Physomitrellopsis africana BRAKER genome annotation

Genome 1 refers to the initially assembled genome (in the scripts this is the "old genome"), and Genome 2 refers to the genome after assembling with flye and multiple rounds of medaka polishing (referred to the new genome in the scripts)

Summary of all results is documented on this spreadsheet

Input files for BRAKER annotation

1. Genome files (Genome 1 and Genome 2)
2. RNA-seq library generated for P. africana
3. Protein files
   1. Protein file with both P. africana and Physomitrium patens
   2. Only P. africana proteins

BUSCO scores for the genome

BUSCO was run for the genome produced after the genome asssembly of P. africana. The genome was run against the eukaryota and viridiplantae databases.

Mapping rates of transcriptomic libraries using HISAT2

Ran HISAT2 to check mapping rates of the for:

Transcriptome input	Genome input	Mapping rate
P. africana trimmed transcriptomic reads	Genome 1	90.06%
P. africana untrimmed transcriptomic reads	Genome 1	69.90%
P. patens trimmed reads	Genome 1	42.62%
P. africana trimmed transcriptomic reads	Genome 2	90.62%

With this, we know that the RNA-seq libraries are definitely of P. africana based on the higher mapping rates compared to P. patens

BRAKER runs with Genome (repeated for both Genome 1 and Genome 2)

Multiple iterations of BRAKER were run (repeated for BRAKER v2.0.5 and BRAKER v2.1.5)

1. Only genome + bam file from transcriptome
2. Genome + bam + protein from P. africana and P. patens

There were additional runs of BRAKER run, for troubleshooting purposes (for only v2.1.5):

1. Genome + P. patens bam file
2. Genome + bam + protein from P. africana