Genomic collinearity

Collinearity is mainly used to describe the position relationship of genes on the genome, that is, the type and relative order of genes between different species derived from the same ancestral type. The size of collinear fragments is closely related to the differentiation time between species: species with shorter differentiation time accumulate less variation and retain more traits inherited from ancestors. On the contrary, the accumulation of variation between species with longer differentiation time leads to fewer common features and shorter collinear fragments.

The PairwiseAligner of Bio.Align package in Biopython was employed to globally align all the complete iridovirus genomes to obtain genomic pairwise identity after all virus genomes were corrected to guarantee that the putative major capsid protein (MCP) gene is the first gene in the genome (5'-3') for a more accurate number. View the image in high definition

The nucmer in MUMmer was employed to calculate the collinearity between two iridovirus genomes, with subsequent visualization achieved using mummerplot and gnuplot. The genomic collinearity analysis did not include incomplete virus genomes, and the virus genomes used for analysis were not sequentially adjusted.

There are 35,569 collinearity from 346 genomic sequences of 310 virus isolates.