This data is part of a publication in process ("Characterizing Hox genes in mayflies (Ephemeroptera), with Hexagenia limbata as a new mayfly model"). The CLC contig data and original read sequencing methodology is also described in the masters thesis of coauthor Christopher Gonzalez (thesis title: "Evolutionary Developmental Biology in the Mayfly Hexagenia limbata, with a Focus on Hox Genes.") H_limbata_CLC_contigs.fa, H_limbata_ORP_contigs.fa The two contig assemblies were assembled from the same set of transcriptome reads (NCBI SRA accession SRX6489924), which were sequenced from a pooled sample of approximately 100 μl of whole-body nymphs, most 1st instar and some 2nd instar. The transcriptomes differ in their assembly methods, with CLC referring to assembly within CLC Genomics WorkBench v.6.0.4 (CLCBio, Boston, MA), while ORP refers to contig assembly via the Oyster River Protocol v2.2.6 (MacManes, 2018). Hexagenia_ORP_peps.fa Peptide sequences generated via TransDecoder v5.5.0 (https://github.com/TransDecoder/TransDecoder/wiki) from the ORP assembly were used to assess the phylogeny of Hox genes in H. limbata. Note that the generated header names do not match those of the contig or annotation files. H_limbata_ORP_annotation.tsv Protein homology annotations for the ORP assembly were done via Diamond v0.9.24.125 (Buchfink et. al., 2015). All headers refer to the generated contig names in H_limbata_ORP_contigs.fa.