The poster Evolutionary Origin of Orphan Genes by Zebulon Arendsee (BCB/GDCB/CMB), Andrew Wilkey (ISU undergrad in BCBio), Priyanka Bhandary (BCB/GDCB/CMB), and Eve Sykin Wurtele (BCB/GDCB/CMB), was awarded an F1000 Poster Award at the 2016 conference of the International Society for Computational Biology and Bioinformatics (ISCB) in Orlando, Florida.
Abstract: Many of the most powerful tools in biology rely on inference of homologs via sequence-based algorithms. However, many loci are invisible to such methods. Those that are short or rapidly evolving, such as orphan genes and small non-coding RNAs, may yield no significant hits. Whereas low-complexity or high-copy number loci may hide in a crowd of false positives. Searching by context bypasses this problem. We present an algorithm for tracing loci between genomes using a synteny map, and test its efficacy by mapping all Arabidopsis thaliana-specific genes to the genomes of eight related species. By reducing the search space and winnowing false positives, we were able to assess the origin of the individual orphan genes with unprecedented resolution. We traced many to their non-genic cousins, identifying the non-genic footprint from which they arose. We linked others to putative genes in related species from which they diverged beyond recognition. Knowing the approximate location of each gene across species also provides a starting point for future studies. Our pipeline can easily be adapted to contextualize elusive elements such as small RNAs and lineage-specific genes in any species for which reliable synteny maps can be built.
Congratulations, Zeb !