Improved genome assembly and annotation (v6.1) for the doubled monoploid potato DM 1-3 516 R44
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.
JBrowse Genome Browser
Genome Assembly:
- DM_1-3_516_R44_potato_genome_assembly.v6.1.fa.gz - Genome assembly for the doubled monoploid potato DM 1-3 516 R44 - v6.1
- DM_1-3_516_R44_potato_genome_assembly.v6.1.hm.fa.gz - Masked genome assembly for the doubled monoploid potato DM 1-3 516 R44 - v6.1
- DM_1-3_516_R44_potato_genome_assembly.v6.1.sm.fa.gz - Soft masked genome assembly for the doubled monoploid potato DM 1-3 516 R44 - v6.1
Genome Annotation:
- DM 1-3 516 R44 - High Confidence Gene Model Set - v6.1
- DM_1-3_516_R44_potato.v6.1.hc_gene_models.cdna.fa.gz - Transcript sequences (cDNA) of high confidence gene models
- DM_1-3_516_R44_potato.v6.1.hc_gene_models.cds.fa.gz - Coding sequences (CDS) of high confidence gene models
- DM_1-3_516_R44_potato.v6.1.hc_gene_models.pep.fa.gz - Protein sequences of high confidence gene models
- DM_1-3_516_R44_potato.v6.1.hc_gene_models.gff3.gz - High confidence gene models annotation in GFF3 format
- DM 1-3 516 R44 - Representative High Confidence Gene Model Set - v6.1
- DM_1-3_516_R44_potato.v6.1.repr_hc_gene_models.pep.fa.gz - Protein sequences of the representative high confidence gene models
- DM_1-3_516_R44_potato.v6.1.repr_hc_gene_models.gff3.gz - Representative high confidence gene models annotation in GFF3 format
- DM 1-3 516 R44 - Working Gene Model Set - v6.1
- DM_1-3_516_R44_potato.v6.1.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
- DM_1-3_516_R44_potato.v6.1.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
- DM_1-3_516_R44_potato.v6.1.working_models.pep.fa.gz - Protein sequences of working gene models
- DM_1-3_516_R44_potato.v6.1.working_models.gff3.gz - Working gene models annotation in GFF3 format
- DM_1-3_516_R44_potato.v6.1.working_models.func_anno.txt.gz - Functional annotation for the working gene models
- DM 1-3 516 R44 - InterPro and GO term assignment - v6.1
- DM_1-3_516_R44_potato.v6.1.working_models.iprscan_output.tsv.gz - InterProScan search results for the working gene models
- DM_1-3_516_R44_potato.v6.1.working_models.iprscan_go_terms.txt.gz - InterProScan assigned GO terms for the working gene models
- DM_1-3_516_R44_potato.v6.1.working_models.go.txt.gz - GO terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)
- DM_1-3_516_R44_potato.v6.1.working_models.goslim.txt.gz - GOSlim terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)
- DM 1-3 516 R44 - Gene Expression Matrix (TPM) - v6.1
- DM_1-3_516_R44_potato.v6.1.TPM_gene_expression_matrix.xlsx - Gene expression values (TPM) for 219 RNA-seq libraries generated for the DM v6.1 working models
- DM 1-3 516 R44 - SolCAP 69K and PotVar GBS SNPs - v6.1
- solcap_69k_SNPs_DM_v6_1_pos.txt.gz - SolCAP 69K SNP positions on the DM 1-3 516 R44 v6.1 assembly
- potvar_SNPs_DM_v6_1_pos.txt.gz - PotVar SNP positions on the DM 1-3 516 R44 v6.1 assembly
- solcap_69k_potvar_SNP_pos_DM_v6_1.xlsx - SolCAP 69K and PotVar SNP positions on the DM 1-3 516 R44 v6.1 assembly (Excel xlsx file)
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.
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