The updated Jbrowse2 Browser for the annotation (ATL_v3) of the phased assembly for Atlantic tetraploid potato is now available. The browser for the version 2 annotation has been removed.
Updated annotation (ATL_v3) for the phased assembly for Atlantic tetraploid potato is now available. Also, annotation is now available for the updated M82 assembly SollycM82_v1.
The chromosome-scale and haplotype-resolved genome assembly and annotation of a cultivated autotetraploid potato "Cooperation-88" (C88) is now available on SpudDB. The contigs were generated from PacBio HiFi reads and anchored to 48 chromosomes using a genetic population and Hi-C data. The data files and a Jbrowse instance are available on the data access page.
The Buell Lab at the University of Georgia is pleased to make available an updated set of genome annotation (UGA-v1) for the M82 tomato cultivar. We generated transcript and functional annotations for the previously published long-read assembly of the M82 genome (Alonge et al. 2019 Genome Biology) using mRNA-seq and Oxford Nanopore full-length cDNA libraries. The annotation can also be viewed on a Jbrowse genome browser or search on the SpudDB BLAST server.
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 phased tetraploid assemblies, genome annotation, and Jbrowse are available on the data access page.
The chromosome-scale and haplotype-resolved genome assembly and annotation of a heterozygous tetraploid potato Otava is now available on SpudDB. More information about the assembly, download links, and a Jbrowse instance are available on the data access page.
The SpudDB search tools have been updated with the DM v6.1 annotation.
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. The DM v6.1 genome assembly, annotation, and Jbrowse are available on the data access page
The genome annotation for the updated long-read chromosome-scale genome assembly (v6.1) for the doubled monoploid potato S. tuberosum Group Phureja DM 1-3 516 R44 is now available. The v6.1 genome assembly, annotation, and JBrowse are available on the data access page.
The Buell Lab at Michigan State University is pleased to make available an updated long-read chromosome-scale genome assembly (v6.1) for the doubled monoploid potato S. tuberosum Group Phureja DM 1-3 516 R44 . The assembly is being released before publication for use by public and private research communities as a resource to facilitate plant biology discoveries and plant breeding programs. The v6.1 genome assembly is available on the data access page.
The haplotype resolved genome assembly and annotation of the heterozygous diploid potato RH89-039-16 is now avaiaible on SpudDB. More information about the assembly, download links, and a Jbrowse instance are available on the data access page.
The paper Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity been published in The Plant Journal. Thee genome assembly and annotation are available from the Data Dryad data repository.
The Buell lab at Michigan State have created a new pseudomolecule (chrUn) created from assembled DM reads that did not map to v4.03 and released it as v4.04. The pseudomolecules chr00-chr12 remain the same as v4.03. The v4.04 FASTA file can be downloaded from the PGSC Data Release Page and searched against on the SpudDB BLAST server. More details about chrUn can be found in Hardigan et al. (2016)
SNPs for the Solanum tuberosum cultivars Atlantic and Superior are now available as tracks on the Spud DB genome browser
The BLAST tool has been updated and now uses NCBI BLAST instead of the previous WU-BLAST. The output from the BLAST search now includes a graphical summary and an enhanced output layout as well.
An update has been made to the Breeder's Assistant Tools. Searching for SNPs via gene annotation is no longer case sensitive, leading to more complete search results.
A paper describing the resources, tools and data available in Spud DB has been published in the journal The Plant Genome.
The DM and RH RNA-Seq FPKM summary files were regenerated with the corrected PGSC DM v4.03 Pseudomolecule annotation. Please see the PGSC Data Download Page for more information.
The PGSC DM v4.03 Pseudomolecule GFF Files have been updated to correct an error. Please see the PGSC Data Download Page for more information.
A paper describing the construction of the PGSC v4.03 pseudomolecules for S. tuberosum Group Phureja DM1-3 has been published in the journal G3: Genes, Genomes, Genetics. The new pseudomolecules can be downloaded from the PGSC Data Download Page
Release 1 of Spud DB - Potato Genomics Resource.