ReadMe Kate L. Hertweck (k8hertweck@gmail.com) National Evolutionary Synthesis Center (NESCent) Durham, NC, U.S.A May 2013 These data were analyzed as a part of the following publication: "Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales" A separate fasta file for each taxon is available in Dryad. Each sequence in the file represents a contig produced via de novo assembly methods (MSR-CA) that RepeatMasker identified as a transposable element. The header for each sequence includes a contig number (e.g., scf7180000006695) followed by the annotation for that particular element (e.g., LTR/Gypsy). Some sequences had significant hits to multiple types of elements so two annotations may follow the contig number in the header. Complete information about details of sequencing can be found in the original publication describing the data: P. Roxanne Steele, Kate L. Hertweck, Dustin Mayfield, Michael R. McKain, James Leebens-Mack and J. Chris Pires. 2012. Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae. American Journal of Botany. 99:2, 330-348. The following table is provided as reference for accession numbers of our labels for each taxon as well as the location of the raw sequence reads at NCBI: Accession_name Taxon BioProject_number Biosample_number SRA_experiment_number SRA_run_number EL04 Agapanthus_africanus SRP021146 SRS414027 SRX268216 SRR830630 EL47 Allium_fistulosum SRP021147 SRS414028 SRX268217 EL32 Scadoxus_cinnabarinus SRP021149 SRS414029 SRX268218 SRR830636 EL01 Hosta_ventricosa SRP021150 SRS414030 SRX268219 SRR830629 EL59 Aphyllanthes_monspeliensis SRP021151 SRS414031 SRX268220 SRR830641 EL28 Asparagus_officinalis SRP021152 SRS414032 SRX268221 SRR830635 EL103 Dichelostemma_ida-maia SRP021148 SRS414033 SRX268222 SRR830633 EL09 Lomandra_longifolia SRP021145 SRS414034 SRX268223 SRR830632 EL24 Sansevieria_trifasciata SRP021153 SRS414035 SRX268224 SRR830634 EL49 Ledebouria_cordifolia SRP021154 SRS414036 SRX268225 EL50 Haworthia_cymbiformis SRP021155 SRS414037 SRX268226 BioProject http://www.ncbi.nlm.nih.gov/bioproject Biosample http://www.ncbi.nlm.nih.gov/biosample Sequence Read Archive (SRA) http://www.ncbi.nlm.nih.gov/sra