The genome assembly for M. incognita, M. arenaria and M. javanica is described in the pre-print :
The following lines describe the methods used for assign sub-genome for Meloidogyne species, based in synteny and ks values.
##Separating sub-genomes in Meloidogyne
1- Run McScanX for each species using the default settings
2- Using the collinearity file, run add_kaks_to_MCScanX.pl (Reubwn)
3- Format the ka/ks file using calculate_collinearity_metric.pl (Reubwn)
4- Select only the synteny groups bigger than 10 genes
python3 groups_bigger_10.py
5- Format file "groups_bigger_than_10.txt"
awk '$0 !~/#/ {print $3 "\t" $4 "\t" $7}' groups_bigger_than_10.txt > species_values_kaks.txt
6- Retrieve the gff file (four columns: contig, gene, start, end) used for McScanX analysis, and run the script on jupyter notebook
Assign_subgenomes_script.py
7- To calculate the euclidean distance based on ks values (script by https://github.com/DjampaKozlowski)
genome_structure.py