Binomen Opsin Length Start

Manwaring, Katie F., Whiting, Michael F., Wilcox, Edward & Bybee, Seth M., 2016, A study of common scorpionfly (Mecoptera: Panorpidae) visual systems reveals the expression of a single opsin, Organisms Diversity & Evolution (New York, N. Y.) 16 (1), pp. 201-209 : 204-206

Order Family Binomen Opsin Length Start /stop codons Data source Accession no.

Coleoptera Tenebrionidae Tribolium castaneum

Lampyridae Luciola cruciata

Dytiscidae Thermonectus marmoratus

Diptera Culicidae Culex quinquefasciatus Aedes aegypti

Therevidae Hoplosathe frauenfeldi Empididae Empis sp. Apsilocephalidae Clesthentia sp. Apsilocephalidae Apsilocephala sp. Hybotidae Bicellaria sp. Hymenoptera Apidae Apis cerana

Apidae Apis mellifera

Apidae Bombus impatiens Pteromalidae Nasonia vitripennis Tenthredinidae Athalia rosae

Lepidoptera Nymphalidae Heliconius sapho Heliconius doris Eueides lineata Dione juno Dryas iulia Speyeria mormonia Agraulis vanillae Danaus plexippus Heliconius pachinus Heliconius erato Euphydryas chalcedona Nymphalis antiopa Vanessa cardui Danaus plexippus Neominois redingsii Riodinidae Apodemia mormo Lycaenidae Lycaena helloides

Lycaena nivalis

Mecoptera Boreidae Boreus coloradensis

Boreus coloradensis Panorpidae Panorpa pryeri

Panorpa japonica

Panorpa lewisi

Panorpa nebulosa

UVS LWS LWS UVS LWS UVS UVS UVS LWS LWS LWS LWS LWS BS UVS LWS BS LWS UVS UVS LWS LWS BS UVS UVS UVS UVS LWS LWS LWS LWS LWS LWS LWS LWS LWS LWS LWS BS LWS LWS BS LWS UVS LWS LWS LWS LWS LWS

1086 −/− GenBank XM_965251 726 +/+ GenBank DQ029113 1143 +/+ GenBank AB300328 1149 +/− GenBank AB300329 1155 +/+ GenBank EU921225 1143 +/+ GenBank EU921226 1407 +/− GenBank XM_001861603 1146 +/+ GenBank DQ440445.1 452 −/− GenBank AY267595

443 −/− GenBank AY267594

449 −/− GenBank AY267593

511 −/− GenBank AY267591

487 −/− GenBank Y267592

1134 +/+ GenBank AB355817 1116 +/+ GenBank AB355816.1 1134 +/+ GenBank AB355818 1134 +/+ GenBank NM_001011606 1134 +/+ GenBank NM_001011639 1116 +/+ GenBank NM_001011605 1290 +/+ GenBank AY655163 1911 +/+ GenBank NM_001170908 1729 +/− GenBank AB437365 1143 +/− GenBank GU324692 1134 +/+ GenBank GQ451897 1137 +/− GenBank HM366555 1137 +/− GenBank HM366553 1422 +/− GenBank GQ451890 1716 +/+ GenBank DQ924366 1488 +/+ GenBank DQ924367 1146 +/+ GenBank AY605545 1400 −/− GenBank AF126756

1143 +/+ GenBank AY918907.1 1561 +/+ GenBank DQ924373.1 1612 +/+ GenBank AY740907 1573 +/+ GenBank AF385333 1396 +/+ GenBank AY847475 1533 +/+ GenBank DQ924377 1705 +/+ GenBank AY587907 1016 +/+ GenBank DQ517943 1269 +/+ GenBank DQ517949 1596 +/+ GenBank DQ517951 1125 +/+ Current Study

1140 + / + Current Study

1128 +/+ Current Study

1391 −/− GenBank AY722614

981 −/− GenBank AY722617

987 −/− GenBank AY722619

992 −/− GenBank AY722620

995 −/+ Current Study cDNA followed by gel purification using a 1 % SeaKem GTG Agarose. From this gel, we used a Caliper LabChip to collect the correct size range prior to loading the samples. The cDNA was then included in an emulsion PCR and prepared for 454 sequencing using the GS FLX Titanium General Library Preparation Method Manual. Transcriptome sequencing was performed on the Roche 454 platform through the BYU DNA Sequencing Center.

Assembly: Transcriptomes were assembled using de novo assembly in Newbler ( Margulies et al. 2005) under default parameters. Various genes, including opsins, were isolated from the assembled transcriptomes using BLASTN software downloaded from ftp://ftp.ncbi.nih.gov/blast/db. A blastx search was conducted against Panorpid and Drosophila opsins as well as a database of D. melanogaster phototransduction genes ( Table 1) using a relaxed e-value cut off (10 e-5). The purpose of these searches was to measure the quality of the transcriptomes.

Boreidae transcriptome RNA was extracted from the eye of the boreid using NucleoSpin columns (Clontech) and reverse-transcribed into a cDNA library using the Illumina TruSeq RNA v2 sample preparation that both generates and amplifies full-length cDNAs. The prepped mRNA libraries were sequenced on an Illumina GAiiX in the Brigham Young University sequencing center, Provo, Utah, USA. Transcriptome assembly: We performed quality control, assembly, annotation, and transcriptome analysis to facilitate downstream phylogenetic analyses. RNAseq reads were trimmed using the Mott algorithm implemented in PoPoolation ( Kofler et al. 2011), with a minimum read length =40 and quality threshold=20. The de novo assembly of the transcriptome contigs was carried out using Trinity ( Grabherr et al. 2011) under the default parameters. Opsin genes: Potential light-interacting genes were isolated from each transcriptome by utilizing the Phylogenetically-Informed Annotation (PIA) tool ( Speiser et al. 2014; http://galaxy-dev.cnsi.ucsb.edu/pia/), implemented in Galaxy ( Giardine et al. 2005; Goecks et al. 2010; Blankenberg et al. 2010). As the PIA tool is optimized to identify an array of light-interacting genes involving circadian cycles, eye development, phototransduction, pigment synthesis, etc., resultant matches in the transcriptomes were then vetted for opsin-specific genes. All individual contigs isolated by the PIA tool were BLASTed, implemented in Geneious®, utilizing the B nr^ database option (GenBank, RefSeq, EMBL, DDBJ, and PDB databases), and the B blastn^ program set to 100 maximum hits. All nonopsin contigs were ignored, and all putative opsin reads, regardless of length, were mapped in SWISS-MODEL (available from http://swissmodel.expasy.org/) ( Arnold et al. 2006; Kiefer et al. 2009; Biasini et al. 2014) to verify the presence of seven trans-membrane regions and aid in the exclusion of partial contigs. A blastx search was conducted against a database of D. melanogaster phototransduction genes (download from Kegg, ID dme04745) using a relaxed e-value cut off (10 e-5).

recovered in two Panorpa species and one Boreus species