Rapid isolation of gene homologs across taxa: Efficient identification and isolation of gene orthologs from non-model organism genomes, a technical report

Here we present an approach - Rapid Isolation of Gene Homologs across Taxa (RIGHT) - to efficiently isolate specific members of gene families. RIGHT is based upon modification and a combination of degenerate polymerase chain reaction (PCR) and gene-specific amplified fragment length polymorphism (AFLP). It allows targeted isolation of specific gene family members from any organism, only requiring genomic DNA. We describe this approach and how we used it to isolate members of several different gene families from diverse arthropods spanning millions of years of evolution.RIGHT facilitates systematic isolation of one gene from large gene families. It allows for efficient gene isolation without whole genome sequencing, RNA extraction, or culturing of non-model organisms. RIGHT will be a generally useful method for isolation of orthologs from both distant and closely related species, increasing sample size and facilitating the tracking of molecular evolution of gene families and regulatory networks across the tree of life.One focus of evolutionary biologists is to understand how changes in regulatory and coding regions of genes contribute to species evolution and adaptation [1,2]. This requires sequence comparisons across distantly related taxa as well as among closely related species. A major limitation in studying molecular evolution is the amount of comprehensive sequence data available to track these changes in genes and their networks. Standard approaches include comparisons across widely divergent model organisms, comparison of gene sequences that have been deposited in databases, and comparisons of whole genome sequences. This can result in an incomplete matrix of information about the lineages of particular gene families, making it difficult to trace steps leading to functional changes in regulatory and coding sequences. Additionally, the sequence conservation of duplicated and diverged genes within gene families [3,4] poses a challenge: How can we identify a par