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Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from
Daniel I Speiser1,2, M Sabrina Pankey3, Alexander K Zaharoff4
1Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. speiser@mailbox.sc.edu.
BMC Bioinformatics
|November 20, 2014
Summary
Phylogenetically-Informed Annotation (PIA) is a new computational method that efficiently annotates genes in non-model organisms. This approach uses pre-calculated gene family trees to rapidly identify genes, aiding the study of evolutionary biology.
Area of Science:
- Evolutionary biology
- Genomics
- Bioinformatics
Background:
- High-throughput sequencing and de novo assembly enable transcriptome analysis for diverse organisms.
- Identifying gene sequences, especially from non-model organisms, remains a significant challenge in biology.
- Phylogenetic analyses are useful but time-consuming for assigning gene identities.
Purpose of the Study:
- To develop a computationally efficient, tree-based method for annotating transcriptomes and genomes.
- To introduce Phylogenetically-Informed Annotation (PIA) for placing uncharacterized genes into pre-calculated gene family phylogenies.
- To create a valuable resource for researchers studying the evolution of light-interacting structures.
Main Methods:
- Generated maximum likelihood trees for 109 Light Interaction Toolkit (LIT) genes from 29 sequenced genomes.
- Utilized the Evolutionary Placement Algorithm (RAxML) to place potential LIT gene sequences onto pre-calculated trees.
- Implemented PIA within the Galaxy workflow management system for high-throughput transcriptome annotation.
Main Results:
- Successfully annotated 28 newly-sequenced transcriptomes from various organisms, including cephalopods, arthropods, and cnidarians, for LIT genes.
- Developed and made available new maximum likelihood trees for LIT genes.
- Demonstrated the utility of PIA on a publicly accessible web server.
Conclusions:
- The new LIT gene trees serve as a valuable resource for studying the evolution of light-interacting structures.
- PIA offers a high-throughput method for identifying genes in non-model organisms using phylogenetic relationships.
- The PIA method can be adapted to search for different gene sets or annotate data from taxa beyond Metazoa.
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