Citrus_segregation_landscapes

Datasets for haplotype reshuffling shatters the Mendelian equilibrium of asexual lineages This data repository stores datasets generated in the study of segregation distortion uncovered during the evolutionary transition from apomixis to sexual reproduction in Citrus hindsii. These files are provided to support full reproducibility of all analyses in the corresponding manuscript.The deposited data include key intermediate results across three major research components: Genome assembly and pangenome construction: haplotype-resolved genome assemblies of PN and DB, genome annotation files (gene models, repeat annotation, TE annotation, LTR annotation), variation calls (inversions, presence/absence variants), pangenome graphs, and supporting alignment files. Haplotype-specific marker development and progeny haplotype reconstruction: haplotype-diagnostic markers, high-density genotype calls of the mapping population, recombination breakpoint coordinates, haplotype origin assignments along chromosomes, and genome-wide haplotype shuffling landscapes. Tree for these datasets:├── breakpoints_bins_haplotype│ ├── Shuffle_interval_DB_PN_chr1.txt│ ├── Shuffle_interval_DB_PN_chr2.txt│ ├── Shuffle_interval_DB_PN_chr3.txt│ ├── Shuffle_interval_DB_PN_chr4.txt│ ├── Shuffle_interval_DB_PN_chr5.txt│ ├── Shuffle_interval_DB_PN_chr6.txt│ ├── Shuffle_interval_DB_PN_chr7.txt│ ├── Shuffle_interval_DB_PN_chr8.txt│ └── Shuffle_interval_DB_PN_chr9.txt├── genome_and_annotations│ ├── DB.hap1.EDTA.TEanno.gff3│ ├── DB.hap1.fa│ ├── DB.Hap1.Final.gff3│ ├── DB.hap2.EDTA.TEanno.gff3│ ├── DB.hap2.fa│ ├── DB.Hap2.Final.gff3│ ├── PN.hap1.EDTA.TEanno.gff3│ ├── PN.hap1.fa│ ├── PN.Hap1.Final.gff3│ ├── PN.hap2.EDTA.TEanno.gff3│ ├── PN.hap2.fa│ └── PN.Hap2.Final.gff3├── pangenome_and_variation│ ├── DBhap1.specific.0.vcf│ ├── DBhap1.specific.1.vcf│ ├── DBhap2.specific.0.vcf│ ├── DBhap2.specific.1.vcf│ ├── KumquatPG.gfa.gz│ ├── KumquatPG.vcf.gz│ ├── PNhap1.specific.0.vcf│ ├── PNhap1.specific.1.vcf│ ├── PNhap2.specific.0.vcf│ └── PNhap2.specific.1.vcf└── progeny_and_variation ├── DB.male.markers.map ├── merged_queries.raw.vcf.gz └── PN.female.markers.map