We are trying to annotate a de novo plant genome.
Originally, we annotated this genome (CAA, 1041 scaffolds) in 2016. Currently,
we have updated the genome assembly of CAA (14 chromosomes + 737 scaffolds). We
have a problem, there has been a loss in the number of genes in the new
annotation (old genome=43289, new genome=38.633). Do you have any idea where
these genes have been lost and any advice on how to get these genes back (some of
these genes are really important, were well supported with AED and now are gone)?
Thank you in advance.
Best wishes, Kasuni
Graduate student Pepper Lab Texas A & M University