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Perl scripts from: The genomes of ancient date palms germinated from 2,000-year-old seeds

Citation

Gros-Balthazard, Muriel; Flowers, Jonathan (2021), Perl scripts from: The genomes of ancient date palms germinated from 2,000-year-old seeds, Dryad, Dataset, https://doi.org/10.5061/dryad.kkwh70s3w

Abstract

Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.

Usage Notes

Perl scripts from Gros-Balthazard et al. (2021) PNAS - The genomes of ancient date palms germinated from 2,000-year-old seeds

Usage may be found within each script.

1. vcf2polymorphism_count.pl
This script counts the number of biallelic snps in a subset of samples in a vcf.

2. vcf2private_alleles.pl
This script evaluate a vcf for private alleles.

3. vcf2singleton_mutation_profiles2.pl
This script reports sample-specific mutation profiles at singleton sites.

4. vcf2singleton_indels.pl
This script reports singleton indels from an input vcf.

Funding

New York University Abu Dhabi Research Institute, Award: 1205H

Zegar Family Foundation, Award: A168

National Science Foundation, Award: IOS-1546218