The all data in this paper could be found in https://zenodo.org/record/5826754
If you have any questions, please contact me at email wangnan9394@163.com. I am happy to hear from you.
coverage_depth_stats.py--python script for catch the coverages in target regions. align_the_circle_genome_by_identical_seeds.py--mitogenome as a circle genome if necessary to align with a same start seqs(position).
Circos_plot: conf file, a input file for circos software; pi.txt, a genetic diversity cacultaed based on 184 samples; SNP.distribution, a density of SNP in mitogenome based on 184 samples.
MT_haplotype_NU_LD_blocks: GWAS_GEMMA.worksteps, the workflow to perform GWAS base on nuclear LD blocks and mitogenome haplotypes GO_10kb_region_for_selected_genes_and_anno.py--python script for grep candidate genes surround the siginificant SNPs(10kb region); GO-analysis-out.xlsx, the result of GO analysis.
RNA_seqs_analysis_in_replacement_samples: All_mitgenome_G1_G1+HB_HB_TPMvalues.txt, the result of TPM values in mitogenome(based on RNA anno(100 bp steped windows)); Conserved_genes_G1_G1+HB_HB_TPMvalues.txt, the 100 bp steped windows related to conserved genes or fragements; G1.anno.100.SAF, the predicted gene structure(100 bp steped windows); make-SAF.py--python script to make a SAF file for featureCount.
chimera-orfs-detected: test_chimeraORFs_in_intergenic_region.py--python script detect the chimera ORFs related to conserved genes or fragments in intergenic regions of mitogenome; split_conservaedgenes_to_30bp.py--python script to split conserved genes or fragments into 30 bp short seqs; Folders:the 14 assembles and chimera resutls.
genetic_load_results: genetic_load_based_on_pops.txt, the genetic load estimated in 184 samples,'At'(atalantia) as a outgroup (ancestry sequences).
paternla_leaksge_heteroplasmy: lemon_paternal_leakage.xlsx, the result of heteroplasmy mediated by paternal leakage in sour_orange and grapefruit populations; sour_orange(subgroup1 and subgroup2)_paternal_leakage.xlsx, the result of heteroplasmy mediated by paternal leakage in sour_orange and grapefruit populations.
The population genomic tools, workflows and scripts could be find in wangnan9394/apomixis_parallel_evolution [https://github.com/wangnan9394/apomixis_parallel_evolution] and wangnan9394/conservation_genomics. [https://github.com/wangnan9394/conservation_genomics]