Fig. 1

Avian and non-avian reptilian landscapes of protein encoding genes. A set of 15,135 common vertebrate genes was sorted in the order of the human reference genome, alternating grey/white bars represent the different chromosomes. A sliding window of a centered gene and its 100 neighbors was taken to calculate the regional genomic average for each variable. a Presence index (red) and length index (blue) of the genes in the eight avian genomes. The areas in orange dots define the genes where the presence index is below the threshold of 0.70. In light blue it is shown where the length index is higher than the threshold of 1.46. In panel b, we have displayed the GC content of mRNA transcripts of the best annotated of the 4 studied non-avian reptiles (black, Chrysemys picta) and eight studied birds (red, Pseudopodoces humilis). The highest peaks of GC content are often seen in areas of a low presence index. c and d Landscapes of the cumulative presence of GARP% (encoded by GC-rich codons, green) or FYMINK% (encoded by AU-rich codons, purple) in the Pseudopodoces humilis (c) and Chrysemys picta (d) genome. The amount of GARP% and GC content are strongly correlated (R = 0.92 for Chrysemys picta and R = 0.91 for Pseudopodoces humilis)