Daucus carota genome V.3 SSR Detection with MISA

Resource Type:

Analysis

Name:

Description:

SSRs were detected in the Daucus carota V.3 assembly 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.

RESULTS OF MICROSATELLITE SEARCH
================================

Total number of sequences examined:                  11
Total size of examined sequences (bp):      441,119,442
Total number of identified SSRs:                148,264
Number of SSR containing sequences:                  11
Number of sequences containing more than 1 SSR:      11
Number of SSRs present in compound formation:    12,941


Distribution to different repeat type classes
---------------------------------------------

Unit size  Number of SSRs
2          52,385
3          30,622
4          38,281
5          16,265
6           7,217
7           2,622
8             872

128,207 designed primer pairs

File:


File	Type
DCARv3 SSR Detection with MISA	GFF3

Publication:

Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2003 Feb; 106(3):411-22.
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.
Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers.. Methods in molecular biology (Clifton, N.J.). 2000; 132:365-86.

Relationship:

There is 1 relationship.
Relationships
The analysis, Daucus carota genome V.3 SSR Detection with MISA, is a part of analysis, Carrot Genome Assembly DH1 v3.0.

Program, Pipeline, Workflow or Method Name:

misa + primer3

Program Version:

1 + 2.3.7

Date Performed:

Thursday, October 10, 2019 - 11:45

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.