Data from: De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A

Date Published: August 22, 2013

DOI: http://dx.doi.org/10.5061/dryad.h5t68

 

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Title Agave deserti transcriptome profiling (RPKM values)
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Description A table of the normalized RPKM values for Agave deserti transcripts in various tissues.
Download a_deserti_normalized_rpkm.txt.gz (7.814 Mb)
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Title Sequences of Agave deserti commensal organisms and contaminants
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Description FASTA file of assembled contigs that DO NOT appear to be Agave deserti sequences. Possible sources are commensal microbes, lab contaminants, and mis-assemblies.
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Title Pfam and InterPro annotations of Agave deserti proteins
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Description Pfam and InterPro annotations of Agave deserti proteins.
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Title Sequences of Agave deserti proteins
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Description FASTA file of Agave deserti proteins
Download agave_deserti_proteins.fa.gz (7.580 Mb)
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Title Sequences of Agave deserti transcript contigs
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Description FASTA of Agave deserti transcript contigs.
Download agave_deserti.fa.gz (31.09 Mb)
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Title Sequences of Agave tequilana commensal organisms and contaminants
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Description Assembled contigs that DO NOT display evidence of Agave tequilana origin. Likely sources include commensal microbes, lab contaminants, and mis-assemblies.
Download agave_tequilana_contaminants.fa.gz (13.57 Mb)
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Title Agave tequilana transcriptome profiling (RPKM values)
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Description Table of normalized RPKM values for Agave tequilana transcripts across various tissues.
Download agave_tequilana_normalized_rpkm.txt.gz (7.112 Mb)
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Title Pfam and InterPro annotations of Agave tequilana proteins
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Description Table of Pfam and InterPro annotations for Agave tequilana proteins.
Download agave_tequilana_pfam_interpro_annotations.txt.gz (1.473 Mb)
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Title Sequences of Agave tequilana proteins
Downloaded 214 times
Description FASTA file of Agave tequilana proteins.
Download agave_tequilana_proteins.fa.gz (7.444 Mb)
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Title Sequences of Agave tequilana transcript contigs
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Description FASTA file of Agave tequilana assembled transcript contigs.
Download agave_tequilana.fa.gz (51.11 Mb)
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Title Pacific Biosciences long-read sequences, unaltered
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Description Pacific Biosciences sequencing of Agave tequilana transcriptome. These are unassembled subreads directly output from a Pacific Biosciences RS.
Download 17618_filtered_subreads.fasta.gz (5.435 Mb)
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Title Illumina-corrected Pacific Biosciences long-read data
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Description FASTA of Pacific Biosciences subreads of file 17618_filtered_subreads.fasta.gz after correction by Agave tequilana Illumina data. Only subreads passing filtering metrics are reported.
Download corrected_pacbio.fasta.gz (647.3 Kb)
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Title OrthoMCL clustering
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Description OrthoMCL grouping of proteins within the Phytozome Tester Set. #OrthoMCL clusters with Agave high confidence proteins and the Phytozome Tester Set. Abbreviations are as follows: ateq - A. tequilana, ades - A. deserti, atha - A. thaliana, bdis - B. distachyon, crei - C. reinhardtii, gmax - G. max, mtru - M. truncatula, osat - O. sativa, ptri - P. trichocarpa, rcom - R. communis, sbic - S. bicolor, sita - S. italica, zmay - Z. mays
Download orthomcl_clusters.txt.gz (3.269 Mb)
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Title Comparison of Agave and Phytozome Tester Set protein lengths
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Description File agave_and_PTS_protein_lengths.txt contains information about the median protein lengths of Agaves and other species in the Phytozome tester set, grouped by OrthoMCL orthologous protein group (aka, PlantOG). ades = Agave deserti, ateq = A. tequilana, atha = A. thaliana, bdis = B. distachyon, crei = C. reinhardtii, gmax = G. max, mtru = M. truncatula, osat = O. sativa, ptri = P. trichocarpa, rcom = R. communis, sbic = S. bicolor, sita = S. italica, zmay = Z. mays
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Title Agave deserti Variant Call Format (VCF)
Downloaded 16 times
Description VCF file of SNPs and indels of the Agave deserti transcriptome, using the most abundant transcript isoform (v1) contigs as a reference sequence.
Download agave_deserti.vcf.gz (44.43 Mb)
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Title Agave tequilana Variant Call Format (VCF) file
Downloaded 17 times
Description VCF format file of SNPs and indels in Agave tequilana, using the most abundant (v1) transcript isoforms as a reference sequence.
Download agave_tequilana.vcf.gz (143.0 Mb)
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When using this data, please cite the original publication:

Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A (2013) De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 14: 563. http://dx.doi.org/10.1186/1471-2164-14-563

Additionally, please cite the Dryad data package:

Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A (2013) Data from: De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.h5t68
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