive fruit at full ripening, and DEGs between two different olive tissues, ripe fruit and their AZ, were also identified. Regarding the cross-talk between fruit and AZ, using qRT-PCR, we confirmed a set of TF genes that were differentially expressed, revealing profiles of expression that have not previously been reported, this offering a promising beginning for studies on the different transcription regulation in such tissues.
在肉质果实中，完全成熟果实的脱落是一个与成熟过程密切相关的过程。在许多果树物种中，如橄榄（油橄榄 cv. 皮夸尔），完全成熟与离层区（AZ）的激活是相互关联的。尽管完全成熟的果实与其离层区在生理上存在显著差异，但基因表达的差异尚未得到充分研究。本研究使用 mRNA-Seq 监测了橄榄果实及其离层区组织在成熟最后阶段的转录组。
罗氏 454 大规模平行焦磷酸测序使我们能够生成 397,457 条高质量 EST 序列，其中 199,075 条来自成熟果实的果皮，198,382 条来自离层区组织。我们将这些序列组装成 19,062 个重叠群，归类为 17,048 个单基因簇。利用每个注释单基因簇的读数（共 15,671 个），我们鉴定出 7,756 个转录本。对成熟果实果皮和离层区的转录谱进行比较分析表明，果实和离层区中有 4,391 个基因是差异表达基因（DEGs）。对差异表达基因的功能分类显示，离层区组织对外部刺激的反应明显高于成熟果实，这表明生长素信号基因以及木质素分解代谢和生物合成途径、芳香族氨基酸生物合成途径、类异戊二烯生物合成途径、蛋白质氨基酸去磷酸化、氨基酸转运和光合作用的表达较高。相比之下，果实中富集的转录本参与了与质子运输偶联的 ATP 合成、糖酵解和细胞壁组织。此外，还鉴定出了 150 多个编码假定转录因子（TFs）的转录本（37 个果实 TF 和 113 个离层区 TF），我们从中随机选择了 8 个基因，并使用定量 RT-PCR 确认了它们的表达模式。
我们从完全成熟的橄榄果实中生成了一组 EST 序列，并鉴定了成熟果实及其离层区这两种不同橄榄组织之间的差异表达基因。关于果实和离层区之间的相互作用，我们使用 qRT-PCR 确认了一组差异表达的 TF 基因，揭示了以前未报道过的表达谱，这为研究此类组织中不同的转录调控提供了一个有希望的开端。
