Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An atlas of small RNAs from potato

ABSTRACT: Small RNAs, including microRNAs (miRNAs), phased secondary small interfering RNAs (phasiRNA), and heterochromatic small interfering RNAs (hc-siRNA) are an essential component of gene regulation. To establish a broad potato small RNA atlas, we constructed an expression atlas of leaves, flowers, roots, and tubers of Desiree and Eva, which are commercially important potato (Solanum tuberosum) cultivars. All small RNAs identified were observed to be conserved between both cultivars, supporting the hypothesis that small RNAs have a low evolutionary rate and are mostly conserved between lineages. However, we also found that a few miRNAs showed differential accumulation between the two potato cultivars, and that hc-siRNAs have a tissue specific expression. We further identified dozens of reproductive and non-reproductive phasiRNAs originating from coding and noncoding regions that appeared to exhibit tissue-specific expression. Together, this study provides an extensive small RNA profiling of different potato tissues that might be used as a resource for future investigations.

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE213986 | GEO | 2022/11/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Quantitative proteomic analysis of differentially expressed proteins in tubers of potato plants differing in resistance to Dickeya solani

Project description:To identify differently expressed proteins in tuber tissue of potato cultivars and diploid interspecific hybrids of Solanum, differing in resistance to Dickeya solani, comparative analysis was performed. Two highly resistant (Bea and Humalda) and three susceptible (Irys, Katahdin, Ulster Supreme) potato cultivars, as well as the highly resistant (DG 00-270) and the susceptible (DG 08-305) diploid clones, were studied. DG 00-270 exhibited higher resistance to D. solani than the cultivars Bea and Humalda. Proteins were extracted from wounded potato tubers inoculated with bacteria at an early symptomatic phase and from controls, i.e., intact tubers and wounded mock-inoculated tubers. Protein profiles were analyzed using nano-liquid chromatography coupled with tandem mass spectrometry (LC-MS-MS/MS).

2019-05-21 | PXD013009 | Pride

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (PARE)

Project description:Maize anthers, the male reproductive floral organs, express two classes of phased, small interfering RNAs (phasiRNAs). RNA profiling from ten sequential cohorts of staged maize anthers plus mature pollen revealed that 21-nt phased siRNAs (21-phasiRNAs) from 463 loci appear abruptly after germinal and initial somatic cell fate specification and then diminish, while 24-nt phased siRNAs (24-phasiRNAs) from 176 loci coordinately accumulate during meiosis and persist as haploid gametophytes differentiate into pollen. RNA sequencing of anther developmental mutants, together with in situ RNA hybridization detection of phasiRNA biogenesis factors, demonstrated that 21-phasiRNAs and 24-phasiRNAs are independently regulated. Furthermore, 21-phasiRNAs require epidermal cells while 24-phasiRNAs require functional tapetal cells. Maize phasiRNAs and mammalian PIWI-interacting RNAs (piRNAs) illustrate convergent evolution of small RNAs to support male reproduction. Examination of maize phasiRNAs by high throughput sequencing for RNA-seq, small RNA, and PARE profiling

2015-02-11 | E-GEOD-52297 | biostudies-arrayexpress

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (RNA-seq)

2015-02-11 | E-GEOD-52290 | biostudies-arrayexpress

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (small RNA-seq)

2015-02-11 | E-GEOD-52293 | biostudies-arrayexpress

PVY-NTN elicits diverse gene expression response in different potato genotypes in the first 12 hours after inoculation

Project description:Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. While cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers, cv. Sante is resistant and thus not affected by the virus. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN interaction. Moreover, the differences in the response of the sensitive and resistant cultivar can pinpoint the genes involved in differential sensitivity of the cultivars. Differential gene expression in the early response of potato cvs. Igor and Sante to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 0.5 and 12 hours after inoculation.

2008-07-09 | GSE12041 | GEO

Senescent Sweetening in Potato Tubers is Associated with a Reduction in Plastidial Glucose-6-Phosphate/Phosphate Encoding Transcripts: Microarray set 1

Project description:Senescent sweetening results in the accumulation of reducing sugars in potato tubers following extended periods of storage at moderate temperatures, used to avoid the separate condition of cold-induced sweetening. Transcriptional profiling was performed using microarrays on potato genotypes with contrasting response; cultivars Arsenal and VR808, were considered to be senescent sweetening susceptible and resistant, respectively. Tubers were stored at 13 °C for two weeks prior to the application of chlorpropham (CIPC) to inhibit sprouting, and then transferred for long-term storage in the dark at 9 °C for different periods. Data indicated changes in carbohydrate metabolism were associated with the onset of senescent sweetening.

2021-07-01 | E-MTAB-10145 | biostudies-arrayexpress

Senescent Sweetening in Potato Tubers is Associated with a Reduction in Plastidial Glucose-6-Phosphate/Phosphate Encoding Transcripts: Microarray set 2

2021-07-01 | E-MTAB-10146 | biostudies-arrayexpress

Early response of potato plants to virus (PVY-NTN) inoculation

Project description:Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. The cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN interaction. Differential gene expression in early response of potato cv. Igor plants to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 12 hours after inoculation, in four biological replicates. Keywords: direct comparison

2008-03-21 | GSE10903 | GEO

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (PARE)

2015-02-11 | GSE52297 | GEO

Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (small RNA-seq)

2015-02-11 | GSE52293 | GEO