I am working with several diploid fungal genomes but confused on how I deal with the duplicated genes. I started by assembling the diploid genomes using dipSPAdes, then gene finding with Maker. The reported number of genes is ~20,000 genes, which is about 2x as many genes that are reported for haploid genomes of the same genus. So my question is, is it okay to go forward with functional gene annotation, or do I need to somehow get rid of the duplicate genes in the genome? I have been confused about whether it is appropriate to publish the diploid version of the genome, or if it is necessary to report the haploid version. I hope this makes sense!
Thanks in advance, Morgan