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Identification of candidate genes related to astringency in cucumber via RNA-seq based transcriptome profiling

ABSTRACT: Identification of candidate genes related to astringency in cucumber via RNA-seq based transcriptome profiling

PROVIDER: PRJNA448682 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6936850_1.fastq.gz	Fastqsanger.gz
	SRR6936850_2.fastq.gz	Fastqsanger.gz
	SRR6936851_1.fastq.gz	Fastqsanger.gz
	SRR6936851_2.fastq.gz	Fastqsanger.gz
	SRR6936846_1.fastq.gz	Fastqsanger.gz

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Identification of candidate genes related to astringency in cucumber via RNA-seq based transcriptome profiling

Project description:Cucumber (Cucumis sativus L.) is one of the most important fruit vegetable crops and is widely grown worldwide (FAO STAT 2016, http://faostat3.fao.org). Astringency greatly affects the flavor quality of cucumber fruits and can be irritating due to the unpleasant oral sensation it causes. However, there are no available report addressing the molecular mechanisms driving the development of cucumber fruit astringency at the transcriptome level. A few relatively basic research efforts have been carried out in our previous studies. In this study, genome-wide analysis of gene expression in the highly astringent cucumber inbred line ‘YB’ was performed using RNA-seq. The aims of this research were to identify the genes responsible for fruit astringency development and to provide new insights into the mechanism underlying the synthesis of astringent compounds in cucumber fruits.

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Grafting changed silicon metabolism and expression of bloom-forming related genes of cucumber pericarp

Project description:Cucumber (Cucumis sativus L.) is an economically important vegetable cultivated all over the world. Grafting can produce bloomless or sparse-bloom cucumber, which is welcomed by increasing consumers. Bloom granule is tine glandular hair, which is hard and rare studied on its formation and related genes. Mutifunctional RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing and has been recently applied to a wide variety of organisms, which provide us reliable technical means detect bloom formation and related genes. In this study, we chose a cucumber inbred line (Shannong No.5) and two pumpkin rootstock lines as materials, and constructed four tested cucumbers, grew plants in “Yamazaki cucumber nutrient solution formula” prepared by deionized water, treated plants with or without 1.7mM potassium silicate 2 hours before collecting pericarp. Each treatment were duplicated twice.16 cDNA libraries were constructed from pericarp of a cucumber inbred line (own-rooted cucumber), C/C (self-grafted cucumber), M/C (More bloom, cucumber grafted onto “3225” rootstock) and L/C(Less bloom, cucumber grafted onto “3212” rootstock). We obtained 17,215,769~17,529,047 high quality reads, and 18,804~19,358 genes from each sample. All reads can be mapped to the cucumber genome (Version 2). By RPKM comparing, we got 38 comparing combinations with differentially expressed genes (DEGs), obtained 38 significantly expressed combinations by FDR≤0.001 and the absolute value of log2Ratio≥1 as the thresholds. These results suggest that there are many differences and genes expression mode among effects of grafting or added silicon. This study addresses a preliminary analysis and offers a foundation for future genomic research in the bloom formation of cucumber.

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

Project description: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 to dissect the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.

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

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A Functional Allele of CsFUL1 Regulates Fruit Length through Repressing CsSUP and Inhibiting Auxin Transport in Cucumber

Project description:Cucumber (Cucumis sativus L.) is an important vegetable crop bearing fleshy pepo fruits that harvested immature. The fruit length is one of the most important agricultural traits that directly determine the fruit yield and affects fruit quality, but the regulatory mechanism of fruit length variation remains elusive. Here we found a FRUITFULL-like MADS-box gene CsFUL1 functions as a key repressor for fruit length regulation in cucumber. The expression of CsFUL1 is highly enriched in male flowers and fruits, and negatively correlated with fruit length in different cucumber lines. Notably, a key SNP in CsFUL1 was selected during cucumber domestication for long fruit. Ectopic expression of CsFUL1 was unable to rescue the indehiscent fruit phenotype of ful-1 in Arabidopsis. Overexpression of CsFUL1 resulted in increased floral organs and reduced fruit length, whereas knockdown of CsFUL1 led to elongated fruit in cucumber. Transcriptome and biochemical analyses showed that CsFUL1 regulates fruit length through two pathways: one by inhibiting the PIN-FORWED (PIN1/7)-mediated auxin transport and thus downregulates auxin related genes in the fruit, and the other by forming a tetramer with other MADS-box genes to repress the CsSUP-mediated cell division and cell expansion. In addition, we found that CsFUL1 promotes locule number variation through the classical CsWUS-CsCLV pathway. Our findings uncover the regulatory commonality and specificity during development of different fruit types, and provide an important candidate gene to customize fruit length during cucumber breeding.

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Project description:The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. We identified 279 sea cucumber miRNAs, including 15 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA; after at least 15 days of continuous torpor) were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 30 differentially expressed miRNAs ([RPM (reads per million) >10, |FC| (|fold change|) ≥1, FDR (false discovery rate) <0.01]) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-124, miR-124-3p, miR-79, miR-9 and miR-2010 were significantly over-expressed during deep aestivation compared with non-aestivation animals, suggesting that these miRNAs may play important roles in metabolic rate suppression during aestivation. analyze the global profile of small RNAs in non-aestivation (NA) and deep aestivation (DA) sea cucumbers' respiratory tree using Solexa sequencing technology

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