Carrot Genome Assembly DCARv2

Resource Type: 
Genome Assembly
Carrot Genome Assembly DCARv2

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:

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

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.
Cross Reference: 
Genbank AssemblyLoading content
NCBI AssemblyLoading content
NCBI BioProjectLoading content
NCBI BioSampleLoading content
NCBI GenomeLoading content
NCBI WGSLoading content
Refseq AssemblyLoading content

The overall goal of this project is to leverage the current genetic and genomic resources in carrot to develop an integrated genomic sequence of carrot including physical map, genetic maps, transcriptomes and SNP database. An integrated and annotated genomic sequence can significantly advance our understanding of agricultural traits, increase genetic gain by making informed selections and shorten breeding cycles by incorporating marker-assisted and genomic selection strategies for breeding carrot and close relatives. Our Goal is to have an annotated sequence of carrot contig N50 30 kb and scaffold N50 of >500 kb.

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NameCommon NameComment
For a general overview of carrot, see the Carrot Facts Page
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NameUniquenameStock Type
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There are 44480 CDS features
There are 4826 DNA features
There are 500482 exon features
There are 68097 gene features
There are 76593 mRNA features
There are 4973 ncRNA features
There are 76593 polypeptide features
There are 2170 transcript features
There are 441 tRNA features
Total: 778655
Program, Pipeline, Workflow or Method Name: 
SOAPdenovo; GapCloser for SOAPdenovo; integration with linkage maps (SOAPdenovo v. 2.04; GapCloser for SOAPdenovo v. 1.12; integration with linkage maps v. NOV-2013). de-novo assembly
Program Version: 
Genome assembly version 2.0
de-novo assembly
Date Performed: 
Friday, November 13, 2015 - 00:00
Data Source: 
Source Name
: LNRQ01000000
Source Version
: 1
Source URI