DH1

Resource Type: 
Breeding Research Material
Image File: 
There are 3 images.
ImageAnnotations
  • breeding research material: DH1
  • date: 2018-10-26
  • File Name: DH1_3.jpg
  • legend: Image of root grown in Hancock, Wisconsin USA taken 2018-10-26
  • photo provider: USDA ARS VCRU
  • breeding research material: DH1
  • date: 2019-05-10
  • File Name: DH1_1.jpg
  • legend: Image of root grown in Hancock, Wisconsin USA taken 2019-05-10
  • photo provider: USDA ARS VCRU
  • breeding research material: DH1
  • date: 2019-05-10
  • File Name: DH1_2.jpg
  • legend: Image of root grown in Hancock, Wisconsin USA taken 2019-05-10
  • photo provider: USDA ARS VCRU
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    Accession: 
    breeding_research_material/290810
    Name: 
    DH1
    Identifier: 
    DH1
    Description: 

    An orange Nantes type cultivated carrot doubled haploid line used in the Carrot Genome Assembly DCARv2.

    This doubled haploid line has been assigned NCBI biosample accession SAMN03216637, please see this record for more details.

    This material is not available from any germplasm repository.

    Project: 
    NameDescription

    The objectives of this study were to evaluate the response of diverse carrot germplasm to salinity stress, identify salt-tolerant carrot germplasm that may be used by breeders, and define appropriate screening criteria for assessing salt tolerance in germinating carrot seed.

    The objectives of this study were to evaluate the response of diverse carrot germplasm to heat stress, identify heat-tolerant germplasm that may be used by plant breeders, and define the appropriate temperature for assessing heat tolerance in germinating carrot seed.

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    Analysis: 
    NameDescription

    An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4.

    There are a few different naming schemes for this assembly. First there is the
    Authors' original naming scheme: Sequences with DCARv2 prefix are the original assembly as submitted to NCBI. These are labelled DCARv2_Chr1 through DCARv2_Chr9 for the chromosome pseudomolecules, DCARv2_MT and DCARv2_PT for the organellar assemblies, DCARv2_B1 and up for unincorporated superscaffolds, DCARv2_S26.1 and up for unincorporated scaffolds, and DCARv2_C10542132 and up for unincorporated contigs. A file with sequences using this naming scheme can be downloaded from the File: link below.
    These sequences can be viewed in JBrowse here.

    Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0

    LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926.

    Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence.

    RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records.

    The NCBI Sequence report lists the correspondences between the various naming methods

    Link to the LNRQ01000000.1 master record at NCBI

    Raw Reads: Link to SRA accessions used for the genome assembly

    This genome is available in the CarrotOmics Blast Search

    Pacific Bioscience, Oxford Nanopore, Illumina Paired-End (PE) and Hi-C sequencing data were used to develop an improved genome assembly and annotation of the doubled haploid orange Nantes-type carrot DH1, NCBI BioSample SAMN03216637. The new DH1 v3 assembly spans 440.7 Mb, assembled into nine chromosomes which represent ~93% of the estimated nuclear genome size (473 Mb).

    This genome is available in the CarrotOmics Blast Search

    Images from carrot roots grown in 2018 used by the SCRI Project

    Grown at the University of Wisconsin Hancock Agricultural Research Station (44.117850, -89.552265) from May to October 2018.

    Images from carrot roots grown in 2019 used by the SCRI Project.

    Grown at the University of California - Desert Research and Extension Center (32.816363, -115.441595) from October 2018 to March 2019

    This assembly represents the NCBI GenBank record for the Daucus carota DH1 Chromosome level assembly published in 2016. This is based on the same assembly as described in CarrotOmics record Carrot Genome Assembly DCARv2

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    Cross Reference: 
    NCBI BioSampleLoading content
    Origin Country: 
    The Netherlands
    Alias: 
    SAMN03216637
    Publication: 
    Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, Bowman M, Iovene M, Sanseverino W, Cavagnaro P, Yildiz M, Macko-Podgórni A, Moranska E, Grzebelus E, Grzebelus D, Ashrafi H, Zheng Z, Cheng S, Spooner D, Van Deynze A, Simon P. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.. Nature genetics. 2016 06; 48(6):657-66.
    Relationship: 
    There are 2 relationships.
    Relationships
    The sample, DH1_10.21273/HORTSCI13333-18, is sample of breeding_research_material, DH1.
    The sample, DH1_10.21273/HORTSCI14144-19, is sample of breeding_research_material, DH1.
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