skip to main content
Idioma:
Primo Search
Clear Search Box
Search in: Busca Geral
Busca Avançada
Busca por Índices

Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms

Speiser, Daniel I ; Pankey, M Sabrina ; Zaharoff, Alexander K ; Battelle, Barbara A ; Bracken-Grissom, Heather D ; Breinholt, Jesse W ; Bybee, Seth M ; Cronin, Thomas W ; Garm, Anders ; Lindgren, Annie R ; Patel, Nipam H ; Porter, Megan L ; Protas, Meredith E ; Rivera, Ajna S ; Serb, Jeanne M ; Zigler, Kirk S ; Crandall, Keith A ; Oakley, Todd H

BMC bioinformatics, 2014-11, Vol.15 (1), p.350-350, Article 350 [Periódico revisado por pares]

England: BioMed Central Ltd

Texto completo disponível

Citações Citado por
  • Título:
    Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms
  • Autor: Speiser, Daniel I ; Pankey, M Sabrina ; Zaharoff, Alexander K ; Battelle, Barbara A ; Bracken-Grissom, Heather D ; Breinholt, Jesse W ; Bybee, Seth M ; Cronin, Thomas W ; Garm, Anders ; Lindgren, Annie R ; Patel, Nipam H ; Porter, Megan L ; Protas, Meredith E ; Rivera, Ajna S ; Serb, Jeanne M ; Zigler, Kirk S ; Crandall, Keith A ; Oakley, Todd H
  • Assuntos: Algorithms ; Analysis ; Animals ; Arthropoda ; Colleges & universities ; Evolution ; Eye Proteins - genetics ; Genes ; Genome ; High-Throughput Nucleotide Sequencing ; Light ; Likelihood Functions ; Marine ; Metazoa ; Molecular Sequence Annotation - methods ; Organisms ; Phylogenetics ; Phylogeny ; Physiological aspects ; Sequence Analysis, Protein ; Software ; Transcriptome ; Vision, Ocular - genetics
  • É parte de: BMC bioinformatics, 2014-11, Vol.15 (1), p.350-350, Article 350
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
  • Descrição: 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. 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/ ). 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.
  • Editor: England: BioMed Central Ltd
  • Idioma: Inglês
Links
Voltar para lista de resultados

  • Realização: ABCD-USP USP   Logos de Redes Sociais: Freepik

Buscando em bases de dados remotas. Favor aguardar.