NCDs of Dffa and Dffb are encoded mainly by its exon 1 and exon 2, respectively (Fig 3a,d).
However, the emergence of GAPD-1 and GAPD-2 is surely not a result of a retroposition, as it was concluded in early studies [ 54, 55], documented by similar exon structures of the isoenzymes.
To determine the false positive rate, we also compared the exon structure accuracy by calculating the exon coverage rate by mRNA short reads.
The exon structure was confirmed by comparing the cDNA with nucleotide contig NT_009866.
All genes have a three exon structure with a large exon 2 flanked by two small exons, except Mal7P1.175, where the small exon 1 appears to be missing (or fused to exon 2).
This program, designed by Siepel and Haussler, identifies evolutionarily conserved protein-coding exons using a phylogenetic hidden Markov model, which simultaneously describes exon structure and exon evolution [ 16].
Type I genes are characterized by the presence of the MADS-box and by a simple intron-exon structure, while Type II genes possess additional conserved domains and a more complex gene structure [ 15, 16].
Such conclusion presented here is further supported by the high degree of conservation of exon structures (Figure 2) and paralogon analysis (Figure 3).
Is the evolution of novel function primarily facilitated by changes to the intron-exon structure of the derived copy relative to its progenitor as manifest in partial and chimeric duplicates or do regulatory changes (rapid promoter evolution or the gain of novel promoters) play a significant role?
Curation was aided by the absolutely conserved intron-exon structure and the presence of just 6 internal indels within the aligned proteins, verified by EST sequences from several genes.
