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

Abstract

BackgroundTools 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.ResultsWe 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/).ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0350-x) contains supplementary material, which is available to authorized users.

Eye-independent, light-activated chromatophore expansion (LACE) and expression of phototransduction genes in the skin of Octopus bimaculoides

“…Additionally, opsin expression by itself is weak evidence for the ability of skin to detect light. Other essential r-opsin cascade genes, including G-protein α (q) and phospholipase C, are also expressed in the skin of O. bimaculoides, suggesting that the necessary genes for functional opsin-based phototransduction are expressed in octopus skin (Speiser et al, 2014). Finally, the LACE action spectrum is also consistent with our hypothesis.…”

Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata

“…Additionally, we used PIA (Speiser et al . ) with default parameters to identify opsins that could be missed by the HMMER search using raw Trinity transcriptomes. All redundant (identical) opsin sequences identified by both approaches were removed using CD‐HIT.…”

Opsins inLimuluseyes: Characterization of three visible light-sensitive opsins unique to and co-expressed in median eye photoreceptors and a peropsin/RGR that is expressed in all eyes

“…In the present study we report that in a transcriptome analysis of ME (Speiser et al, 2014), we detected two rhabdomeric opsins (r-opsins) that had not been identified previously in transcriptomes of VE and LE, and in a BLAST analysis of a recent assembly of the Limulus genome (http://www.ncbi.nlm.nih.gov/bioproject/ PRJNA20489), we detected an additional r-opsin sequence closely related to one found in the ME transcriptome. We call these opsins LpOps6, LpOps7 and LpOps8.…”