Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phylogeny of the saffron-crocus species group, Crocus series Crocus (Iridaceae)

ABSTRACT: Phylogeny of series Crocus

PROVIDER: PRJEB25396 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2570770.fastq.gz	Fastqsanger.gz
	ERR2570771.fastq.gz	Fastqsanger.gz
	ERR2570772.fastq.gz	Fastqsanger.gz
	ERR2570773.fastq.gz	Fastqsanger.gz
	ERR2570764.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 14

Similar Datasets

Epigenetic variability among saffron crocus (Crocus sativus L.) accessions characterised by different phenotypes

Project description:This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analysed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions’ alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualise sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.

2021-03-24 | GSE166350 | GEO

Disentangling a polyploid complex within Crocus series Verni

Project description:Disentangling a polyploid complex within Crocus series Verni

| PRJEB57934 | ENA

Crocus sativus (saffron crocus) whole genome shutgun Illumina sequencing

Project description:Saffron (Crocus sativus) is an autotriploid hybrid derived from wild Crocus cartwrightianus cytotypes

| PRJEB29021 | ENA

Crocus sativus isolate:Saffron JU | cultivar:Saffron

Project description:Crocus sativus isolate:Saffron JU | cultivar:Saffron Genome sequencing and assembly

| PRJNA734464 | ENA

Crocus doerteae KERNDORFF species nova

Project description:Crocus doerteae KERNDORFF species nova (Liliiflorae, Iridaceae), a new member of Series Scardici

| PRJEB44177 | ENA

Crocus cobbii KERNDORFF, PASCHE & HARPKE species nova (Liliiflorae, Iridaceae) and its relatives

Project description:Description of the new species Crocus cobbii

| PRJEB43897 | ENA

Epigenetic variability among saffron crocus (Crocus sativus L.) accessions characterised by different phenotypes

Project description:Epigenetic variability among saffron crocus (Crocus sativus L.) accessions characterised by different phenotypes

| PRJNA700580 | ENA

<i>Crocus speciosus</i> (Iridaceae)-A New Species for the Bulgarian Flora.

Project description:This is the first report on the autumn-flowering species Crocus speciosus, belonging to C. ser. Speciosi from the Bulgarian flora. The species was found in Southeastern Bulgaria, in the area between Ahtopol and Rezovo. Re-examining the Bulgarian collections, the earliest specimen was collected in 1975, was probably overlooked, and most likely determined as C. pulchellus. The nearest known localities of the species are on the territory of Türkiye. In this study, we compared C. pulchellus and C. ibrahimii using DNA sequence data from the nuclear ITS1/2 region and morphological features. Our study showed a close relationship between the specimens from Bulgaria and the recently deposited data of C. speciosus and their separation from the closely related C. pulchellus. Together with the previously cited white anthers as a key feature for determination, the molecular data confirmed a clear distinction between the samples with white anthers in the two species. The morphological data of our taxon overlapped with the description of C. ibrahimii. The molecular data strongly supported the affiliation of C. speciosus s.l., but did not support the recognition of C. ibrahimii as a separate species and it should be referred to as a subspecies of C. speciosus subsp. ibrahimii Rukšāns.

| S-EPMC9965344 | biostudies-literature

Rediscovery of Crocus biflorus var. estriatus (Iridaceae)

Project description:Rediscovery of Crocus biflorus var. estriatus (Iridaceae), and its taxonomic characterisation

| PRJEB27989 | ENA

Saffron Transcriptome and Gene Expression

Project description:In this study, we aim to present a global transcriptome analysis of medicinal/spice plant, Crocus sativus. We generated about 206 million high-quality reads from five tissues (corm, leaf, Tepal, stamen and stigma) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples.

2016-03-04 | GSE65103 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data