Commentary - (2021) Volume 5, Issue 1
The recent rapid growth of genomic data has made it possible to identify genes having the same inferred function, even among distantly related species, such as humans and invertebrates. Assessing evolutionary relationships provides a way to interpolate or extrapolate gene attributes among species . For such evolutionary analyses, we developed a web tool called ORTHOSCOPE . By uploading gene sequences of interest and by selecting species genomes from >450 bilaterians (Figure 1), users can infer their functions and copy numbers, according to results reported by ORTHOSCOPE in the form of gene trees. That is, ORTHOSCOPE can estimate the evolutionary history of a gene with one click.
ORTHOSCOPE , Web tool , Genome , Gene tree , Species tree , Bilaterians
Many studies involving genome comparisons focus only on the presence of genes belonging to selected species or lineages. In addition to the presence of genes in a lineage, ORTHOSCOPE can also evaluate their absence by selecting several representative species. For example, users can explore the evidence of horizontal gene transfer by showing the presence or absence of genes among lineages. Using Orthosocpe, we showed that the prokaryotic cellulose synthase gene (CesA) was horizontally transferred into the genome of a tunicate ancestor from a bacterium [1-3]. Tunicates are the only metazoans that can synthesize cellulose, a biological function associated with bacteria and plants, but not animals. Also, ORTHOSCOPE can be applied to such enigmas in human genomes (Figure 1). The possibility of horizontally acquired genes has been debated since publication of the first human genomes .
ORTHOSCOPE users can determine the number of gene copies of a species. For this purpose, ORTHOSCOPE employs a genome-scale protein-coding gene database (coding and amino acid sequence data sets) constructed for each species using only the longest sequence, when transcript variants exist for single locus. By examining 48 fish species with full genome sequences, using ORTHOSCOPE, Ishikawa et al.  found that multiple freshwater ray-finned fishes show a convergent increase in copies of a single gene (Fads2, fatty acid desaturase 2). This convergence suggests the importance of Fads2 gene in colonization of freshwater. Also, ORTHOSCOPE can be applied to find a solution to Peto’s paradox: contrary to expectation, there is little relationship between cancer incidence and the number of cells in an organism. In fact, recent studies of the African elephant genome suggest that multiple copies of tumor suppressor gene P53 hold the answer .
ORTHOSCOPE can be used to select candidate genes for future directions in stem-cell or medical studies. The GLIS family transcription factors, GLIS1 and GLIS3, potentiate generation of induced pluripotent stem cells (iPSCs), although another GLIS family member, GLIS2, suppresses cell reprograming. Using ORTHOSCOPE, Yasuoka et al  showed that GLIS1 and GLIS3 originated during vertebrate whole genome duplication, whereas GLIS2 is a sister group to GLIS1/3. This study highlights the importance of carefully considering evolutionary relationships among genes without preconceptions or misconceptions stemming from classical gene names. It clearly indicates that as the first step, future reprograming studies should focus on GLIS1/3 rather than on GLIS2.
The web tool, ORTHOSCOPE, ensures the same environment for genome comparisons. For example, users can reproduce the same analysis used in a published paper. Thus, ORTHOSCOPE can be a standard tool for genome comparative studies.