Brassica nigra
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA18141 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR12205303.fastq.gz | Fastqsanger.gz | |||
| ERR12245635_1.fastq.gz | Fastqsanger.gz | |||
| ERR12245635_2.fastq.gz | Fastqsanger.gz | |||
| ERR12245636_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 22 |
Similar Datasets
Project description:GC-TOF-MS, Brassica nigra / MeJA + herbivory
2019-02-06 | ST001134 | MetabolomicsWorkbench
Project description:MicroRNAs and siRNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still less understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in a high oil content and a low oil content Brassica napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 11 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large amount of 23-nt small RNAs with specific nucleotide composition preference were also identified, which may present new classes of functional small RNAs.
2011-12-28 | GSE34727 | GEO
Project description:Brassica oleracea and Brassica nigra Raw sequence reads
| PRJNA954599 | ENA
Project description:An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome M-bM-^@M-^\shockM-bM-^@M-^] and instability occur during this process, whereas chromosome doubling results in doubling and reconstructing the genome dosage. Recent studies have demonstrated that small RNAs, mainly siRNAs and miRNAs, play an important role in maintaining the genome reconstruction and stability. However, to date, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling, which is essential to elucidate the mechanism of polyploidisation. Therefore, the genetic and DNA methylation alterations and changes in the siRNA and miRNA were assessed during the formation of an allodiploid (genome: AB) and its allotetraploid (genome: AABB) between Brassica rapa (M-bM-^YM-^@) and Brassica nigra (M-bM-^YM-^B) in the present study.The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid. The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid. The high-throughput sequencing results obtained for the small RNAs showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively. Moreover, the percentages of miRNAs increased with an increase in the polyploidy levels, but the percentages of siRNAs and DNA methylation alterations decreased with an increase in the polyploidy levels. Furthermore, 320 known and 52 novel miRNAs were obtained from the parents in both the allodiploid and allotetraploid. However, quantitative real-time polymerase chain reaction (qRT PCR) analysis showed that the expression levels of the targets genes were negatively corrected with the expressed miRNAs.The study showed that siRNAs and DNA methylation play an important role in maintaining the genome stability in the formation of an allotetraploid. The miRNAs regulate gene expression and induce the phenotype variation, which may play an important role in the occurrence of heterosis in the allotetraploid. The findings of this study may provide new information for elucidating that the allotetraploids have a growth advantage over the parents and the allodiploids. High throughput sequence of the parents (Brassica rapa and Brassica nigra) and their hybrids (allodiploid and allotetraploid)
2014-09-30 | E-GEOD-61872 | biostudies-arrayexpress
Project description:Understanding the regulation of lipid metabolism is vital for genetic engineering of Brassica napus (B. napus) to increase oil yield or modify oil composition. We report the application of Illumina Hiseq 2000 for transcriptome profiling of seeds of B. napus at different developmental stages, which may uncover the dynamic changes in lipid metabolism and reveal key genes involved in lipid biosynthesis and degradation. Total RNA from developing seeds at 2, 4, 6, and 8 weeks after pollination (WAP) were isolated and sequenced separately. The gene expression levels of all samples were quantified and normalized by the DESeq normalization. We found that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. Two genes, encoding for acetyl-CoA carboxylase and acyl-ACP desaturase, might be critical for fatty acid biosynthesis in oil rape seeds. This study provides insight into the mechanism underlying lipid metabolism and reveals candidate genes that are worthy of further investigation for their values in genetic engineering of B. napus. Whole Transcriptome profiling of developing Brassica napus seeds at 2, 4, 6, 8 WAP by RNA sequencing using Illumina HiSeq 2000.
2016-02-06 | E-GEOD-77637 | biostudies-arrayexpress
Project description:Brassica nigra plants, a Brassicaceae close to Arabidopsis thaliana, was used for combined stresses experiments. In this study, we performed a whole-genome microarray analysis on five-week-old plants and compared untreated plants and plants treated with ozone at 70 ppb, larvae of Pieris brassicae or both ozone followed by P. brassicae insect.
2017-02-10 | E-MTAB-5030 | biostudies-arrayexpress
Project description:Compared to ordinary rapeseed, high-oleic acid rapeseed has higher levels of monounsaturated fatty acids and lower levels of saturated fatty acid and polyunsaturated fatty acids, and thus is of high nutritional and health value. In addition, high-oleic acid rapeseed oil imparts cardiovascular protective effects. Based on these properties, high-oleic acid oil crops have been extensively investigated and cultivated. In this study, we employed a microarray analysis with high oleic acid line and low oleic acid line from the developing seeds (27 days after flowering) of Brassica napus.
2018-09-20 | GSE120223 | GEO
Project description:Understanding the regulation of lipid metabolism is vital for genetic engineering of Brassica napus (B. napus) to increase oil yield or modify oil composition. We report the application of Illumina Hiseq 2000 for transcriptome profiling of seeds of B. napus at different developmental stages, which may uncover the dynamic changes in lipid metabolism and reveal key genes involved in lipid biosynthesis and degradation. Total RNA from developing seeds at 2, 4, 6, and 8 weeks after pollination (WAP) were isolated and sequenced separately. The gene expression levels of all samples were quantified and normalized by the DESeq normalization. We found that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. Two genes, encoding for acetyl-CoA carboxylase and acyl-ACP desaturase, might be critical for fatty acid biosynthesis in oil rape seeds. This study provides insight into the mechanism underlying lipid metabolism and reveals candidate genes that are worthy of further investigation for their values in genetic engineering of B. napus.
2016-02-06 | GSE77637 | GEO
Project description:An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome “shock” and instability occur during this process, whereas chromosome doubling results in doubling and reconstructing the genome dosage. Recent studies have demonstrated that small RNAs, mainly siRNAs and miRNAs, play an important role in maintaining the genome reconstruction and stability. However, to date, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling, which is essential to elucidate the mechanism of polyploidisation. Therefore, the genetic and DNA methylation alterations and changes in the siRNA and miRNA were assessed during the formation of an allodiploid (genome: AB) and its allotetraploid (genome: AABB) between Brassica rapa (♀) and Brassica nigra (♂) in the present study.The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid. The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid. The high-throughput sequencing results obtained for the small RNAs showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively. Moreover, the percentages of miRNAs increased with an increase in the polyploidy levels, but the percentages of siRNAs and DNA methylation alterations decreased with an increase in the polyploidy levels. Furthermore, 320 known and 52 novel miRNAs were obtained from the parents in both the allodiploid and allotetraploid. However, quantitative real-time polymerase chain reaction (qRT PCR) analysis showed that the expression levels of the targets genes were negatively corrected with the expressed miRNAs.The study showed that siRNAs and DNA methylation play an important role in maintaining the genome stability in the formation of an allotetraploid. The miRNAs regulate gene expression and induce the phenotype variation, which may play an important role in the occurrence of heterosis in the allotetraploid. The findings of this study may provide new information for elucidating that the allotetraploids have a growth advantage over the parents and the allodiploids.
2014-09-30 | GSE61872 | GEO
Project description:Brassica nigra cultivar:Sangam Genome sequencing and assembly
| PRJNA642332 | ENA