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