Phased Genome Assemblies and Annotation of Tetraploid Potato: Atlantic, Castle Russet, Avenger, Altus, Colomba, Spunta

January 11, 2022 - The paper "Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity" by Hoopes et al. has been published in Molecular Plant.

The genome assembly and annotation files are available below. The entire data set for the paper is available on Data Dryad at https://doi.org/10.5061/dryad.3n5tb2rhw.

Atlantic Genome Assembly (v3):

Updated Annotation (v3) for the Phased Assembly of Atlantic Tetraploid Potato

February 17, 2023 - The Buell Lab at the University of Georgia is pleased to make available an updated set of genome annotation for the Atlantic genome assembly (ATL_v3). ATL_v3 was annotated as described in (Hoopes et al. 2022 ) with new RNA-seq libraries and Oxford Nanopore (ONT) cDNA libraries. The methods for processing the new RNA-seq and ONT cDNA libraries as are follows:

RNA-seq libraries were processed for genome annotation by first cleaning with Cutadapt(Martin 2011, v2.10) using a minimum length of 100 nt and quality cutoff of 10 then aligning the cleaned reads to the respective genome using HISAT2(Kim et al. 2019, v2.1.0). Oxford Nanopore (ONT) cDNA reads were processed with Pychopper (v2.5.0; github.com/epi2me-labs/pychopper) and trimmed reads greater than 500 nt were aligned to the respective genome using minimap2(H. Li 2018, v2.17-r941) with a maximum intron length of 5,000 nt. The aligned RNA-seq and ONT cDNA reads were each assembled using Stringtie (Kovaka et al. 2019, v2.2.1) and transcripts less than 500 nt were removed.

Note: the previous Atlantic v2.0 assembly and annotation can be found at Data Dryad at https://doi.org/10.5061/dryad.3n5tb2rhw.

JBrowse Genome Browser

• Genome browser for the Atlantic v3 assembly and annotation
• Genome browser for the phased chromosome-scale genome assembly and annotation of S. tuberosum cv. Castle Russet v2

Genome Assembly:

• ATL_v3.asm.fa.gz - Genome assembly for Atlantic - v3
• ATL_v3.asm.hm.fa.gz - Masked genome assembly for Atlantic - v3
• ATL_v3.asm.sm.fa.gz - Soft masked genome assembly for Atlantic - v3

Genome Annotation:

• High Confidence Gene Model Set
• ATL_v3.hc_gene_models.cdna.fa.gz - Transcript sequences (cDNA) of the high confidence gene models
• ATL_v3.hc_gene_models.cds.fa.gz - Coding sequences (CDS) of the high confidence gene models
• ATL_v3.hc_gene_models.pep.fa.gz - Protein sequences of the high confidence gene models
• ATL_v3.hc_gene_models.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.

• ATL_v3.hc_gene_models.repr.cdna.fa.gz - Transcript sequences (cDNA) of the the representative high confidence gene models
• ATL_v3.hc_gene_models.repr.cds.fa.gz - Coding sequences (CDS) of the representative high confidence gene models
• ATL_v3.hc_gene_models.repr.pep.fa.gz - Protein sequences of the representative high confidence gene models
• ATL_v3.hc_gene_models.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.

• ATL_v3.working_models.cdna.fa.gz - Transcript sequences (cDNA) of the working gene models
• ATL_v3.working_models.cds.fa.gz - Coding sequences (CDS) of the working gene models
• ATL_v3.working_models.pep.fa.gz - Protein sequences of the working gene models
• ATL_v3.working_models.gff3.gz - Working gene models annotation in GFF3 format
• ATL_v3.functional_annotation.txt.gz - Functional annotation for the working gene models
• ATL_v3.working_models.go_slim.obo.gz - GO Slim annotation for the working gene models


• Representative Working Gene Model Set

The representative working gene models are a subset of the working gene model set. Each representative gene model is the isoform with the longest CDS at each locus.

• ATL_v3.working_models.repr.cdna.fa.gz - Transcript sequences (cDNA) of the representative working gene models
• ATL_v3.working_models.repr.cds.fa.gz - Coding sequences (CDS) of the representative working gene models
• ATL_v3.working_models.repr.pep.fa.gz - Protein sequences of the representative working gene models

Castle Russet Genome Assembly:

• CR_v2.0_pseudomolecules.fasta.gz - Castle Russet genome assembly with phased and unphased pseudomolecules
• CR_v2.0_asm.fasta.gz - Castle Russet genome assembly with phased pseudomolecules, unphased pseudomolecules, and unplaced scaffolds
• CR_v2.0_unplaced_scaffolds.fasta.gz - Castle Russet genome assembly with unplaced scaffolds
• Potato_POR06V12_Phased_scaffolds.fasta.gz - Castle Russet DeNovoMagic^TM genome assembly with phased scaffolds
• Potato_POR06V12_Phased_Unplaced_scaffolds.fasta.gz - Castle Russet DeNovoMagic^TM genome assembly with unphased scaffolds
• CR_v2.0_asm.hm.fasta.gz - Repeat masked Castle Russet v2.0 genome assembly
• CR_v2.0_asm.sm.fasta.gz - Soft repeat masked Castle Russet v2.0 genome assembly

Castle Russet Genome Annotation:

• Castle Russet v2.0 Pseudomolecules - High Confidence Gene Model Set
• cr.hc.pm.cdna.fasta.gz - Transcript sequences (cDNA) of high confidence gene models
• cr.hc.pm.cds.fasta.gz - Coding sequences (CDS) of high confidence gene models
• cr.hc.pm.pep.fasta.gz - Protein sequences of high confidence gene models
• cr.hc.pm.locus_assign.gff3.gz - High confidence gene models annotation in GFF3 format


• Castle Russet v2.0 Pseudomolecules - 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.

• cr.hc.repr.pm.pep.fasta.gz - Protein sequences of the representative high confidence gene models
• cr.hc.repr.pm.locus_assign.gff3.gz - Representative high confidence gene models annotation in GFF3 format


• Castle Russet v2.0 Pseudomolecules - 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.

• cr.working_models.pm.cdna.fasta.gz - Transcript sequences (cDNA) of working gene models
• cr.working_models.pm.cds.fasta.gz - Coding sequences (CDS) of working gene models
• cr.working_models.pm.pep.fasta.gz - Protein sequences of working gene models
• cr.working_models.pm.locus_assign.gff3.gz - Working gene models annotation in GFF3 format
• cr.pm.functional_annotation.txt.gz - Functional annotation for the working gene models
• Castle Russet v2.0 Pseudomolecules - InterPro and GO term assignment
• cr.pm.iprscan_output.tsv.gz - InterProScan search results for the working gene models
• cr.pm.iprscan_go_terms.txt.gz - InterProScan assigned GO terms for the working gene models
• cr.pm.gene_models.go.txt.g - GO terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)
• cr.pm.gene_models.go_slim.txt.gz - Plant GOSlim terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)

Avenger Genome Assembly:

• Avenger_NRQ-11019_Fully_phased_scaffolds.fasta.gz - Avenger DeNovoMagic^TM genome assembly with phased scaffolds
• Avenger_NRQ-11019_Unphased_scaffolds.fasta.gz - Avenger DeNovoMagic^TM genome assembly with unphased scaffolds
• avenger_phased_asm.hm.fa.gz - Repeat masked Avenger genome assembly
• avenger_phased_asm.sm.fa.gz - Soft repeat masked Avenger genome assembly

Avenger Genome Annotation:

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


• Avenger Phased Scaffolds - 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.

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


• Avenger Phased Scaffolds - 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.

• avenger.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
• avenger.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
• avenger.working_models.pep.fa.gz - Protein sequences of working gene models
• avenger.working_models.gff3.gz - Working gene models annotation in GFF3 format
• avenger.functional_annotation.txt - Functional annotation for the working gene models
• Avenger Phased Scaffolds - InterPro and GO term assignment
• avenger.iprscan_output.tsv.gz - InterProScan search results for the working gene models
• avenger.iprscan_go_terms.txt.gz - InterProScan assigned GO terms for the working gene models
• avenger.gene_models.go.txt.gz - GO terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)
• avenger.gene_models.go_slim.txt.gz - Plant GOSlim terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)

Altus Genome Assembly:

• Altus_Fully_phased.scaffolds.fasta.gz - Altus DeNovoMagic^TM genome assembly with phased scaffolds
• Altus_Unphased.scaffolds.fasta.gz - Altus DeNovoMagic^TM genome assembly with unphased scaffolds
• altus_phased_asm.hm.fa.gz - Repeat masked Altus genome assembly
• altus_phased_asm.sm.fa.gz - Soft repeat masked Altus genome assembly

Altus Genome Annotation:

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


• Altus Phased Scaffolds - 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.

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


• Altus Phased Scaffolds - 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.

• altus.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
• altus.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
• altus.working_models.pep.fa.gz - Protein sequences of working gene models
• altus.working_models.gff3.gz - Working gene models annotation in GFF3 format
• altus.functional_annotation.txt - Functional annotation for the working gene models
• Altus Phased Scaffolds - InterPro and GO term assignment
• altus.iprscan_output.tsv.gz - InterProScan search results for the working gene models
• altus.iprscan_go_terms.txt.gz - InterProScan assigned GO terms for the working gene models
• altus.gene_models.go.txt.gz - GO terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)
• altus.gene_models.go_slim.txt.gz - Plant GOSlim terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)

Colomba Genome Assembly:

• Colomba_fully_phased.scaffolds.fasta.gz - Colomba DeNovoMagic^TM genome assembly with phased scaffolds
• Colomba_Unphased.scaffolds.fasta.gz - Colomba DeNovoMagic^TM genome assembly with unphased scaffolds
• colomba_phased_asm.hm.fa.gz - Repeat masked Colomba genome assembly
• colomba_phased_asm.sm.fa.gz - Soft repeat masked Colomba genome assembly

Colomba Genome Annotation:

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


• Colomba Phased Scaffolds - 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.

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


• Colomba Phased Scaffolds - 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.

• colomba.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
• colomba.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
• colomba.working_models.pep.fa.gz - Protein sequences of working gene models
• colomba.working_models.gff3.gz - Working gene models annotation in GFF3 format
• colomba.functional_annotation.txt - Functional annotation for the working gene models
• Colomba Phased Scaffolds - InterPro and GO term assignment
• colomba.iprscan_output.tsv.gz - InterProScan search results for the working gene models
• colomba.iprscan_go_terms.txt.gz - InterProScan assigned GO terms for the working gene models
• colomba.gene_models.go.txt.gz - GO terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)
• colomba.gene_models.go_slim.txt.gz - Plant GOSlim terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)

Spunta Genome Assembly:

• Spunta_NRQ_11022_fully_phased_scaffolds.fasta.gz - Spunta DeNovoMagic^TM genome assembly with phased scaffolds
• spunta_NRQ_11022_unphased_scaffolds.fasta.gz - Spunta DeNovoMagic^TM genome assembly with unphased scaffolds
• spunta_phased_asm.hm.fa.gz - Repeat masked spunta genome assembly
• spunta_phased_asm.sm.fa.gz - Soft repeat masked spunta genome assembly

Spunta Genome Annotation:

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


• Spunta Phased Scaffolds - 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.

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


• Spunta Phased Scaffolds - 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.

• spunta.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
• spunta.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
• spunta.working_models.pep.fa.gz - Protein sequences of working gene models
• spunta.working_models.gff3.gz - Working gene models annotation in GFF3 format
• spunta.functional_annotation.txt - Functional annotation for the working gene models
• Spunta Phased Scaffolds - InterPro and GO term assignment
• spunta.iprscan_output.tsv.gz - InterProScan search results for the working gene models
• spunta.iprscan_go_terms.txt.gz - InterProScan assigned GO terms for the working gene models
• spunta.gene_models.go.txt.gz - GO terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)
• spunta.gene_models.go_slim.txt.gz - Plant GOSlim terms assigned to the working gene models by best hit to the Arabidopsis proteome (TAIR10)