Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme

Resource Type: 
File
File Type: 
FASTA format
Download: 
Download File NameAvailable atSizeMD5
130.DHv2.fna.gzCarrotOmics108.18MB3ecd06322e7b9ab4d5393e81ba86cd1c
Description: 

This file contains the carrot genome assembly sequences with the authors' original naming scheme, and is the version used for the JBrowse instance available here. See the referenced analysis below for more details.

There are 6 relationships.
Relationships
The FASTA format, Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme, is reference genome VCF, DCARv2 Y2 Mapping Variants JBrowse VCF.
The FASTA format, Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme, is reference genome VCF, DCARv2 L8708 x Z020 Linkage Map Variants JBrowse VCF.
The FASTA format, Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme, is reference genome VCF, DCARv2 Genome Paper Variants 2016 JBrowse VCF.
The FASTA format, Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme, is reference genome VCF, 10.1002/csc2.20333 Unimputed Variants.
The FASTA format, Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme, is reference genome VCF, 10.1002/csc2.20333 Unfiltered Variants.
The FASTA format, Carrot Genome Assembly DCARv2 Sequence Original Naming Scheme, is reference genome VCF, 10.1002/csc2.20333 Imputed Variants.
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Project: 
NameDescription

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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Analysis: 
NameDescription

The assembled sequences from the 2011 Carrot EST Assembly were mapped to the carrot genome assembly DCARv2 using blastn. Resulting hits were converted to gff3 format for use in the CarrotOmics JBrowse. This file can be downloaded from the link below.

Data from this analysis can be viewed in JBrowse here.

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

SSRs were detected in the Daucus carota V.2 assembly (LNRQ01) using misa, and when possible primers were designed with primer3.

misa detection parameters 2-6 3-4 4-3 5-3 6-3 7-3 8-3 and interruptions 10

This analysis has not been published.

Data from this analysis can be viewed in JBrowse here.

The assembled sequences from the 2020 transcriptome assembly were mapped to the carrot genome assembly DCARv2 using blastn. Resulting hits were converted to gff3 format for use in the CarrotOmics JBrowse. This file can be downloaded from the link below.

Data from this analysis can be viewed in JBrowse here.

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Organism: 
NameCommon NameComment
Carrot
For a general overview of carrot, see the Carrot Facts Page
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Biomaterial: 
NameDescription

This biosample is also known by its germplasm accession of DH1, please see this record for more details.

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License: 
NameAttribution 4.0 International (CC BY 4.0)
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