title: Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.
abstract: BACKGROUND
  Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families.
  
  
  RESULTS
  We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository ( http://bitbucket.org/osiris_phylogenetics/pia/ ) and we demonstrate PIA on a publicly-accessible web server ( http://galaxy-dev.cnsi.ucsb.edu/pia/ ).
  
  
  CONCLUSIONS
  Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.
authors.affiliation: Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. speiser@mailbox.sc.edu.|Department of Biological Sciences, University of South Carolina, Columbia, SC, USA. speiser@mailbox.sc.edu.
authors.forename: Daniel I
authors.initials: DI
authors.lastname: Speiser
authors.affiliation: Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. abrinas@gmail.com.
authors.forename: M Sabrina
authors.initials: MS
authors.lastname: Pankey
authors.affiliation: Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. sashazaharoff@gmail.com.
authors.forename: Alexander K
authors.initials: AK
authors.lastname: Zaharoff
authors.affiliation: The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA. Battelle@whitney.ufl.edu.
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Battelle
authors.affiliation: Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA. hbracken@fiu.edu.
authors.forename: Heather D
authors.initials: HD
authors.lastname: Bracken-Grissom
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, FL, USA. jessebreinholt@gmail.com.
authors.forename: Jesse W
authors.initials: JW
authors.lastname: Breinholt
authors.affiliation: Department of Biology, Brigham Young University, Provo, UT, USA. seth.bybee@gmail.com.
authors.forename: Seth M
authors.initials: SM
authors.lastname: Bybee
authors.affiliation: Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA. cronin@umbc.edu.
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Cronin
authors.affiliation: Department of Biology, Marine Biological Section, University of Copenhagen, Copenhagen, Denmark. algarm@bio.ku.dk.
authors.forename: Anders
authors.initials: A
authors.lastname: Garm
authors.affiliation: Department of Biology, Portland State University, Portland, OR, USA. arl3@pdx.edu.
authors.forename: Annie R
authors.initials: AR
authors.lastname: Lindgren
authors.affiliation: Department of Molecular and Cell Biology & Department of Integrative Biology, University of California, Berkeley, CA, USA. nipam@uclink.berkeley.edu.
authors.forename: Nipam H
authors.initials: NH
authors.lastname: Patel
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, SD, USA. Megan.Porter@usd.edu.
authors.forename: Megan L
authors.initials: ML
authors.lastname: Porter
authors.affiliation: Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, USA. meredith.protas@dominican.edu.
authors.forename: Meredith E
authors.initials: ME
authors.lastname: Protas
authors.affiliation: Department of Biology, University of the Pacific, Stockton, CA, USA. arivera@pacific.edu.
authors.forename: Ajna S
authors.initials: AS
authors.lastname: Rivera
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA. serb@iastate.edu.
authors.forename: Jeanne M
authors.initials: JM
authors.lastname: Serb
authors.affiliation: Department of Biology, Sewanee: The University of the South, Sewanee, TN, USA. kzigler@sewanee.edu.
authors.forename: Kirk S
authors.initials: KS
authors.lastname: Zigler
authors.affiliation: Computational Biology Institute, George Washington University, Ashburn, VA, USA. kcrandall@gwu.edu.|Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA. kcrandall@gwu.edu.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Crandall
authors.affiliation: Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. todd.oakley@lifesci.ucsb.edu.
authors.forename: Todd H
authors.initials: TH
authors.lastname: Oakley
mesh_terms: D000465:Algorithms; D000818:Animals; D005136:Eye Proteins / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008027:Light; D016013:Likelihood Functions; D058977:Molecular Sequence Annotation / Q000379:methods*; D010802:Phylogeny; D020539:Sequence Analysis, Protein; D059467:Transcriptome; D014785:Vision, Ocular / Q000235:genetics*
chemical_list: D005136:Eye Proteins