Genome Annotation - Pgenerosa_v070 and v074 Top 18 Scaffolds Feature Count Comparisons

After annotating Pgenerosa_v074 on 20190701, we noticed a large discrepancy in the number of transcripts that MAKER identified, compared to Pgenerosa_v070. As a reminder, the Pgenerosa_v074 is a subset of Pgenerosa_v070 containing only the top 18 longest scaffolds. So, we decided to do a quick comparison of the annotations present in these 18 scaffolds Pgenerosa_v070 and Pgenerosa_v074.

Briefly, used grep to pull out features identified in the same 18 scaffolds in the Pgenerosa_v074 assembly from Pgenerosa_v070 annotated GFF from 20190228 and then counted the number of features identified in this newly subsetted GFF. It’s all documented in the Jupyter Notebook below.

Jupyter Notebook (GitHub):


Output folder:

GFF subset:


GENOME CDS exon gene mRNA
Pgen_v070 169460 175006 53035 53035
Pgen_v070_top18_scaffolds 41187 43554 8404 8404
Pgen_v074 10764 10940 1712 1712

Well, we definitely see a difference between annotations of those top 18 scaffolds (~6-fold difference). However, there is still a huge difference between the full Pgenerosa_v070 annotation and the top 18 scaffolds from the Pgenerosa_v070 annotation.

I’ll be performing some RNAseq alignments to these various assemblies. That should provide us with some evidence that we can use to support/refute some of the annotations that are present/absent.