Brassica oleracea var. italica
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ABSTRACT:
PROVIDER: PRJNA382165 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: The goals of this study are to analyze the transcriptome of five time point in broccoli seed germination and sprout development and to find the putative glucosinolate metabolism genes in the stage. Methods: Total mRNA of germinated seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas of wild-type broccoli were harvested. Each sample was harvested in three independent biological replicates with equal weight and subsequently pooled together for sequencing. The sequence reads that passed quality filters were de novo assembled using VELVET followed by OASES. Then the assembled unigenes were used for the abundance and functional analysis. Results: A total of ~85million 251bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and Nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues,as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolismgenes sharing 62.04-89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinaseTGG2 was 20-130 times higher.These results along with the previous reports that glucosinolate concentration decreased exponentially once after germination indicate the breakdown products of glucosinolates may play important roles in broccoli seed germination and sprout development. Conclusion: Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts to develop functional vegetables containing high levels of the anticarcinogenic glucosinolates. They will also provide new insight into the genomic research of this species and its relatives.
2014-03-18 | GSE53298 | GEO
Project description:Warmer temperature is predicted to have negative effects on transition from vegetative to reproductive development in plants. The production of floral head in broccoli (Brassica oleracea var. italica) is dramatically reduced because of the high temperature stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of signalling pathway during the broccoli head formation under heat stress is limited. In this study, heat-tolerance (HT) and heat-sensitive (HS) broccoli genotypes were used to determine the effects of temperatures on the floral head development. We compared the transcription level of the HT and HS genotypes transcriptome under different temperatures ranging from 15 to 27 C. According to weighted correlation network analysis, the high temperature (27 C) activated calcium signalling pathways and mitogen-activated protein kinase cascades in both HT and HS lines. Noticeably, the genes involved in these pathways were expressed to lower level in HT than those of HS. The expression level of genes coding for heat-shock elements was lower in HT than HS. BoFLC1, a key regulator of flowering initiation, was expressed significantly lower in HT at 22 and 27 C but expressed higher in HS. Other FLC homologues were expressed to similar levels between HT and HS.
2017-04-08 | GSE97528 | GEO
Project description:Purpose: The goals of this study are to analyze the transcriptome of five time point in broccoli seed germination and sprout development and to find the putative glucosinolate metabolism genes in the stage. Methods: Total mRNA of germinated seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas of wild-type broccoli were harvested. Each sample was harvested in three independent biological replicates with equal weight and subsequently pooled together for sequencing. The sequence reads that passed quality filters were de novo assembled using VELVET followed by OASES. Then the assembled unigenes were used for the abundance and functional analysis. Results: A total of ~85million 251bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and Nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues,as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolismgenes sharing 62.04-89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinaseTGG2 was 20-130 times higher.These results along with the previous reports that glucosinolate concentration decreased exponentially once after germination indicate the breakdown products of glucosinolates may play important roles in broccoli seed germination and sprout development. Conclusion: Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts to develop functional vegetables containing high levels of the anticarcinogenic glucosinolates. They will also provide new insight into the genomic research of this species and its relatives. Wild-type broccoli mRNA profiles of seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas were generated by deep sequencing, three biological replicates pooling together for each tissue, using Illumina Myseq platform.
2014-03-18 | E-GEOD-53298 | biostudies-arrayexpress
Project description:Identification and comparative analysis of miRNAs and their targets associated with curd-forming capacity at high temperature in two broccoli genotypes
| PRJNA217918 | ENA
Project description:Broccoli miRNA
| PRJNA323999 | ENA
Project description:Expression data from 11-day-old antisense BoEMF2.1 broccoli
| PRJNA157349 | ENA
Project description:Differentially expressed transcripts (DETs) at two growth stages in kohlrabi and broccoli
| PRJDB14212 | ENA
Project description:Blindness, characterized by apical abortion, is a physiological condition that affects the Brassica family. While exposure to low temperatures during early development has been associated with blindness, the underlying causes and their impact on proper development remain unknown. This study aims to investigate the mechanisms involved in blindness occurrence in broccoli plants.
2023-07-18 | E-MTAB-13076 | biostudies-arrayexpress
Project description:Brassica oleracea var. italica cultivar:broccoli Assembly
| PRJNA361430 | ENA
Project description:In this study, the annotation of protein in broccoli was used the cds sequence predicted by RNA-Seq De novo assembly. The libraries of RNA extracted from the broccoli were employed for sequencing and analysis. Our results demonstrated that alicylic acid (SA) and ethylene (ET) biosynthesis were more susceptible to being induced by wounding with lower intensities, whereas, jasmonic acid (JA) biosynthesis was more susceptible to being activated by wounding with higher intensities. Some carbohydrate metabolic pathways and amino acid biosynthesis-related pathways such as phenylalanine, cysteine and methionine metabolic pathways were significantly up-regulated, which promotes the precursor levels for phenolic substances and glucosinolate synthesis. Biosynthesis of secondary metabolites was activated by wounding through regulation of critical proteins involved in the corresponding metabolic pathways.
2021-01-22 | GSE165229 | GEO