RNA-Seq analysis and transcriptome assembly for Blackberry (Rubus sp. Var. Lochness) fruit
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Project description:RNA-Seq analysis and transcriptome assembly for Blackberry (Rubus sp. Var. Lochness) fruit
| PRJEB6680 | ENA
Project description:BackgroundThere is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties.ResultsDe novo RNA-seq of ripe blackberries grown under field conditions was performed using Illumina Hiseq 2000. Almost 9 billion nucleotide bases were sequenced in total. Following assembly, 42,062 consensus sequences were detected. For functional annotation, 33,040 (NR), 32,762 (NT), 21,932 (Swiss-Prot), 20,134 (KEGG), 13,676 (COG), 24,168 (GO) consensus sequences were annotated using different databases; in total 34,552 annotated sequences were identified. For protein prediction analysis, the number of coding DNA sequences (CDS) that mapped to the protein database was 32,540. Non redundant (NR), annotation showed that 25,418 genes (73.5%) has the highest similarity with Fragaria vesca subspecies vesca. Reanalysis was undertaken by aligning the reads with this reference genome for a deeper analysis of the transcriptome. We demonstrated that de novo assembly, using Trinity and later annotation with Blast using different databases, were complementary to alignment to the reference sequence using SOAPaligner/SOAP2. The Fragaria reference genome belongs to a species in the same family as blackberry (Rosaceae) but to a different genus. Since blackberries are tetraploids, the possibility of artefactual gene chimeras resulting from mis-assembly was tested with one of the genes sequenced by RNAseq, Chalcone Synthase (CHS). cDNAs encoding this protein were cloned and sequenced. Primers designed to the assembled sequences accurately distinguished different contigs, at least for chalcone synthase genes.ConclusionsWe prepared and analysed transcriptome data from ripe blackberries, for which prior genomic information was limited. This new sequence information will improve the knowledge of this important and healthy fruit, providing an invaluable new tool for biological research.
| S-EPMC4311454 | biostudies-literature
Project description:Rubus armeniacus (Himalayan blackberry), drRubArme1
| PRJNA1131409 | ENA
Project description:Rubus armeniacus (Himalayan blackberry) genomic and transcriptomic data
| PRJNA1131426 | ENA
Project description:Rubus armeniacus (Himalayan blackberry) genome assembly, drRubArme1, principal haplotype
| PRJNA1155727 | ENA
Project description:Rubus armeniacus (Himalayan blackberry) genome assembly, drRubArme1, alternate haplotype
| PRJNA1155729 | ENA
Project description:Rubus chingii Hu, indigenous to China, is very rich in flavonoids. With the exception of anthocyanin, fruit flavonoids were much higher than most berries including other raspberry species, which partly contributed to its high phenolics and antioxidant capability. In contrast to other raspberries, anthocyanin and other flavonoids decreased as fruit matured. We investigated four typical phases of fruit maturation using transcriptomics, proteomics and metabolomics. The results indicate that the down-regulation of phenylpropanoid, flavonoid and anthocyanin biosynthesis are responsible for the metabolic decrease. The down-regulation of RcCHS (CL6140.Contig5) and RcCHI (Unigene14858 and Unigene22344) at gene and protein levels were associated with decreases of naringenin/naringenin chalcone respectively. Down-regulation of RcLAR (CL9527.Contig3) at gene and protein levels was consistent with decreases of afzelechin/epiafzelechin, catechin/epicatechin, and gallocatechin/epigallocatechin. However, multiple genes/proteins involved in the enzymatic pathways were divergent and differently regulated, e.g. Rc4CL genes/proteins were down-regulated while Rc4CL-like was maintained at constantly low levels.
2021-08-05 | PXD021977 | Pride
Project description:‘Crumbly’ fruit is a developmental disorder in red raspberry (Rubus idaeus) that results in malformed fruit with poor adherence of drupelets to one another. In terms of quality and yield, crumbly fruit has become a serious problem in the raspberry industry resulting in unsaleable fruit and waste. A microarray experiment, using pools of progeny from a segregating mapping population (Glen Moy x Latham) with either 'normal' or 'crumbly' fruit at three different fruit developmental stages ('closed'; 'open'; 'green'), identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within three quantitative trait loci (QTL) identified. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of the crumbly fruit phenotype.
2021-04-16 | E-MTAB-10049 | biostudies-arrayexpress
Project description:Rubus chingii var. suavissimus cultivar:wanfu1 Genome sequencing
| PRJNA728443 | ENA
Project description:Six stages of flower and fruit materials from S. lycopersicum var. Moneymaker (MM), S. lycopersicum var. cerasiforme LA1310 (CC) and Solanum pimpinellifolium PI365967 (PP) including 5DPA, 20DPA, mature green, break stage and red ripen fruits and -2DPA flower
2018-01-01 | GSE74828 | GEO