Brassica
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA451077 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We explored the transcriptomic changes of synthetic Brassica allohexaploid by comparing to its parents using a high-throughput RNA-Seq method. A total of 35644409 sequence reads were generated, and 32642 genes were aligned from the data. There were 29260, 29060 and 29697 genes identified in Brassica rapa, Brassica carinata, and Brassica allohexaploid, respectively. We screened differentially expressed genes (DEGs) by a standard of two-fold or greater change in expression and false discovery rate (FDR) no more than 0.001. As a result, 7397 DEGs were detected between Brassica hexaploid and its parents. A large proportion of the 3184 DEGs between Brassica hexaploid and its paternal parent B. rapa was involved in biosynthesis of secondary metabolites, plant-pathogen interaction, photosynthesis, and circadian rhythm. Between Brassica hexaploid and its maternal parent B. carinata, 2233 DEGs were screened. A lot of them had functions of plant-pathogen interaction, plant hormone signal transduction, ribosome, limonene and pinene degradation, photosynthesis, and also biosynthesis of secondary metabolites. In addition, we found many transcription factor genes, methyltransferase and methylation genes that showed differential expression between Brassica hexaploid and its parents. Leaf mRNA profiles of Brassica rapa, Brassica carinata, and Brassica allohexaploid
2014-10-10 | E-GEOD-46299 | biostudies-arrayexpress
Project description:We explored the transcriptomic changes of synthetic Brassica allohexaploid by comparing to its parents using a high-throughput RNA-Seq method. A total of 35644409 sequence reads were generated, and 32642 genes were aligned from the data. There were 29260, 29060 and 29697 genes identified in Brassica rapa, Brassica carinata, and Brassica allohexaploid, respectively. We screened differentially expressed genes (DEGs) by a standard of two-fold or greater change in expression and false discovery rate (FDR) no more than 0.001. As a result, 7397 DEGs were detected between Brassica hexaploid and its parents. A large proportion of the 3184 DEGs between Brassica hexaploid and its paternal parent B. rapa was involved in biosynthesis of secondary metabolites, plant-pathogen interaction, photosynthesis, and circadian rhythm. Between Brassica hexaploid and its maternal parent B. carinata, 2233 DEGs were screened. A lot of them had functions of plant-pathogen interaction, plant hormone signal transduction, ribosome, limonene and pinene degradation, photosynthesis, and also biosynthesis of secondary metabolites. In addition, we found many transcription factor genes, methyltransferase and methylation genes that showed differential expression between Brassica hexaploid and its parents.
2014-10-10 | GSE46299 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Illumina mRNA-Seq is comparable to microarray analysis for transcript quantification but has increased sensitivity and, importantly, the potential to distinguish between homoeologous genes in polyploids. Using a novel curing process, we adapted a reference sequence that was a consensus derived from ESTs from both Brassica A and C genomes to one containing A and C genome versions for each of the 94,558 original unigenes. We aligned reads from Brassica napus to this cured reference, finding 38% more reads mapping in resynthesised lines and 28% in natural lines. Where the A and C versions differed at single nucleotide positions, termed inter-homoeologue polymorphisms (IHPs), we were able to apportion expression in the polyploid to the A or C genome homoeologues. 43,761 unigenes contained at least one IHP, with a mean frequency of 10.5 per kb unigene sequence. 6,350 of the unigenes with IHPs were differentially expressed between homoeologous gene pairs in resynthesised B. napus. 3,212 unigenes showed a similar pattern of differential expression across a range of natural B. napus crop varieties and, of these, 995 were in common with resynthesised B. napus. Functional classification showed over-representation in gene ontology categories not associated with dosage-sensitivity.
2011-10-18 | E-MTAB-4340 | biostudies-arrayexpress
Project description:Brassica rapa, Brassica oleracea and Brassica napus Raw sequence reads
| PRJNA874461 | ENA
Project description:Brassica napus, Brassica rapa, Brassica oleracea, Brassica carinata, Brassica juncea raw sequence reads
| PRJNA298501 | ENA
Project description:Brassica oleracea and Brassica nigra Raw sequence reads
| PRJNA954599 | ENA