A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history

This webpage accompanies the article:

Scott MF, Botigúe LR, Brace S, Stevens C, Mullin V, Stevenson A, Thomas MG, Fuller DQ, Mott R (2019) A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nature Plants 5 1120-1128

For an overview of the major findings, see this News and Views article by Breen & Rabanus-Wallace (2019) , articles in The Scientist and The Conversation , and this blog post.

Sequence data for two specimens are deposited at the ENA, study number PRJEB31103 (sample accession numbers ERS3135152 and ERS3574944).

We provide a VCF file of the main set of 99k SNP genotypes used for the majority of the analyses. These are genotype calls for sample S1 with at least 2 alignments that have mapQ>30 covering each site. To mitigate reference allele bias from the alginment of short aDNA reads, the alignments have also been filtered for those that don't align when either the reference genome or the reads are modified to carry the alternate allele, following the method in Günther & Nettelblad (2019). These called genotypes are a subset of those from the Avni et al. (2017) paper describing the wild Emmer wheat reference genome.

These genotypes called in the ancient Egyptian emmer wheat accession are also viewable via the GrainGenes browser.

The full set of analysis scripts can be found on GitHub.