FAIRDOMHub

8 items tagged with 'data retrieval'.

_p_stRT

Assay: _A_03.2_components Short Name: 03.2_components Assay Class: DRY Assay Type: components Title: Components: tr2aacds headers, cdhit-2d Description: Components: tr2aacds headers, cdhit-2d; post-filtering redefinition of paralogue clusters pISA Assay creation date: 2019-10-22 pISA Assay creator: Ziva Ramsak Phenodata: None Featuredata: Data:

Submitter: Maja Zagorscak

Biological problem addressed: Annotation

Investigation: _I_STRT

Study: _S_03_stCuSTr

Organisms: Solanum tuberosum

Models: No Models

SOPs: No SOPs

Data files: /input/input.tar, /intermediate_4_cdhit-2d.tar.gz, /output/output.tar, /scripts/scripts.tar

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1171.1

Created: 7th Nov 2019 at 18:06, Last updated: 15th Nov 2019 at 21:07

/presentations/Figure2.pdf

_p_stRT

_p_stRT/_I_STRT pipeline

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3157.1

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 16th Nov 2019 at 11:49, Last updated: 25th Nov 2019 at 00:33

/reports/SupplementaryTableS1

_p_stRT

Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies. Raw and processed reads summary. Layer _p_stRT/_I_STRT/ _S_01_sequences/reports

Creators: Maja Zagorscak, Marko Petek

Submitter: Maja Zagorscak

DOI: 10.15490/fairdomhub.1.datafile.3090.1

Investigations: _I_STRT

Studies: SupplementaryInformation

Assays: Supplementary Information

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Created: 6th Nov 2019 at 15:25, Last updated: 8th Apr 2020 at 18:39

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

_p_stRT

(Show All)

Abstract (Expand)

Background: Although the reference genome of Solanum tuberosum group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid group … Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research and its subsequent applications in breeding. Results: For the DM genome assembly, two only partially-overlapping gene models exist differing in a unique set of genes and intron/exon structure predictions. First step was to merge and manually curate the merged gene model, creating a union of genes in Phureja scaffold. We next compiled available RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using CLC, Trinity, Velvet, and rnaSPAdes de novo assemblers using different settings to test for optimal outcome. In addition, for cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Revised EvidentialGene redundancy-reducing pipeline was employed to produce accurate and complete cultivar-specific transcriptomes from assemblers output, as well as to attain the pan-transcriptome. Due to being the most diverse dataset in terms of tissues (stem, seedlings and roots) and experimental conditions, cv. Désirée was the most complete transcriptome (95.8% BUSCO completeness). For cv. Rywal and breeding clone PW363 data were available for leaf samples only and the resulting transcriptomes were less complete than cv. Désirée (89.8% and 89.3% BUSCO completeness, respectively). Cross comparison of these cultivar-specific transcriptomes and merged DM gene model suggests that the core potato transcriptome is comprised of 16,339 genes. The pan-transcriptome contains a total of 95,779 transcripts, of which 54,614 transcripts are not present in the Phureja genome. These represent the variants of the novel genes found in the potato pan-genome. Conclusions: Our analysis shows that the available gene model of double-monoploid potato from group Phureja is, to some degree, not complete. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput -omics analyses, and future breeding programmes.

Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden

Date Published: No date defined

Publication Type: Not specified

DOI: 10.1101/845818

Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato

Created: 19th Nov 2019 at 12:48, Last updated: 8th Dec 2022 at 18:26

Graph based storage and retrieval of computational models

SysMO DB