The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids

Abstract

Potato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.

Fig. 1

The haplotypes of the phased Solanum okadae (OKA15) genome.

Fig. 2

The k-mer coverage plots of each of 23 genome sequences from potato wild relatives (Solanum sp).

Fig. 3

BUSCO quality assessment results of short reads de novo genome assemblies for 24 potato wild relatives or hybrid clones (Solanum sp). The bar plot shows the percent of BUSCO genes (Viridiplantae dataset) present in each genome assembly. Species information and accession numbers are detailed in Table 1.

Fig. 4

The number of high-confidence genes and transcripts found in 22 potato wild relatives accessions (Solanum sp). The two columns for each genome represent the total number of predicted genes and transcripts (larger number on top of bar) along with their proportions of functional annotations (smaller number inside bar). Species information and accession numbers are detailed in Table 1.

Fig. 5

A whole genome presence-absence variation (PAV) based phylogenetic tree showing the relatedness of potato wild relatives (Solanum sp). The S. etuberosum genome sequence was used as an outgroup. The numbers at the nodes represent bootstrap support values. For clarity of the figure, only key values are given, and the ones omitted are all 100.

Fig. 6

A plastome sequence based phylogenetic tree of 24 potato wild relatives (Solanum sp). The S. etuberosum was used as an outgroup. The numbers at the nodes represent bootstrap support values.