Appendix 4-figure 6: Preliminary maximum likelihood phylogeny of luciferase homologs
datasetposted on 2018-08-13, 17:30 authored by Timothy FallonTimothy Fallon, Sarah Sander LowerSarah Sander Lower
From our reference genesets, a protein BLAST search detected 24, 20, 32, and 2 luciferase homologs (E-value < 1x10-60) to P. pyralis luciferase (PpyrLuc1; Genbank accession AAA29795) from the P. pyralis, A. lateralis, I. luminosus genesets, and Drosophila melanogaster respectively. We defined the luciferase co-orthology as followings; (1) shows an BLASTP E-value lower than 1.0x10-60 towards DmelPACS (CG6178), (2) phylogenetically sister to DmelPACS, which is the most similar gene to firefly luciferase in D. melanogaster, based on a preliminary maximum likelihood (ML) phylogenetic reconstruction (Appendix 4-figure 6). Preliminary ML phylogenetic reconstruction was performed as follows: The sequences of luciferase homologs from Mengenilla moldrzyki, Pediculus humanus, Limnephilus lunatus, Ladona fulva, Frankliniella occidentalis, Zootermopsis nevadensis, Onthophagus taurus, Anoplophora glabripennis, Agrilus planipennis, Harpegnathos saltator, Blattella germanica, Acyrthosiphon pisum, Tribolium castaneum, Bombyx mori, Anopheles gambiae, Apis mellifera, Leptinotarsa decemlineata, and Dendroctonus ponderosae were obtained from OrthoDB (https://www.orthodb.org). The sequences which show 99% similarity were filtered by CD-HIT (v4.7). The resulting sequences and beetle luciferases were aligned using (MAFFT v7.309) using the BLOSUM62 matrix and filtered for spurious sequences and poorly aligned regions using trimAl (v.1.2rev59) (parameters: -strict). The final alignment was 385 blocks and 264 sequences. Then, the best fit amino acid substitution model, LG+F Gamma, was estimated by Aminosan (v1.0.2016.11.07) using the Akaike Information Criterion. Finally, a maximum likelihood gene phylogeny was estimated using RAxML (v8.2.9; 100 bootstrap replicates). Supporting files such as multiple sequence alignment, gene accession numbers, and other annotations are available on FigShare (DOI: 10.6084/m9.figshare.6687086).