I noticed that some genes on my maker runs were annotated like fragmented pieces instead of a single gene.
For example, for a gene composed by 4 exons, I was expecting to have the 4 exons concatenated in a single protein sequence. I performed annotations in several species and for some of them I have only one gene annotated, i.e with the 4 exons merged in a single protein sequence. But for other species, with the same protein evidence and maker.ctl parameters I got 4 "genes" evidence instead of one. Actually on the blast results is pretty clear how they are part of the same gene at different positions. This is an issue because I'm doing gene families expansions and contraction and the analysis detects as this gene is being expanded, as it has 3 more copies, but in reality they are part of the same gene.
Have you seen this before? Could you help me to seek for a solution?