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.
Highlights
Background & SummaryAt 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]
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]
Different breeding programmes have resulted in accumulation of smaller genome modifications, e.g. SNPs and INDELs
Summary
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]. 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. We consolidated representative cultivar-specific sequences to generate a potato pan-transcriptome (StPanTr) These transcriptomes will improve high throughput sequencing analyses, from RNA-Seq and sRNA-Seq to more specific ones like ATAC-Seq, by providing a more comprehensive and accurate mapping reference. The knowledge generated regarding variations in transcript sequences between cultivars, such as SNPs, insertions and deletions, will be a key instrument in assisting potato breeding programmes
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