Generating synteny comparison between Foc TR4 genomes

Here is the code used to generate an overview of the synteny between our genome assembly of Fusarium oxysporum f. sp. cubense TR4 versus several relevant reference genome sequence assemblies.

• Warmington RJ, Kay W, Jeffries A, et al. High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic. Microbiol Resour Announc. 2019;8(36):e00904-19. Published 2019 Sep 5. doi:10.1128/MRA.00904-19
• Asai S, Ayukawa Y, Gan P, et al. High-Quality Draft Genome Sequence of Fusarium oxysporum f. sp. cubense Strain 160527, a Causal Agent of Panama Disease. Microbiol Resour Announc. 2019;8(29):e00654-19. Published 2019 Jul 18. doi:10.1128/MRA.00654-19
• Wang B, Yu H, Jia Y, et al. Chromosome-Scale Genome Assembly of Fusarium oxysporum Strain Fo47, a Fungal Endophyte and Biocontrol Agent. Mol Plant Microbe Interact 2020;33(9):1108-1111. doi:10.1094/MPMI-05-20-0116-A
• Ma LJ, van der Does HC, Borkovich KA, et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010;464(7287):367-373. doi:10.1038/nature08850

It uses the MCscan function with the JCVI libraries:

• https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)
• Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo. 10.5281/zenodo.31631.

Download the CDS and GFF files from NCBI:

Note that we can only use genome assemblies for which CDS have been provided. This eliminates most of the chromosome-scale assemblies in NCBI

### UK0001 TR4 
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/994/515/GCA_007994515.1_ASM799451v1/GCA_007994515.1_ASM799451v1_cds_from_genomic.fna.gz
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/994/515/GCA_007994515.1_ASM799451v1/GCA_007994515.1_ASM799451v1_genomic.gff.gz

### RIKEN 160527 
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/005/930/515/GCA_005930515.1_ASM593051v1/GCA_005930515.1_ASM593051v1_cds_from_genomic.fna.gz
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/005/930/515/GCA_005930515.1_ASM593051v1/GCA_005930515.1_ASM593051v1_genomic.gff.gz

### Fo47 reference sequence
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/085/055/GCA_013085055.1_ASM1308505v1/GCA_013085055.1_ASM1308505v1_cds_from_genomic.fna.gz
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/085/055/GCA_013085055.1_ASM1308505v1/GCA_013085055.1_ASM1308505v1_genomic.gff.gz

### Fol 4287 reference sequence
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/149/955/GCF_000149955.1_ASM14995v2/GCF_000149955.1_ASM14995v2_cds_from_genomic.fna.gz
wget --no-clobber https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/149/955/GCA_000149955.2_ASM14995v2/GCA_000149955.2_ASM14995v2_genomic.gff.gz


gunzip *.fasta.gz *.gff.gz

Generate BED files

python -m jcvi.formats.gff bed --type=mRNA --key=locus_tag GCA_007994515.1_ASM799451v1_genomic.gff -o UK0001.bed
python -m jcvi.formats.gff bed --type=mRNA --key=locus_tag GCA_005930515.1_ASM593051v1_genomic.gff -o RIKEN_160527.bed
python -m jcvi.formats.gff bed --type=mRNA --key=locus_tag GCA_013085055.1_ASM1308505v1_genomic.gff -o Fo47.bed
python -m jcvi.formats.gff bed --type=mRNA --key=locus_tag GCA_000149955.2_ASM14995v2_genomic.gff -o Fol4287.bed

Generate properly formatted CDS FastA files

perl reformat_fasta_with_locus_tags.pl GCA_007994515.1_ASM799451v1_cds_from_genomic.fna > UK0001.cds
perl reformat_fasta_with_locus_tags.pl GCA_005930515.1_ASM593051v1_cds_from_genomic.fna > RIKEN_160527.cds
perl reformat_fasta_with_locus_tags.pl GCA_013085055.1_ASM1308505v1_cds_from_genomic.fna > Fo47.cds
perl reformat_fasta_with_locus_tags.pl GCF_000149955.1_ASM14995v2_cds_from_genomic.fna > Fol4287.cds

Compare UK0001 against RIKEN_160527

python -m jcvi.compara.catalog ortholog RIKEN_160527 UK0001 --no_strip_names 

python -m jcvi.compara.synteny screen --minspan=30 --simple RIKEN_160527.UK0001.anchors RIKEN_160527.UK0001.anchors.new

python -m jcvi.graphics.karyotype seqids layout --keep-chrlabels --font=Arial --figsize=25x15

Compare UK0001 against Fo47

python -m jcvi.compara.catalog ortholog Fo47 UK0001 --no_strip_names 

python -m jcvi.compara.synteny screen --minspan=30 --simple Fo47.UK0001.anchors Fo47.UK0001.anchors.new

Compare RIKEN versus Fol4287

python -m jcvi.compara.catalog ortholog RIKEN_160527 Fol4287 --no_strip_names 

python -m jcvi.compara.synteny screen --minspan=30 --simple RIKEN_160527.Fol4287.anchors RIKEN_160527.Fol4287.anchors.new

python -m jcvi.graphics.karyotype seqids layout --keep-chrlabels --font=Arial --figsize=25x15

Generate macrosynteny plot

python -m jcvi.graphics.karyotype seqids layout --keep-chrlabels --font=Arial --figsize=20x15 --nocircles -o karyotype-no-labels.pdf

python -m jcvi.graphics.karyotype seqids layout --keep-chrlabels --font=Arial --figsize=20x15  -o karyotype-with-labels.pdf