(a) Two ohnologous scaffolds (177 and 179) are aligned, showing the perfect conservation of ohnologous gene (green) order typically found in most ohnologous scaffolds. When no onhologous copy was annotated, the singleton gene copy (yellow) was used to build a gene model when possible, leading to five possible outcomes: functional (orange), pseudogene (purple), incomplete gene model (grey), absent (that is, no match, white) or ambiguous (blue). Normalised expression values are shown for each annotated protein-coding gene for 15 tissues. (b) The plots show the result of the LastZ alignment of the genomic DNA sequence of two scaffolds. The histogram underneath indicates the local percentage of nucleotide sequence identity of each LastZ High-scoring Segment Pair (HSP). The section in red corresponds to the region shown in panel (a). (c) Whisker plots (with whiskers representing the range of the distribution, excluding the 5% most extreme values) showing the distribution of percentage of nucleotide sequence identity between LastZ HSPs of 579 ohnologous scaffolds (n=85,050, red), and the percentage of amino-acid sequence identity between single-copy genes and their pseudogene model (n=1,344, green) or ohnologous gene copies between each other (n=4,032, green).