Gene Prediction Challenges and Strategies for Phytophthora meadii

[mathavanpu]

Hi there,
I am currently working on gene prediction for the pseudo-fungus Phytophthora meadii. Unfortunately, I couldn't locate any relevant gene models associated with this species. Is it possible to use a gene model from the available fungus species, or how can I create a new gene training model specific to Phytophthora meadii? The genome is accessible on NCBI through the following link: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_032432875.1/. Could you please guide how to proceed?

'Thanks
Mathavan M

[KatharinaHoff]

I recommend that you run BRAKER with --fungus flag.

[mathavanpu]

Okay, thank you very much for the response. I have referred to Ramesh R. Vetukuri et al. (2018), where they mentioned that Augustus (Stanke et al., 2004) was utilized for gene prediction by employing the previously sequenced plant pathogenic relative, Phytophthora capsici, as a training model. I am seeking your guidance to build the Augustus training model for the pseudofungi Phytophthora capsici."

Reference :
Vetukuri RR, Tripathy S, Malar C M, Panda A, Kushwaha SK, Chawade A, Andreasson E, Grenville-Briggs LJ, Whisson SC. Draft genome sequence for the tree pathogen Phytophthora plurivora. Genome Biology and Evolution. 2018 Sep;10(9):2432-42.