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ABSTRACT:
PROVIDER: PRJNA608853 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:EST derived SSR markers in Jatropha curcas L.: Development, characterization, polymorphism and across species/genera transferability
| PRJNA79645 | ENA
Project description:Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genome-wide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intra-provenance cross (north-north cross, 58th parallel) and an inter-provenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a wide-spread North American forest tree. Results: A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar’s 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the inter-provenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar’s distribution, and higher photosynthetic assimilation rates and water-use efficiency at high-latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs, may in fact represent efficient adaptive variations against fast-evolving pathogens.
2018-09-11 | GSE119764 | GEO
Project description:Whole-genome DNA methylation profiling of oral cancer in patients from North-Eastern states of India. The Illumina Infinium 450k Human DNA methylation BeadChip was used to screen the entire DNA methylation profiles across approximately 485,577 CpGs in matched oral cancer samples. Samples included 12 paired samples (12 cancer and 12 normal).
2019-04-09 | GSE97784 | GEO
Project description:Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India
| PRJEB37902 | ENA
Project description:Development of Ensete ventricosum SSR markers
| PRJNA217866 | ENA
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
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