Marko Petek (Author), Maja Zagorščak (Author), Živa Ramšak (Author), Sheri Sanders (Author), Špela Tomaž (Author), Elizabeth Tseng (Author), Mohamed Zouine (Author), Anna Coll Rius (Author), Kristina Gruden (Author)

Abstract

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. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated 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 several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.

Keywords

RNA interferenca (RNAi);dsRNA;utišanje genov;RNAi za zatiranje škodljivcev;analiza preživetja;Leptinotarsa decemlineata (Say);poljski poskus;E coli HT115 (DE3);

Data

Language: English
Year of publishing:
Typology: 1.01 - Original Scientific Article
Organization: NIB - National Institute of Biology
UDC: 577
COBISS: 27695619 Link will open in a new window
ISSN: 2052-4463
Views: 19
Downloads: 8
Average score: 0 (0 votes)
Metadata: JSON JSON-RDF JSON-LD TURTLE N-TRIPLES XML RDFA MICRODATA DC-XML DC-RDF RDF

Other data

Secondary language: Slovenian
Secondary keywords: RNA interferenca (RNAi);dsRNA;utišanje genov;RNAi za zatiranje škodljivcev;analiza preživetja;Leptinotarsa decemlineata (Say);poljski poskus;E coli HT115 (DE3);
Source comment: Nasl. z nasl. zaslona; Opis vira z dne 9. 9. 2020;
Pages: str. 1-15
Volume: ǂVol. ǂ7
Issue: ǂarticle no. ǂ249
Chronology: 2020
DOI: 10.1038/s41597-020-00581-4
ID: 24574232