Quick BUSCO karyotyping 🦋 🔀 🦋

Mapping BUSCO genes from a reference genome to a new assembly to enable more consistent chromosome numbering and crudely infer large scale fissions/fusions

Dependencies

• Python 3
• (Python 3 module) Biopython
• (Python 3 module) seaborn
• (Python 3 module) reportlab

Usage

run BUSCO (tested with version 3) for a given reference genome and a query genome. Ensure that chromosomes in the reference are labelled suitably. I used ChrXX for autosomes (e.g. Chr10) and Chr1z for the Z.

For Lepidoptera, I typically run like this:

screen -L python run_BUSCO.py -i ./Heliconius_melpomene_melpomene_Hmel2.5.scaffolds.fa -m geno -c 60 -o Hmel2.5 --limit 4 -z -l ~/bin/busco_v3/DB/endopterygota_odb9 -sp heliconius_melpomene1 --long

Required options

-q (query fasta)
-t (BUSCO "full_table_" output file from query fasta)
-r (BUSCO "full_table_" output file reference fasta)

Run with defaults

python3.8 BUSCO_2_Chrom.py -q GCA_902806685.1_iAphHyp1.1_genomic.fna -t Query_table.txt -r Px_full_table.txt

Outputs 🔬

1. Prints the original scaffold name with a more detailed and less detailed appendix based on identity and amount of reference BUSCO genes. For example, LR761654.1_Chr10(36)Chr12(59), denotes the original scaffold name and that it contains 36 BUSCO genes derived from reference chromosome 10 and 59 BUSCO genes derived from chromosome 12.

2. Outputs a pdf file (default -o output.pdf) effectively displaying one side of an alignment. Specifically, the query genome karyotype along with the specific identity and reference chromosome information of individual BUSCO genes. Requires magnification/zoom! 🔍