Sweet potato (Ipomea batatas)
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ABSTRACT:
PROVIDER: PRJNA312883 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sweet potato virus disease (SPVD) is one of the most devastating diseases affecting sweetpotato (Ipomoea batatas), an important food crop in developing countries. SPVD develops when sweetpotato plants are dually infected with sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus (SPCSV). In the current study, global gene expression between SPVD affected plants and virus-tested control plants (VT) were compared in the susceptible ‘Beauregard’ and resistant ‘NASPOT 1’ (Nas) sweetpotato cultivars at 5, 9, 13 and 17 days post inoculation (DPI).
2010-01-29 | GSE18869 | GEO
Project description:Two complementary protein extraction methodologies coupled with an automated proteomic platform were employed to analyze tissue-specific proteomes and characterize biological and metabolic processes in sweet potato. A total of 74,255 peptides corresponding to 4,321 nonredundant proteins were successfully identified. Data were compared to predicted protein accessions for Ipomea species and mapped on the sweet potato transcriptome and haplotype-resolved genome. A proteogenomics analysis successfully mapped 12,902 peptides against the transcriptome or genome, representing 90.4% of the total 14,275 uniquely identified peptides, predicted 741 new protein-coding genes, and specified 2726 loci where annotations can be further improved. Overall, 39,916 peptides mapped to 3,143 unique proteins in leaves, and 34,339 peptides mapped to 2,928 unique proteins in roots; 32% and 27% unique identified proteins were leaves- and roots-specific, respectively.
2019-05-30 | PXD012999 | Pride
Project description:Global gene expression signatures was analysed through microarray expression profiling as a discovery platform to identify up and down regulated ESTs that represent genes involved in metabolic pathways in the leaf, fibrous root and storage root (tuber forming root) of sweetpotato (Ipomoea batatas) as affcted by high temperature stress (40oC) compared to ambient temperature (30oC). Also Global gene expression signatures was analysed by the same procedure to explore up and down regulated ESTs in tuberous root of sweet potato in comparison with fibrous root of Ipomoea cornea and identify unique ESTs that represent genes involved in tuber formation in sweet potato.
2015-10-01 | GSE51862 | GEO
Project description:To screen genes related to the development of sweet potato tuberous roots, the high throughput sequencing of different stages of sweet potato tuberous roots was performed. The fibrous roots (FR; roots at 20 dap), developing tuberous roots (DR; roots at 60 dap) and mature tuberous roots (MR; roots at 120 dap) of Ipomoea batatas (L.) Taizhong 6 and MBP3 overexpressed lines were used for transcriptome analysis. Totally, we identified 5488 differentially expressed genes between different stage tuberous roots of Taizhong6 and 14312 differentially expressed genes between the tuberous roots of Taizhong6 and MBP3 overexpressed lines, by calculating the gene FPKM in each sample and conducting differential gene analysis. This study provides a foundation for the mechanism analysis of sweet potato tuberous root development.
2023-10-12 | GSE245185 | GEO
Project description:More than 3.5 million raw DGE tags were obtained in each library. The clean tags in each sample ranged from 3.35 to 3.63 million, and the distinct clean tags ranged from 93,593 to 139,389. The 21 bp DGE clean tags were mapped to sweet potato transcripts. Then, we compared 7 libraries pair-wisely so that 21 pairs of comparisons were implemented. Among these comparisons, we found that 4,721 to 12,151 transcripts had significant changes in expression, and the average number was 9,657. We also observed a large number of specifically expressed transcripts between each two libraries. The expression profiles of those genes involved in root development and carbohydrates accumulation were characterized. Moreover, other genes of interest, such as potentially abiotic stress tolerance and insect resistance, were also characterized. 7 samples are examined: young leaves, mature leaves, stems, fibrous roots, initial tuberous roots, expanding tuberous roots and harvest tuberous roots.
2012-02-18 | E-GEOD-35929 | biostudies-arrayexpress
Project description:we performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of sweet potato challenged with Fob using Illumina Hiseq technology. A total of 89,944,188 clean reads were generated and were assembled into 101,988 unigenes with an average length of 666bp, 62,605(61.38%) of them were functional annotated in the non-redundant(nr) protein database from NCBI by using BLASTX with a cut-off E-value of 10-5, and COG,GO and KEGG annotations were examined for better understand their functions. Five DGE libraries were constructed from the sweet potato cultivar JS57 (high resistance) and XZH (high susceptible) challenged with pathogenic and Nonpathogenic Fob. The differentially expressed genes including up- and down-regulation in five libraries were identified and calculated based on comparisons of transcriptomes, showing differences in gene expression profiles among the samples. A set of differentially expressed genes involved disease response were identified, including 40 WRKY and seven NAC transcription factors, four resistance genes, 22 pathogenesis-related genes, and six genes involved in SA signal pathway. Our study is the first to provide the transcriptome sequence resource of sweet potato challenged with pathogenic and non-pathogenic Fob and demonstrate its digital expression profiling. We discovered a set of genes involved in disease resistance. These data provides comprehensive sequence resource of sweet potato for genetic and genomic studies and will accelerate the understanding of molecular mechanism of disease resistance.
2018-02-13 | GSE89290 | GEO
Project description:Three potato cultivars infected by Phytophthora infestans
| PRJEB4212 | ENA
Project description:More than 3.5 million raw DGE tags were obtained in each library. The clean tags in each sample ranged from 3.35 to 3.63 million, and the distinct clean tags ranged from 93,593 to 139,389. The 21 bp DGE clean tags were mapped to sweet potato transcripts. Then, we compared 7 libraries pair-wisely so that 21 pairs of comparisons were implemented. Among these comparisons, we found that 4,721 to 12,151 transcripts had significant changes in expression, and the average number was 9,657. We also observed a large number of specifically expressed transcripts between each two libraries. The expression profiles of those genes involved in root development and carbohydrates accumulation were characterized. Moreover, other genes of interest, such as potentially abiotic stress tolerance and insect resistance, were also characterized.
2012-02-18 | GSE35929 | GEO
Project description:Basil downy mildew (BDM) caused by Peronospora Belbahrii leads to losses in sweet basil cultivation across the world. Though resistant cultivars of basil exist, the formation of sterile offspring and the introduction of unwanted phenotypic and chemotypic traits slows breeding. Previous work by the Simon lab at Rutgers University identified pair of sweet basil cultivars; one resistant to BDM, MRI, and one susceptible, SB22. They predicted that three genes in MRI confer increased BDM resistance. RNA from infected MRI and SB22 plants was harvested during the first 3 days of infection at 4 timepoints in order to capture as many early phases of plant-pathogen interaction as possible. The goal is to develop resistance markers for use in breeding experiments.
2020-11-04 | GSE111387 | GEO
Project description:Potato plants (cv. Russet Burbank) were grown as in vitro plantlets, and transplanted into 12-cm pots in Sunshine Mix #2 (peat/perlite mix) supplemented with slow release fertilizer (Osmocoat) in the greenhouse. The experiment was conducted in the summer of 2004 at Moscow, ID. Plantings were staggered to facilitate collection of volatiles and leaf samples during a short harvest window for all times of all treatments. Infectious Green Peach Aphids were raised on PLRV-infected potato plants; test plants were infected by placing 10 infectious aphids on a leaf in a clip cage for 48 h. The control plants for PLRV were similarly treated with aphids that had been raised on uninfected potato plants. A local isolate of PVYO was inoculated mechanically using purified virus (5 ìg ml-1) in buffer (50 mM Na2HPO4, 20 mM Na2SO3 pH 7.0) lightly rubbed onto a leaf previously dusted with carborundum. Control plants for PVY were treated in the same manner using buffer without PVY. The RNA samples were made from systemically affected leaves, excluding the actual leaves inoculated by aphids or that received the mechanical infection. Leaf volatiles were concurrently collected from equivalent plants; aliquots of frozen leaf samples were sent for metabolite analysis prior to RNA extraction. Leaf harvests were made 1, 3, 7, 14, and 28 d post-inoculation. Keywords: Direct comparison
2007-09-01 | GSE8213 | GEO