[maker-devel] Assistance on MAKER annotation

[D Mudiyanselage Kasuni Daundasekara]

Hello Yandell lab,

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
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