Carrot Genome Assembly DH1 v3.0 Repetitive DNA Annotation

Resource Type:

Analysis

Name:

Description:

De novo identification of carrot repetitive DNA was carried out with RepeatModeler v.2.0.1. Annotation of the consensus sequences was performed using a curated database of carrot LTR-RTs, Helitrons and MITE, carrot satellite repeats, dicot plant repeats from RepBase (v.23.05) and DANTE. Masking was performed using RepeatMasker.

File:


File	Type
DCARv3 Repetitive DNA Annotation	GFF3

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 is 1 relationship.
Relationships
The analysis, Carrot Genome Assembly DH1 v3.0 Repetitive DNA Annotation, is a part of analysis, Carrot Genome Assembly DH1 v3.0.

Program, Pipeline, Workflow or Method Name:

RepeatModeler + RepeatMasker

Program Version:

v.2.0.1 + v.4.1.0

Date Performed:

Tuesday, November 10, 2020 - 09:20

Data Source:

Source Name: : Carrot Genome Assembly DH1 v3.0

Organism:


Name	Common Name	Comment
Daucus carota subsp. sativus	Carrot	For a general overview of carrot, see the Carrot Facts Page

Biomaterial:


Name	Description
SAMN03216637	This biosample is also known by its germplasm accession of DH1, please see this record for more details.

Project:


Name	Description
Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot	The project goals are to improve the assembly of the genome of cultivated carrot, and improve gene predictions using this improved assembly.