What's New
September 16, 2024
The SpudDB website has been updated. The genome browsers for all the genome assemblies have been updated to Jbrowse2. The DM v6.1 gene expression and coexpression data and webpages have also been updated. There is also a new DM v6.1 syntelogs page for an updated Potato syntelog data set. The website has also been upgraded to use HTTPS for security and better compatibility with modern web browsers.
February 17, 2023
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.
February 11, 2022
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.
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 phased tetraploid assemblies, genome annotation, and Jbrowse are available on the data access page.
September 14, 2021
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.
December 1, 2020
The SpudDB search tools have been updated with the DM v6.1 annotation.
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. The DM v6.1 genome assembly, annotation, and Jbrowse are available on the data access page
June 4, 2020
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.
May 22, 2020
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.
March 14, 2020
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.
Feb 5, 2018
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.
Feb 1, 2016
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)
March 28, 2014
A paper describing the resources, tools and data available in Spud DB has been published in the journal The Plant Genome.
November 1, 2013
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
September 4, 2013
Release of Spud DB - Potato Genomics Resource.
|
|
|
|