![]() This concept has been extended to pan-transcriptomes, where the presence or absence of variations is not bound only to gene content, but also to genetic and epigenetic regulatory elements. The latter leads to the concept of species specific pan-genomes, namely the core genome present in most individuals and the dispensable genome comprised of genes present only in a subset of individuals, which results in the emergence of particular subgroup-specific phenotypes. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.Īt species level, genomes of individuals can differ in single nucleotide polymorphisms (SNPs), short insertions and deletions (INDELs), gene copy numbers, and presence or absence of genes 1. 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. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Next, we compiled available and newly generated RNA-Seq datasets (cca. 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. This lack of knowledge hinders further progress in potato research. 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.
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