Carrot Genome Assembly DH1 v3.0

Core Data

integrated_assembly

Name

Carrot Genome Assembly DH1 v3.0

Type

genome assembly

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

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

Data Source Name

PRJNA798760

Data Source URI

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA798760

Relationship

The Analysis NCBI Daucus carota subsp. sativus Annotation Release GCF_001625215.2-RS_2024_03 is a part of Carrot Genome Assembly DH1 v3.0
The Analysis Carrot Genome Assembly DH1 v3.0 Regulatory Gene Annotation is a part of Carrot Genome Assembly DH1 v3.0
The Analysis Carrot Genome Assembly DH1 v3.0 Resistance Gene Annotation is a part of Carrot Genome Assembly DH1 v3.0
The DCAR V3.0 Gene Prediction is a part of Carrot Genome Assembly DH1 v3.0
The Analysis Carrot Genome Assembly DH1 v3.0 Repetitive DNA Annotation is a part of 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 Carrot Genome Assembly DH1 v3.0
The Analysis Carrot Genome Assembly DCARv3 Gaps is a part of Carrot Genome Assembly DH1 v3.0
The Analysis Daucus carota genome V.3 SSR Detection with MISA is a part of Carrot Genome Assembly DH1 v3.0
The Analysis Carrot Genome Assembly DH1 v3.0 Tandem Repeats annotation by trf is a part of Carrot Genome Assembly DH1 v3.0

Database Reference Annotations

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.

Project

Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot

Biological Sample

SAMN03216637

Sequence Feature

DCARv3_Chr1
DCARv3_Chr2
DCARv3_Chr3
DCARv3_Chr4
DCARv3_Chr5
DCARv3_Chr6
DCARv3_Chr7
DCARv3_Chr8
DCARv3_Chr9
DCARv3_MT
DCARv3_PT

Organism

Daucus carota subsp. sativus

Germplasm

DH1