De novo assembled transcriptome for hybrids betwen Epidendrum fulgens and E. puniceoluteum (Orchidaceae)

A “hybrid transcriptome” was <i>de novo</i> assembled to be used as a reference for differential gene expression analysis among Epidendrum fulgens, Epidendrum puniceoluteum and and their natural hybrids. To do so, we merged reads from all sampled hybrids into a single dataset, and filtered low-quality bases (Phred score&lt;30) and adapters using the Fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Filtered data were normalized using the “normalize_by_kmer_coverage” procedure of the Trinity v. 2.6.6 pipeline. Subsequently, a <i>de novo</i> assembly was performed using the MIRA assembler v. 4.9.4 under the following settings: quality clipping on (-CL:qc=yes), spoiler detection on (−AS:sd=yes), minimum base quality = 5 (-CL:qcmq=5), length of the window for quality clipping = 5 (−CL:qcwl=5); relative percentage of exact word matches = 70% (-SK:pr=70, Stepping increment = 2 (−SK:kss=2); maximum mega-hub ratio = 1 (−SK:mmhr=1), and minimum number of reads to discard sequences = 3 (−AS:mrpc=3). To avoid chimeric contigs, we discarded reads mapped in more than one contig or mapped more than once within the same contig using the blast_check tool. This reference transcriptome was filtered for contigs longer than 200 bp with a minimum of 5x coverage.