The 454 EST libraries were sequenced on GS-FLX machines at the Indiana Universit y Center for Genomics and Bioinformatics (http://cgb.indiana.edu/ http://cgb.ind iana.edu/), the David H. Murdock Research Institute (DHMRI; http://www.dhmri.org /about.html), or Genome Quebec (http://www.genomequebec.com/v2009/home/) using t he standard Titanium Chemistry (http://www.454.com/). 454 sequences were cleaned using Snowhite (Barker et al., 2010) or ESTclean (http://sourceforge.net/projec ts/estclean/). Cleaned sequences were initially assembled with MIRA (Chevreux et al., 2004), using the “accurate,est,denovo,454” assembly mode. However, because in our experience MIRA can be too aggressive in splitting up contigs with high coverage, we took the MIRA contigs and singletons and re-assembled with CAP3 at 94% identity (Huang and Madan, 1999). The Illumina EST libraries were sequenced on Illumina GAII machines at the UC Da vis Genome Center (http://www.genomecenter.ucdavis.edu/), Indiana University Cen ter for Genomics and Bioinformatics (above), or at DHMRI (above). Illumina data were cleaned with customized scripts (http://code.google.com/p/atgc-illumina/) a nd assembled with CLC (http://www.clcdenovo.com/) using the default settings, or with Trinity (http://trinityrnaseq.sourceforge.net/) using --bfly_opts "--edge- thr=0.05 -V 5" to increase its ability to distinguish close paralogs.