Mapping and chromosomal segmentation in theEimeria tenellagenome. One segment of the integrated map (IHM01) is shown, aligned with the supercontigs from the 2010 assembly and the contigs from the 2007 assembly. Labels “Cxxxxxx” are contig numbers in the 2007 assembly; labels “SCxx.y” indicate the supercontig (xx) and contig (y) of the 2010 assembly; HAPPY markers are named as “Ewgxxxxx”. To the right are shown the pseudomolecules for this map segment (built from the 2007 contigs) and for the previously-sequenced Chromosome 1 . The diameter of the inner “spindle” indicates A/T content (5 kb sliding window; wider portions are higher in A/T), and colored bands indicate blocks of repeats of CAG (red), the telomere-like repeat unit AGGTTT (green) or other simple-sequence repeats (blue); sequence gaps are grey. The outer transparent “shell” indicates the information content (3rd order Markov entropy) of the sequence (5 kb sliding window) – wider regions correspond to a higher information content, narrower regions to more repeat-rich sequence; the blue-tinted regions are R-segments, whilst the untinted regions are P-segments.
Lim et al. BMC Genomics 2012 13:389 doi:10.1186/1471-2164-13-389