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
File:
| File | Type |
|---|---|
| Carrot Genome Assembly DCARv3 Sequence Original Naming Scheme | FASTA format |
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:
| 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. |
Cross Reference:
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:
| Name | Common Name | Comment |
|---|---|---|
Carrot | For a general overview of carrot, see the Carrot Facts Page |
Biomaterial:
| Name | Description |
|---|---|
This biosample is also known by its germplasm accession of DH1, please see this record for more details. |
Stock:
| Name | Uniquename | Stock Type |
|---|---|---|
DH1 | breeding_research_material |
Project:
| Name | Description |
|---|---|
The project goals are to improve the assembly of the genome of cultivated carrot, and improve gene predictions using this improved assembly. |
Feature:
Core Data:
integrated_assembly