Pipeline publication

[…] s during the evolution of ants. Using codon analysis, we detected signatures of positive selection on the lineage-specific expansion Or gene clades from the 9-exon subfamily, which are candidates for cuticular hydrocarbon receptors in ants [, ]. This study supports the hypothesis that highly specialized olfactory sense in ants, in this case lineage-specific chemical communication evolved under positive selection., We identified the remaining Or family members in these two genomes following the partially automated approach of Ref. []. Briefly, the amino acid sequences of the odorant receptors (ORs) from P. barbatus, S. invicta, Ca. floridanus, L. humile and Ce. biroi were used as queries for tBLASTn searches against the At. cephalotes and Ac. echinatior genome databases at the Ant Genomes Portal (Acep_1.0 and Aech_V2.0 Scaffold assembly, respectively; http://hymenopteragenome.org/ant_genomes) []. Search parameters were set as default except that Expect threshold (E value) was changed to 1000 to allow the detection of highly divergent sequences. Blast results were used to build draft gene models in a text editor. The DNA sequences of putative gene regions were retrieved using the GBrowse tool and compared with ORs that are closely related using GeneWise []. GeneWise allows the prediction of coding proteins based on similarity of translated DNA and input protein sequence. Putative ORs inferred from GeneWise were aligned with known ant ORs, and problem regions of models and pseudogenes were refined. We performed the BLAST and following annotation steps for multiple iterations until no new genes were discovered., Gaps in the genome assemblies prevent the building of some full-length gene models. We only kept gene models that encode more than 250 amino acids (i.e. more than 60 % of the average full-length ant OR protein) in our final gene set. We added suffices after gene names to indicate incomplete gene models in a similar way to previous studies [–] as follow: NTE = N terminus missing, CTE = C terminus missing, I = internal sequence missing. If more than one region was missing, the fir […]

Pipeline specifications

Software tools TBLASTN, GBrowse, GeneWise
Organisms Acromyrmex echinatior, Atta cephalotes, Camponotus floridanus, Harpegnathos saltator, Pogonomyrmex barbatus, Linepithema humile, Solenopsis invicta, Apis mellifera
Chemicals Amino Acids