Carrot Genome Sequencing Project

Resource Type:

Project

Name:

Short Description:

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.

Contact:


Name	Description	Type
Carrot Genome Sequencing Consortium	University and Industry sponsors of the carrot genome sequencing project 2012–2016	Research Group

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 6 relationships.
Relationships
The project, Daucus carota subsp. sativus cultivar:DH1 Genome sequencing and assembly, is a subproject of project, Carrot Genome Sequencing Project.
The project, Daucus carota subsp. sativus cultivar:DH1 RefSeq Genome sequencing, is a subproject of project, Carrot Genome Sequencing Project.
The project, Daucus carota subsp. sativus isolate:DH1: Daucus carota subsp. sativus improved genome assembly v3, is a subproject of project, Carrot Genome Sequencing Project.
The project, Daucus carota subsp. sativus cultivar:DH1: Daucus carota subsp. sativus DCARv3 Transcriptome, is a subproject of project, Carrot Genome Sequencing Project.
The project, Resequencing of Daucus carota or close relatives, is a subproject of project, Carrot Genome Sequencing Project.
The project, Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot, is a subproject of project, Carrot Genome Sequencing Project.

Analysis:


Name	Description
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: 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

File:


File	Type
Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme	FASTA format