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pipeline

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DOI: 10.15490/fairdomhub.1.datafile.3157.1

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_p_stRT/_I_STRT/_S_04_stPanTr/_A_04-MSA

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DOI: 10.15490/fairdomhub.1.datafile.3096.1

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/reports/SupplementaryTableS2-Primary_potato_transcriptome_assemblies.xlsx
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_p_stRT/_I_STRT/_S_02_denovo

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DOI: 10.15490/fairdomhub.1.datafile.3091.1

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_p_stRT/_I_STRT/_S_01_sequences

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DOI: 10.15490/fairdomhub.1.datafile.3090.1

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Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
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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 Zagorscak, Ziva Ramsak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll Rius, Kristina Gruden

Date Published: No date defined

Journal: Not specified

Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in Datenablageplattformen für die medizinische Forschung
WG Infrastructure for Translational Research

Abstract

Not specified

Authors: None

Date Published: 24th Oct 2017

Journal: Not specified

/input/README.MD
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pISA/README.MD at projects · NIB-SI/pISA · GitHub
pISA-tree, _p_stRT

pISA-tree: Standard project directory tree (ISA-tab compliant) - NIB-SI/pISA
https://github.com/NIB-SI/pISA/

Creators: Maja Zagorscak, Andrej Blejec

Contributor: Maja Zagorscak

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_p_stRT/_I_STRT/_S_04_stPanTr

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Creators: Maja Zagorscak, Kristina Gruden, Marko Petek, Ziva Ramsak, Anna Coll Rius

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