Ontology highlight
ABSTRACT:
PROVIDER: PRJNA680907 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Studies have shown that Respiratory Burst Oxidase Homolog B (RBOHB) are involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RBOHB. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.
2017-12-31 | E-MTAB-5560 | biostudies-arrayexpress
Project description:Studies have shown that Rice Salt Sensitive 1 (RSS1) is involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RSS1. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.
2017-12-31 | E-MTAB-5583 | biostudies-arrayexpress
Project description:Development of Simple Sequence Repeat (SSR) and Morphological Markers to Identify Jaboticaba Cultivars
| PRJDB9795 | ENA
Project description:Rhododendron hybridum Hort. (Ericaceae) is an important ornamental species with striking continuous flowering feature. However, few genomic resources are currently available in this species, and the breeding programs were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from four different tissues using RNA-Seq to gain insight on the functional genes and to isolate EST-SSR markers for breeding and conservation purposes. In total 38,050,296 high-quality sequence reads were obtained, and 56,120 unigenes (with N50 = 1,236bp) were assembled. Of which, 32,580 (58.05 %) and 8,788 (15.66 %) were annotated to GO and KEGG database, respectively. Additionally, 38,775 (69.09 %) and 37,409 (66.66 %) R. hybridum unigenes were aligned to the Arabidopsis thaliana and Oryza sativa genome, respectively. A total of 21,103 simple sequence repeat (SSR) motifs were identified in 15,050 contigs. Among them, dinucleotide repeats account for the largest proportion for 49.27%, followed by mono- (35.94%) and trinucleotide (21.5%). This study represents the first transcriptome data of R. hybridum and confirms that the transcriptome assembly data are a useful resource for EST-SSR loci development. Such vast sequence data and markers will be robust tools for genomic research and breeding of R. hybridum and related species.
2020-04-11 | GSE97630 | GEO
Project description:Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) by 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of Expressed Sequence Tags (ESTs) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. Furthermore, over 200 high quality single nucleotide discrepancies were discovered using the Bukang cDNA collection as a reference database. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from over 600 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research. 1 sample TF68 accession examined
2011-09-08 | E-GEOD-29215 | biostudies-arrayexpress
Project description:Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) by 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of Expressed Sequence Tags (ESTs) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. Furthermore, over 200 high quality single nucleotide discrepancies were discovered using the Bukang cDNA collection as a reference database. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from over 600 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.
2011-09-08 | GSE29215 | GEO