Evolutionary analyses and comparative genomics were performed with 16 species: D. melanogaster, A. gambiae, D. pulex, L. salmonis, S.maritima, S. mimosarum, M. martensii, I. scapularis, H. dujardini, C. elegans, B. malayi, T. spiralis, M. musculus, H. sapiens, and B. floridae. For orthologous group analyses, gene families were identified using OrthoFinder (Emms and Kelly, 2015 (link)). The canonical proteome was used as a query in BlastP against proteomes from 16 species to generate a distance matrix for OrthoFinder to normalize and then cluster with MCL. Detailed methods are described in Source code 5. For the comparative BLAST analysis, five additional transcriptome datasets were used from the following crustacean species: Litopenaeus vannamei, Echinogammarus veneris, Eucyclops serrulatus, Calanus finmarchicus, Speleonectes tulumensis.
Kao D., Lai A.G., Stamataki E., Rosic S., Konstantinides N., Jarvis E., Di Donfrancesco A., Pouchkina-Stancheva N., Sémon M., Grillo M., Bruce H., Kumar S., Siwanowicz I., Le A., Lemire A., Eisen M.B., Extavour C., Browne W.E., Wolff C., Averof M., Patel N.H., Sarkies P., Pavlopoulos A, & Aboobaker A. (2016). The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. eLife, 5, e20062.
Publication 2016
C elegans Crustacean D melanogaster Evolutionary Gene Litopenaeus Musculus ProteomesTranscriptome
Corresponding Organization :
Other organizations :
University of Oxford, Janelia Research Campus, Howard Hughes Medical Institute, Imperial College London, Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, University of California, Berkeley, Harvard University, National Museum of Natural History, Humboldt-Universität zu Berlin
Evolutionary analyses and comparative genomics were performed on 16 species: D. melanogaster, A. gambiae, D. pulex, L. salmonis, S.maritima, S. mimosarum, M. martensii, I. scapularis, H. dujardini, C. elegans, B. malayi, T. spiralis, M. musculus, H. sapiens, and B. floridae.
dependent variables
Orthologous group analyses were performed to identify gene families using OrthoFinder.
control variables
The canonical proteome was used as a query in BlastP against proteomes from 16 species to generate a distance matrix for OrthoFinder to normalize and then cluster with MCL.
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