Dataset Information

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.).

ABSTRACT: Olive (Olea europaea.L) is an economically important oleaginous crop and its fruit cold-pressed oil is used for edible oil all over the world. The basic region-leucine zipper (bZIP) family is one of the largest transcription factors families among eukaryotic organisms; its members play vital roles in environmental signaling, stress response, plant growth, seed maturation, and fruit development. However, a comprehensive report on the bZIP gene family in olive is lacking. In this study, 103 OebZIP genes from the olive genome were identified and divided into 12 subfamilies according to their genetic relationship with 78 bZIPs of A. thaliana. Most OebZIP genes are clustered in the subgroup that has a similar gene structure and conserved motif distribution. According to the characteristics of the leucine zipper region, the dimerization characteristics of 103 OebZIP proteins were predicted. Gene duplication analyses revealed that 22 OebZIP genes were involved in the expansion of the bZIP family. To evaluate the expression patterns of OebZIP genes, RNA-seq data available in public databases were analyzed. The highly expressed OebZIP genes and several lipid synthesis genes (LPGs) in fruits of two varieties with different oil contents during the fast oil accumulation stage were examined via qRT-PCR. By comparing the dynamic changes of oil accumulation, OebZIP1, OebZIP7, OebZIP22, and OebZIP99 were shown to have a close relationship with fruit development and lipid synthesis. Additionally, some OebZIP had a significant positive correlation with various LPG genes. This study gives insights into the structural features, evolutionary patterns, and expression analysis, laying a foundation to further reveal the function of the 103 OebZIP genes in olive.

SUBMITTER: Rong S

PROVIDER: S-EPMC7288668 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.).

Rong Siyu S Wu Zhiyang Z Cheng Zizhang Z Zhang Shan S Liu Huan H Huang Qianming Q

Genes 20200505 5

Olive (Olea europaea.L) is an economically important oleaginous crop and its fruit cold-pressed oil is used for edible oil all over the world. The basic region-leucine zipper (bZIP) family is one of the largest transcription factors families among eukaryotic organisms; its members play vital roles in environmental signaling, stress response, plant growth, seed maturation, and fruit development. However, a comprehensive report on the bZIP gene family in olive is lacking. In this study, 103 OebZIP ...[more]

PMID: 32380769

Similar Datasets

Project description:BackgroundAlternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year"), followed by a low-yield or even no crop the following year ("off-year"). Several factors may affect the balance between such developmental phase-transition processes. Among them are the microRNA (miRNA), being gene-expression regulators that have been found to be involved as key determinants in several physiological processes.ResultsSix olive (Olea europaea L. cv. Ayvalik variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on year" and "off year" leaves in July and in November, respectively) and sequenced by high-throughput Illumina sequencing. The RNA was retrotranscribed and sequenced using the high-throughput Illumina platform. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in the olive. In addition, 38 putative novel miRNAs were discovered in the datasets. Expression of olive tree miRNAs varied greatly among the six libraries, indicating the contribution of diverse miRNA in balancing between reproductive and vegetative phases. Predicted targets of miRNA were categorized into 108 process ontology groups with significance abundance. Among those, potential alternate bearing-associated processes were found, such as development, hormone-mediated signaling and organ morphogenesis. The KEGG analyses revealed that the miRNA-targeted genes are involved in seven main pathways, belonging to carbohydrate metabolism and hormone signal-transduction pathways.ConclusionA comprehensive study on olive miRNA related to alternate bearing was performed. Regulation of miRNA under different developmental phases and tissues indicated that control of nutrition and hormone, together with flowering processes had a noteworthy impact on the olive tree alternate bearing. Our results also provide significant data on the miRNA-fruit development interaction and advance perspectives in the miRNA profile of the olive tree.

Project description:Plants regularly experience multiple abiotic and biotic pressures affecting their normal development. The 90-kDa heat shock protein (HSP90) plays a dynamic role in countering abiotic and biotic stresses via a plethora of functional mechanisms. The HSP90 has been investigated in many plant species. However, there is little information available about this gene family in the cultivated Mediterranean olive tree, Olea europaea subsp. europaea var. europaea. In the current study, we systematically performed genome-wide identification and characterization of the HSP90 gene family in O. europaea var. europaea (OeHSP90s). Twelve regular OeHSP90s were identified, which were phylogenetically grouped into two major clusters and four sub-clusters, showing five paralogous gene pairs evolving under purifying selection. All of the 12 proteins contained a Histidine kinase-like ATPase (HATPase_c) domain, justifying the role played by HSP90 proteins in ATP binding and hydrolysis. The predicted 3D structure of OeHSP90 proteins provided information to understand their functions at the biochemical level. Consistent with their phylogenetic relationships, OeHSP90 members were predicted to be localized in different cellular compartments, suggesting their involvement in various subcellular processes. In consonance with their spatial organization, olive HSP90 family members were found to share similar motif arrangements and similar number of exons. We found that OeHSP90 promoters contained various cis-acting elements associated with light responsiveness, hormone signaling pathways and reaction to various stress conditions. In addition, expression sequence tags (ESTs) analysis offered a view of OeHSP90 tissue- and developmental stage specific pattern of expression. Proteins interacting with OeHSP90s were predicted and their potential roles were discussed. Overall, our results offer premises for further investigation of the implication of HSP90 genes in the physiological processes of the olive and its adaptation to stresses.

Dataset Information

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.).

Publications

Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets