The Buell Lab at the University of Georgia is pleased to make available an updated long-read chromosome-scale genome assembly (v6.1) and genome annotation for the doubled monoploid potato S. tuberosum Group Phureja DM 1-3 516 R44.
September 23, 2020 - The paper "Construction of a chromosome-scale long-read reference genome assembly for potato" describing the DM v6.1 assembly and annotation has now been published in Gigascience.
High confidence representative gene models are a subset of the high confidence gene model set. Each representative gene model is the isoform with the longest CDS at each locus.
The set of working gene models contains all loci and isoforms from the annotation pipeline and may include artifacts such as partial gene models.
Gene expression values (TPM) for 219 potato RNA-seq libraries from the SRA were generated using Kallisto (v0.46.2). The spreadsheet contains the gene expression matrix and a table listing the SRA run accession, cultivar, and sample information.
The format of the spreadsheet: 1st column: gene model ID 2nd column: library 1 3rd column: library 2 ... last column: functional annotation of the gene
The SolCAP 69K SNPs (Hamilton et al., 2011) and the PotVar GBS SNPs (Uitdewilligen et al., 2013) were located on the DM v6.1 assembly by mapping the SNP flanking sequences. Each 100 nt flanking sequence was mapped with Vmatch (http://www.vmatch.de) allowing at most 5 mismatches and the top scoring alignment reported. If multiple alignments have the same top score, all of the top scoring alignments are reported and the SNP is marked as multimapping.