S. verrucosum, a Wild Mexican Potato As a Model Species for a Plant Genome Assembly Project

In this project we sequence an inbred self-compatible tuber-bearing wild Mexican diploid potato species S. verrucosum. Using this genome we benchmark the latest Illumina, PacBio long reads, BioNano Genomics optical maps and Dovetail artificial Hi-C data along with Bioinformatics tools to generate scaffold N50s in the multi-megabase range.

We extracted DNA from fresh leaf tissue of a selfed line, from which various Illumina libraries constructed. Analysis of the k-mer profiles indicates that this S. verrucosum accession is highly homozygous as expected. Illumina large insert PCR-free, and DISCOVAR libraries were used for paired end data, Illumina Nextera mate pair libraries for scaffolding, with PacBio long reads for gap filling. The Illumina assemblies were further scaffolded using a Dovetail Genomics cHiCago™ in vitro Hi-C library followed by HiRise™ scaffolding. We are currently using a PacBio only de novo assembly, and additionally BioNano Genomics optical map based hybrid assemblies.

Benchmarking the assemblies consists of assessing the presence of  CEGMA core eukaryotic genes, local assembly accuracy will be compared to BAC inserts, long range scaffolding accuracy based on synteny to S. tuberosum and S. lycopersicum, and correct assembly of repetitive regions as exemplified by R-gene clusters.

Generation of a genome sequence for S. verrucosum will open up further opportunities for its use as a genetic model, and for studying comparative genome structure within the Solanaceae.