Carrot Genome Assembly DH1 v3.0

Resource Type: 
Analysis
Name: 
Carrot Genome Assembly DH1 v3.0
Description: 

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

Publication: 
Coe K, Bostan H, Rolling W, Turner-Hissong S, Macko-Podgórni A, Senalik D, Liu S, Seth R, Curaba J, Mengist MF, Grzebelus D, Van Deynze A, Dawson J, Ellison S, Simon P, Iorizzo M. Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots.. Nature plants. 2023 Oct; 9(10):1643-1658.
Relationship: 
There are 9 relationships.
Relationships
The analysis, Carrot Genome Assembly DH1 v3.0 Tandem Repeats annotation by trf, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, Carrot Genome Assembly DH1 v3.0 Regulatory Gene Annotation, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, Carrot Genome Assembly DH1 v3.0 Resistance Gene Annotation, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, DCAR V3.0 Gene Prediction, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, Carrot Genome Assembly DH1 v3.0 Repetitive DNA Annotation, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, NCBI Daucus carota subsp. sativus Annotation Release GCF_001625215.2-RS_2024_03, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, Carrot Genome Assembly DCARv3 Gaps, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, Daucus carota genome V.3 SSR Detection with MISA, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
The analysis, DCAR Gene annotation V1.0 locations on Carrot Genome Assembly DH1 V3.0, is a part of analysis, Carrot Genome Assembly DH1 v3.0.
Loading content
Program, Pipeline, Workflow or Method Name: 
FALCON 0.3.0; CANU 1.5; Pilon 1.23; SALSA2; PBjelly 15.8.24; RaGOO; LR_Gapcloser
Program Version: 
Genome assembly version 3.0
Algorithm: 
de-novo assembly
Date Performed: 
Tuesday, October 8, 2019 - 00:00
Data Source: 
Source Name
: PRJNA798760
Source URI
: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA798760
Organism: 
NameCommon NameComment
Carrot
For a general overview of carrot, see the Carrot Facts Page
Loading content
Biomaterial: 
NameDescription

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

Loading content
Stock: 
NameUniquenameStock Type
DH1
breeding_research_material
Loading content
Project: 
NameDescription

The project goals are to improve the assembly of the genome of cultivated carrot, and improve gene predictions using this improved assembly.

Loading content
Feature: 
NameUniquenameFeature Type
DCARv3_Chr1
DCARv3_Chr1
DNA
DCARv3_Chr2
DCARv3_Chr2
DNA
DCARv3_Chr3
DCARv3_Chr3
DNA
DCARv3_Chr4
DCARv3_Chr4
DNA
DCARv3_Chr5
DCARv3_Chr5
DNA
DCARv3_Chr6
DCARv3_Chr6
DNA
DCARv3_Chr7
DCARv3_Chr7
DNA
DCARv3_Chr8
DCARv3_Chr8
DNA
DCARv3_Chr9
DCARv3_Chr9
DNA
DCARv3_MT
DCARv3_MT
DNA
Loading content
Core Data: 
integrated_assembly