Data from: A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes

Hodel RG, Gitzendanner MA, Germain-Aubrey CC, Liu X, Crowl AA, Sun M, Landis JB, Segovia-Salcedo MC, Douglas NA, Chen S, Soltis DE, Soltis PS

Date Published: June 16, 2016

DOI: http://dx.doi.org/10.5061/dryad.rb7h0

 

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Title README
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Description ReadMe file describing the data package
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Title LocusInfo
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Description The LocusInfo.zip file is a compressed zip file containing a directory with the microsatellite loci for each species. The the LocusInfo directory contains the microsatellite locus information for the 1096 species for which loci were developed. The loci were from the 1KP project (http://onekp.com) transcriptomes. For some species, there were multiple transcriptomes, either from multiple collections or multiple tissues; these have been combined into a single file for each species.
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Title Scaffolds
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Description The Scaffolds.zip file is a compressed zip file containing a directory with the scaffolds corresponding to the microsatellite loci. The Scaffolds directory contains the sequence of the scaffolds that had microsatellites identified on them. The files are bz2 compressed zip files. The unzipped file is a fasta file with all of the scaffolds corresponding to the loci in the LocusInfo directory.
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Title GCF_000004515.3_V1.1_genomic
Downloaded 14 times
Description The script "BLAST_to_Coding_SSR.R” (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS"). This file is the gff file needed for the script.
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Title G_R_0764-0510-HitTable
Downloaded 18 times
Description The script "BLAST_to_Coding_SSR.R” (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS"). This is the second of three files needed to run the script.
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Title G_R_0803-0253-HitTable
Downloaded 19 times
Description The script "BLAST_to_Coding_SSR.R” (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS"). This is the third of three files needed to run the script.
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Title glycine_max_454_raw_all
Downloaded 9 times
Description A fasta file is necessary to run pal_finder. The file included here is a fasta file of raw 454 genomic reads from Glycine max (NCBI Trace Archive (TI 1732557604-1733276192; Swaminathan et al., 2007)).
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When using this data, please cite the original publication:

Hodel RGJ, Gitzendanner MA, Germain-Aubrey CC, Liu X, Crowl AA, Sun M, Landis JB, Segovia-Salcedo MC, Douglas NA, Chen S, Soltis DE, Soltis PS (2016) A New Resource for the Development of SSR Markers: Millions of Loci from a Thousand Plant Transcriptomes. Applications in Plant Sciences 4(6): 1600024. http://dx.doi.org/10.3732/apps.1600024

Additionally, please cite the Dryad data package:

Hodel RG, Gitzendanner MA, Germain-Aubrey CC, Liu X, Crowl AA, Sun M, Landis JB, Segovia-Salcedo MC, Douglas NA, Chen S, Soltis DE, Soltis PS (2016) Data from: A new resource for the development of SSR markers: millions of loci from a thousand plant transcriptomes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.rb7h0
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