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* Home
* News
* FAQs
* Genome Browser
* S. tuberosum group Phureja DM1-3 v6.1
* S. tuberosum cv. Atlantic v2
* S. tuberosum cv. Castle Russet v2
* S. tuberosum group Phureja DM1-3 v4.03
* S. tuberosum group Tuberosum RH89-039-16 v3
* S. tuberosum cv. Cooperation-88
* S. tuberosum cv. Otava v1
* M82 Tomato (UGA-v1)
* Search Tools
* Download
* DM v6.1
* Phased Tetraploid Potato Assemblies
* Cooperation-88 (C88) v1
* RH89-039-16 v3
* Otava v1
* DM v4.03/v4.04
* M6 Genome Data
* M82 Tomato UGA-v1 Annotation
* Links
* Contact
SOLANACEAE GENOMICS RESOURCE
* 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 26, 2022 - The Buell Lab 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.
* 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 6.1 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 DM v6.1 genome
assembly, annotation, and Jbrowse are available on the data access page.
* May 22, 2020 - The Buell Lab at the University of Georgia 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
genome assembly is available on the DM v6.1 data access page.
* March 14, 2020 - The haplotype resolved genome assembly and annotation of the
heterozygous diploid potato RH89-039-16 is now available on SpudDB. More
information about the assembly, download links, and a Jbrowse instance are
available on the data access page.
* February 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. The genome assembly and annotation are available from the Data Dryad
data repository.
* March 28, 2014 - A paper describing the resources, tools and data available
in Spud DB has been published in the journal The Plant Genome.
POTATO GENOMIC TOOLS
Potato (Solanum tuberosum L.) is the fourth most important crop in the world,
behind wheat, rice, and maize. In 2004, worldwide potato production exceeded 327
million metric tons. Potato also produces more food energy and value per unit of
land area than any other crop. Compared to grain crops, potato is a superior
source of nutrition; however, among major crop plants, potato is arguably the
most intensively managed. In addition, tuber quality requirements are complex
and must be maintained during harvest and storage. The genome sequence of potato
was released and published in 2011 by the International Potato Genome Sequencing
Consortium (PGSC). The assembled potato genome is that of the doubled monoploid
S. tuberosum Group Phureja DM1-3 (DM; AEWC00000000); the genome assembly
represents 726 MB, of which 86%, is anchored to the genetic map and contains
39,031 annotated genes. In addition, BAC and whole genome shotgun sequences were
released from a second clone, S. tuberosum Group Tuberosum RH89-039-16 (RH;
ERP000627).
In 2020, an improved genome assembly of DM (v6.1) (based on Oxford Nanopore
long-read sequencing) and improved genome annotation was released and published.
The new assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb
genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12
chromosomes. The new assembly has improved contiguity with a 595-fold increase
in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase
in N50 scaffold size, and an LTR Assembly Index score of 13.56.
Spud DB houses potato genome browsers for the updated DM v6.1 pseudomolecules
and the legacy PGSC v4.03 pseudomolecules. The potato genome browsers also
contain data from potato RNA-Seq libraries from the SRA, and SolCAP SNP
information , and SolCAP SNP information (Hamilton et al. 2011) (Felcher et al.
2012).
The updated SpudDB Search Tools provide a BLAST server to search the assembly,
annotation, and legacy data sets. Annotation searches by assigned functional
annotation, InterPro, GO and PFAM are also available.
We welcome input from outside researchers. If there is some way in which we can
improve this resource, we would like to hear from you. Please use the comment
form on our contact page to send us your suggestions.
Funding has been provided by awards from the U.S. Department of Agriculture
(2008-35300-18671) and the U.S. National Science Foundation (DBI-0604907,
DBI-0834044, and 1202724). Any opinions, findings, and conclusions or
recommendations expressed in this material are those of the author(s) and do not
necessarily reflect the views of the National Science Foundation.
Spud DB is maintained and hosted by the Buell Lab in the Department of Crop and
Soil Sciences at University of Georgia.
DM V6.1 QUICK SEARCH
Gene ID:
Search terms:
WHAT'S NEW
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 26, 2022
An updated set of genome annotation (UGA-v1) for the M82 tomato cultivar is now
available. 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.
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 6.1 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
An updated and improved 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. See the data access page for more information.
MARCH 14, 2020
The haplotype resolved genome assembly and annotation of the heterozygous
diploid potato RH89-039-16 is now available on SpudDB. More information about
the assembly, download links, and a Jbrowse instance are available on the data
access page..
FEBRUARY 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. The genome assembly
and annotation are available from the Data Dryad data repository.
FEBRUARY 1, 2016
The Buell Lab has released v4.04 of the DM pseudomolecules. More information can
be found on the Download page
MAINTENANCE NOTICE
We have planned server maintenance on the first Wednesday of every month and
therefore, Spud DB web pages may be unavailable or only partially functional
during server maintenance.
Funding has been provided by awards from the U.S. Department of Agriculture
(2008-35300-18671) and the U.S. National Science Foundation (DBI-0604907,
DBI-0834044, and 1202724). Any opinions, findings, and conclusions or
recommendations expressed in this material are those of the author(s) and do not
necessarily reflect the views of the National Science Foundation.
Photos courtesy of C. Robin Buell and the MSU Potato Breeding and Genetics
Program.