Conservation genomics in an endangered citrus relative

Related paper: Conservation genomics insights into the spontaneous integration of multiple reproductive strategies in an endangered citrus relative

Related source: https://github.com/wangnan9394/conservation_genomics

#admixture.zip

This file including population ancestry of Fortunella. The estimated admixture proportions ranged from K=2 to K=5.

#apomixis_locus_200kb_vcf.zip

This file including VCF file of the WILDAPO group. The proportion of introgressions from cultivars and the number of heterozygous introgressed variations in samples from WILDAPO was calculated based on this file.

#deleterious_mutations.zip

This file including the summary of deleterious mutations in Fortunella. The BED file annotated the types of each variation based on the ancestry state.

#fd_and_D_statistics.zip

There are population level D statistic (ABBA-BABA statistic) and genome-wide fd statistic, using the Dsuite, ANGSD and genomic_general programs.

#genome-wide_haplotype_results.zip

We calculated the genome-wide haplontic divergence in each sample from the WILDAPO group, and the summary was zipped in this file.

#PCA_TajimaD_value.zip

The PCA and Tajima’D value were calculated based on the variation map using PLINK. We have included the results of genome-wide Tajima’s D from five groups.

#ROH_500kb.zip

This file including ROH analysis of Fortunella.

#S-locus_analysis.zip

This file including VCF file of the S-locus (Chr. 1). The phylogeny of S-locus were constructed based on this VCF file.

#SMC_files.zip

This file including smc.gz files of five groups (CULAPO, CULSEX, WILDAPO, WILDSEX1, WILDSEX2). The approximate lookup table of each group in this zipped file.

#SSMs.zip

We calculated the introgression based on the genome-wide species-specific variations (this VCF format file).

#Subtrees_TWISST.zip

The combination of subtrees, which were calculated based on 25 kb non-overlapped windows. The input subtrees and the output files by TWISST in this file.

#treemix.zip

we estimated that the potential migration events ranged from 1 to 3 with five repeats for each test.

#variation_map_kumquats.vcf.gz

we filtered nuclear genomic variations based on depth of coverage and missing rates using VCFtools with the following criteria: variant quality (QD) > 2.0, quality score (QUAL) > 40.0, mapping quality (MQ) > 30.0, genotype calls with a depth > 2 or <100 and with < 20% of genotypes missing across all samples.