Structure and content of the rattlesnake genome. (A) Regional variation in GC content, genomic repeat content, and gene density (for 100-kb windows) are shown on to-scale chromosomes, with centromere locations represented by circles; values above the genome-wide median are red. GD is gene density, or the number of genes per 100-kb window; higher density shown in darker red. (B) Synteny between rattlesnake, chicken, and anole genomes. Colors on chicken and anole chromosomes correspond with homologous rattlesnake sequence. Numbers to the right of chromosomes in the microchromosome inset represent rattlesnake microchromosomes syntenic with a given chicken or anole chromosomes for >80% of their length. Divergence times are shown in millions of years (mya). (C) Patterns of GC content from genome alignment of 12 squamate species, with tree branches colored according to genomic GC content. The heat map to the right depicts GC content in 50-kb windows of aligned sequence, with macro- and microchromosome regions labeled below. (D) Genomic GC isochore structure measured by the standard deviation in GC content among 5-, 20-, and 80-kb windows. (E) Genomic repeat content among 12 squamate species, with tree branches colored by total genomic repeat content.
