Genome assembly and annotation for doubled monoploid potato DM1S1 (v1)

October 31, 2022 - The Douches Lab at Michigan State University and the Buell Lab at the University of Georgia are pleased to make available a long-read chromosome-scale genome assembly (v1) and genome annotation for the doubled monoploid potato S. tuberosum Group Phureja DM1S1.

Genome Assembly:

• DM1S1.final_asm.v1.fa.gz - Genome assembly for DM1S1 (v1)

Genome Annotation:

• High Confidence Gene Model Set
• DM1S1.gene_models.hc.cdna.fa.gz - Transcript sequences (cDNA) of high confidence gene models
• DM1S1.gene_models.hc.cds.fa.gz - Coding sequences (CDS) of high confidence gene models
• DM1S1.gene_models.hc.pep.fa.gz - Protein sequences of high confidence gene models
• DM1S1.v1.gene_models.hc.gff3.gz - High confidence gene models annotation in GFF3 format


• Representative High Confidence Gene Model Set

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.

• DM1S1.gene_models.hc.repr.pep.fa.gz - Protein sequences of the representative high confidence gene models
• DM1S1.v1.gene_models.hc.repr.gff3.gz - Representative high confidence gene models annotation in GFF3 format


• Working Gene Model Set

The set of working gene models contains all loci and isoforms from the annotation pipeline and may include artifacts such as partial gene models.

• DM1S1.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
• DM1S1.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
• DM1S1.working_models.pep.fa.gz - Protein sequences of working gene models
• DM1S1.v1.working_models.gff3.gz - Working gene models annotation in GFF3 format
• DM1S1.functional_annotation.txt.gz - Functional annotation for the working gene models


• 1S1 Variant Calls and Haplotype Assembly
• 1S1_strelka2_filtered_variants.vcf.gz - filtered VCF file of 1S1, variant called by Strelka2(v2.9.10) with default parameters then filtered based on Strelka2 recommended thresholds and to remove multiallelic calls and keep only alternate alleles.
• 1S1_strelka2_filtered_variants.consensus.fasta.gz - fasta file created through consensus of alternate alleles of 1S1 with DM1S1 assembly from strelka2 filtered VCF (1S1_strelka2_filtered_variants.vcf.gz) to represent the second haplotype of 1S1.
• 1S1_freebayes_filtered_variants.vcf.gz - filtered VCF file of 1S1 variant called by Freebayes(v1.3.2) with -C 4 --min-map-quality 30 -min-base-quality 30 parameters and filtered to remove multiallelic calls and keep only alternate alleles.
• 1S1_freebayes_filtered_variants.consensus.fasta.gz - fasta file created through consensus of alternate alleles of 1S1 with DM1S1 assembly from Freebayes(v1.3.2) filtered VCF (1S1_freebayes_filtered_variants.vcf.gz) to represent the second haplotype of 1S1.
• 1S1_gatk_filtered_variants.vcf.gz - filtered VCF file of 1S1 variant called by GATK(v4.1.4.1) with --min-base-quality-score 20 parameter and filtered to remove multiallelic calls and keep only alternate alleles.
• 1S1_gatk_filtered_variants.consensus.fasta.gz - fasta file created through consensus of alternate alleles of 1S1 with DM1S1 assembly from GATK(v4.1.4.1) filtered VCF (1S1_gatk_filtered_variants.vcf.gz) to represent the second haplotype of 1S1.