Scripts used in the comparative physiological investigation of mitochondrial genome function in the parasitic Orobanchaceae
Citation: Cai, Liming, Robert K. Jansen, and Justin C. Havird. "Altered mitochondrial respiration is associated with loss of nuclear-encoded OXPHOS genes in parasitic broomrapes." bioRxiv (2025): 2025-02.
Subfolder contents:
1_Angiosperm_Nmt_survey
Scripts used to fish N-mt genes, clean paralogs, align sequence, and generate preliminary gene trees
2_Species_tree_inference
Further remove paralogs using the phylogeny-based Yang and Smith pipeline, generate one-to-one ortholog for species tree inference
3_Gene_loss_verification
BUSCO evaluation of data quality, phylogentic ANOVA analysis, Fisher's exact test for gene loss
4_Molecular_evolution
N-terminal targeting peptides identification and removal; HyPhy commands for RELAX analysis
5_O2K_statistic_analysis
R script to analyze O2K data