Genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification

184.cp.variations.map.vcf.zip--the chloroplast variation map of 184 samples 184.mt.variations.map.vcf.zip----the mitochondrial variation map of 184 samples aligment1.fa-- the group of grapefruit, sweet orange and sour orange for mitochondrial heteroplasmy analysis aligment2.fa-- the group of lemon for mitochondrial heteroplasmy analysis coverage depth of 184 short reads samples.zip -- the coverage depth of BAMs in mitochondrial variation map in 184 samples Fortunella hindsii mitochondrial genome.gb -- the conservation proteins annotation of kumquat reference mitochondrial genome GWAS-118.samples.input.phenotype.for GWAS.txt -- the inputfiles for GWAS GWAS-LD.linked.input.gwas.vcf.gz -- the LD linked variations for GWAS LD.purning.nuclear.variation.map.vcf.gz -- LD purning nuclear variations for demography analysis normalization.RNA-seqs.txt -- the nomarlization data of expression of mitochondrial genome nuclear.variation.map.vcf.gz -- the nuclaer variation map ORFs annotation based on Augustus.gtf -- the annotation gene structure using Augustus pan-genome and aligned mitochondrial genomes.zip -- the pan-genome(.fa and .gfa) and aligned mitochondrial genomes scaffold-assemblies.zip -- the scaffolds of mitochondrial genomes