(a) Allelic variation evident from mapping RNA-Seq reads to a Trinity-reconstructed full-length whitefly transcript. Top: Shown is a single transcript (top, red bar), orthologous to the D. melanogaster Lamin gene, determined by grouping of allelic variant transcripts generated by Trinity. SNPs: yellow bars, Middle: Cummulative read coverage along the transcripts; colored bars: SNPs; bar height: relative proportions of SNP variants. Blue: C, red: T, orange: G, green: A. Bottom: Individual read coverage. (b) Example of two alternatively spliced transcripts resolved even in the absence of a reference genome. Top: Shown are two isoforms of an ELAV-like gene (top) reconstructed by Trinity (grey boxes, alternative exons). Exon structure is determined for visualization by the D. melanogaster ortholog. Bottom: shown is the protein sequence alignment of the two whitefly isoforms to orthologous proteins from other insects, confirming the splice variants (grey boxes). (c) Comparison of performance in de novo assembly of the whitefly transcriptome. For each of the methods, shown is the number of unique top-matching (blastx) uniref90 protein sequences aligned across the corresponding minimum percent protein length value at >= 80% (blue), >= 90% (green), >= 95% (orange) and 100% (red).