DCARv2 2019 SSR JBrowse GFF3

Resource Type:

File

File Type:

GFF3

Download:


Download File Name	Available at	Size	MD5
01.45.2019SSR.gff3.gz	CarrotOmics	3.38MB	d869397c6ca8480344cadd573fd83ff9

Description:

A published collection of 55,386 SSR primer pairs. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

References:

The following records refer to this file:


Analysis	10.1080/13102818.2019.1701551 2019 SSR
Organism	Daucus carota subsp. sativus

Analysis:


Name	Description
10.1080/13102818.2019.1701551 2019 SSR	A published collection of 55,386 SSR primer pairs. GMATA (Genome-wide Microsatellite Analyzing Tool Package) software was utilized for mining the genome assembly https://www.ncbi.nlm.nih.gov/nuccore/LNRQ00000000 for SSRs and designing primers from the flanking sequences. Applied microsatellite search parameters for mononucleotide repeats were: Min. length (nt): 1, Max. length (nt): 1, Min. repeat-times: 10. Search parameters for tandem repeats of two to six nucleotides were: Min. length (nt): 2, Max. length (nt): 6, Min. repeat-times: 5. Parameters for marker primer design were: Min. amplicon size: 100 bp, Max. amplicon size: 300 bp, Optimal annealing Tm: 60 °C, Flanking sequence length: 400 bp, Max. template length (the genome is partitioned to individual segments for each SSR): 2000 bp. The high-throughput marker design process produced a total of 55,386 primer pairs that are predicted to amplify 67,279 SSR loci, corresponding to an overall average density of 5.38 kilobases (kb)/marker interval. Marker loci were evenly distributed across the nine carrot chromosomes with marker densities ranging from 5.22 kb/marker interval (chromosome 6) to 5.47 kb/marker interval (chromosome 3). The start and end positions of the SSR loci in the chromosome sequences, the repeat motifs, number of repeats, flanking primer sequences and annealing temperatures can be accessed at https://figshare.com/articles/Marker_data/8593337/2 as ‘SSR Locus Information and Primer Data.xls’. Data from this analysis can be viewed in JBrowse here.

Organism:


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

License:


Name	Attribution 4.0 International (CC BY 4.0)
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