Comparative Genomics Visualization Tool Geno2Cir And Its Application In Gymnosperm Chloroplast Genomes Comparison

In recent years, huge amount of genomic sequence data has become a great challenge for traditional methods of data analysis and visualization. How to effectively and quickly compare and visualize sequences in genomic level is a major issue for bioinformatics researchers. Circos is a widely used data visualization tool, but incapable of handling raw sequence data (sequences data, annotations, compositions and so on) by itself, especially for genomic level data, which requires great effort on programming and data mining.Here, we present a tool to bridge raw genomic data to Circos directly-Geno2Cir. This tool is able to deal with aligned genomic sequences, with various user-defined parameters (such as window length, pace length in genomic sequences comparison, the distance threshold for Kimura2-parameters method in sequence distance comparison, choice of reference genome and so on), and to generate files that can be used by Circos directly. This tool not only deals with pair-wise comparison of genomes, but also multiple comparison of genomes. The former one is realized by window-walking method to compare two sequences directly by certain size of window and pace length. The latter one is realized by calculating pair-wise Kimura2-parameter distance, then the overall difference by distance matrix.We have applied this tool to a number of data sets. For example, we used this tool in chloroplast genomes of gymnosperm species, Pinus, and found common and different evolution history footprints, and some sites that might be used as DNA markers for phylogenetic research and species-level taxonomy analysis, especially helpful in plant taxon in which generic DNA barcoding markers are not applicable. The tool can be directly used to analyze and visualize genomic comparison in studies using whole chloroplast genome as single DNA barcode to distinguish closely related species.For distantly related species, those sequences which can be correctly aligned can be compared successfully using this tool, for example, mitochondrial genomes of Papilionoidea species or even further. In summary, this tool is very useful for lots of disciplines such as comparative genomics, systematic biology, phylogenetics, genetics and so on.