DOI: 10.5061/dryad.h5t68
title: Data from: De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

description: Background: Agaves are succulent monocotyledonous plants native to xeric
 environments of North America. Because of their adaptations to their
 environment, including crassulacean acid metabolism (CAM, a
 water-efficient form of photosynthesis), and existing technologies for
 ethanol production, agaves have gained attention both as potential
 lignocellulosic bioenergy feedstocks and models for exploring plant
 responses to abiotic stress. However, the lack of comprehensive Agave
 sequence datasets limits the scope of investigations into the
 molecular-genetic basis of Agave traits. Results: Here, we present
 comprehensive, high quality de novo transcriptome assemblies of two Agave
 species, A. tequilana and A. deserti, built from short-read RNA-seq data.
 Our analyses support completeness and accuracy of the de novo
 transcriptome assemblies, with each species having a minimum of
 approximately 35,000 protein-coding genes. Comparison of agave proteomes
 to those of additional plant species identifies biological functions of
 gene families displaying sequence divergence in agave species.
 Additionally, a focus on the transcriptomics of the A. deserti juvenile
 leaf confirms evolutionary conservation of monocotyledonous leaf
 physiology and development along the proximal-distal axis. Conclusions:
 Our work presents a comprehensive transcriptome resource for two Agave
 species and provides insight into their biology and physiology. These
 resources are a foundation for further investigation of agave biology and
 their improvement for bioenergy development.
description: Agave deserti
 transcriptome profiling (RPKM values)A table of the
 normalized RPKM values for Agave deserti transcripts in various
 tissues.a_deserti_normalized_rpkm.txt.gzSequences of Agave deserti commensal organisms and contaminantsFASTA file of assembled contigs that DO NOT appear to be Agave deserti sequences. Possible sources are commensal microbes, lab contaminants, and mis-assemblies.agave_deserti_contaminants.fa.gzPfam and InterPro annotations of Agave deserti proteinsPfam and InterPro annotations of Agave deserti proteins.agave_deserti_pfam_interpro_annotations.txt.gzSequences of Agave deserti proteinsFASTA file of Agave deserti proteinsagave_deserti_proteins.fa.gzSequences of Agave deserti transcript contigsFASTA of Agave deserti transcript contigs.agave_deserti.fa.gzSequences of Agave tequilana commensal organisms and contaminantsAssembled contigs that DO NOT display evidence of Agave tequilana origin. Likely sources include commensal microbes, lab contaminants, and mis-assemblies.agave_tequilana_contaminants.fa.gzAgave tequilana transcriptome profiling (RPKM values)Table of normalized RPKM values for Agave tequilana transcripts across various tissues.agave_tequilana_normalized_rpkm.txt.gzPfam and InterPro annotations of Agave tequilana proteinsTable of Pfam and InterPro annotations for Agave tequilana proteins.agave_tequilana_pfam_interpro_annotations.txt.gzSequences of Agave tequilana proteinsFASTA file of Agave tequilana proteins.agave_tequilana_proteins.fa.gzSequences of Agave tequilana transcript contigsFASTA file of Agave tequilana assembled transcript contigs.agave_tequilana.fa.gzPacific Biosciences long-read sequences, unalteredPacific Biosciences sequencing of Agave tequilana transcriptome. These are unassembled subreads directly output from a Pacific Biosciences RS.17618_filtered_subreads.fasta.gzIllumina-corrected Pacific Biosciences long-read dataFASTA 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.corrected_pacbio.fasta.gzOrthoMCL clusteringOrthoMCL 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. maysorthomcl_clusters.txt.gzComparison of Agave and Phytozome Tester Set protein lengthsFile 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. maysagave_and_PTS_protein_lengths.txt.gzAgave deserti Variant Call Format (VCF)VCF file of SNPs and indels of the Agave deserti transcriptome, using the most abundant transcript isoform (v1) contigs as a reference sequence.agave_deserti.vcf.gzAgave tequilana Variant Call Format (VCF) fileVCF format file of SNPs and indels in Agave tequilana, using the most abundant (v1) transcript isoforms as a reference sequence.agave_tequilana.vcf.gz