Dataset Information

Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.).

ABSTRACT: Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-Seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation for dissecting the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.

SUBMITTER: Jiang L

PROVIDER: S-EPMC5379036 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.).

Jiang Li L Yan Shuangshuang S Yang Wencai W Li Yanqiang Y Xia Mengxue M Chen Zijing Z Wang Qian Q Yan Liying L Song Xiaofei X Liu Renyi R Zhang Xiaolan X

Scientific reports 20150126

Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-Seq data were used to co ...[more]

PMID: 25619948

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Project description:Background. Ovary culture has been a useful way to generate double haploid (DH) plant in cucumber (Cucumis sativus L.). However, the rate of embryo induction and the ability for induced embryo to grow into normal embryo are quite low. Moreover, the s mechanism of cucumber embryogenesis remains ambiguous. In this study, the molecular basis for cucumber embryogenesis was explored to set up basis for a more efficient ovary culture method. Differentially expressed genes during embryogenesis process, including the early stages of embryo formation, embryo maturation and shoot formation, were investigated using transcriptomic sequencing. Methods. Based on the cytological observation of cucumber ovary culture, the ovary culture can be divided into three stages:early embryo development, embryo maturation (from pre-embryos to cotyledon embryos) and the shoot formation stage. six key time points were selected for transcriptome sequencing and analysis. Results. We firstly conducted cytological observations which suggest that cell enlargement is the symbol for gametophytes to switch to sporophyte development pathway during early embryogenesis stage. In this stage, RNA-seq revealed 3468 up-regulated genes, including hormone signal transduction genes, hormone response genes and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. The total 480 genes that function in protein complex binding, microtubule binding, tetrapyrrole binding, tubulin binding and other microtubule activities were continuously up-regulated during the embryo maturation stage, indicating that the cytoskeleton structure was continuously being built and maintained by the action of microtubule-binding proteins and enzyme modification during embryo development. In shoot formation stage, 1383 genes were up-regulated, which were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, phenylalanine metabolism, and starch and sucrose metabolism. The shoot formation stage might be regulated by 6 transcription factors that contained a B3 domain, 9 genes in the AP2/ERF family and 2 genes encoded WUS homologous domain proteins. Conclusions. These findings offer a valuable framework for explaining the transcriptional regulatory mechanism underlying embryogenesis during cucumber ovary culture.

Project description:BackgroundSignal peptides are essential for plant growth and development. In plants, biological processes including cell-cell communication, cellular proliferation and differentiation, cellular determination of self-incompatibility, and defensive responses, all depend heavily on peptide-signaling networks such as CLE (CLAVATA3/Embryo surrounding region-related). The CLEs are indispensable in different periods of plant growth and development, especially in maintaining the balance between proliferation and differentiation of stem cells in various meristematic tissues. The working system of CLE genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. The distributional patterns of chromosome-level genome assembly in cucumber provide a fundamental basis for a genome-wide comparative analysis of CLE genes in such plants.ResultsA total of 26 individual CLE genes were identified in Chinese long '9930' cucumber, the majority of which belong to unstable short alkaline and hydrophilic peptides. A comparative analysis showed a close relationship in the development of CLE genes among Arabidopsis thaliana, melon, and cucumber. Half of the exon-intron structures of all CsCLEs genes are single-exon genes, and motif 1, a typical CLE domain near the C-terminal functioning in signal pathways, is found in all cucumber CLE proteins but CsCLE9. The analysis of CREs (Cis-Regulatory Elements) in the upstream region of the 26 cucumber CLE genes indicates a possible relationship between CsCLE genes and certain functions of hormone response elements. Cucumber resulted closely related to Arabidopsis and melon, having seven and 15 orthologous CLE genes in Arabidopsis and melon, respectively. Additionally, the calculative analysis of a pair of orthologous genes in cucumber showed that as a part of the evolutionary process, CLE genes are undergoing a positive selection process which leads to functional differentiation. The specific expression of these genes was vigorous at the growth and development period and tissues. Cucumber gene CLV3 was overexpressed in Arabidopsis, more than half of the transformed plants in T1 generation showed the phenomena of obvious weakness of the development of growing point, no bolting, and a decreased ability of plant growth. Only two bolted strains showed that either the pod did not develop or the pod was short, and its development was significantly inferior to that in the wild type.ConclusionsIn this study, 26 CLE genes were identified in Chinese long '9930' cucumber genome. The CLE genes were mainly composed of alkaline hydrophilic unstable proteins. The genes of the CLE family were divided into seven classes, and shared close relationships with their homologs in Arabidopsis and melon. The specific expression of these genes was evaluated in different periods of growth and tissue development, and CLV3, which the representative gene of the family, was overexpressed in Arabidopsis, suggesting that it has a role in bolting and fruit bearing in cucumber.

Dataset Information

Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.).

Publications

Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.).

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