The highly divergent <i>Jekyll</i> genes, required for sexual reproduction, are lineage specific for the related grass tribes Triticeae and Bromeae

<jats:title>Summary</jats:title><jats:p>Phylogenetically related groups of species contain lineage‐specific genes that exhibit no sequence similarity to any genes outside the lineage. We describe here that the <jats:italic>Jekyll</jats:italic> gene, required for sexual reproduction, exists in two much diverged allelic variants, <jats:italic>Jek1</jats:italic> and <jats:italic>Jek3</jats:italic>. Despite low similarity, the Jek1 and Jek3 proteins share identical signal peptides, conserved cysteine positions and direct repeats. The Jek1/Jek3 sequences are located at the same chromosomal locus and inherited in a monogenic Mendelian fashion. <jats:italic>Jek3</jats:italic> has a similar expression as <jats:italic>Jek1</jats:italic> and complements the <jats:italic>Jek1</jats:italic> function in <jats:italic>Jek1</jats:italic>‐deficient plants. <jats:italic>Jek1</jats:italic> and <jats:italic>Jek3</jats:italic> allelic variants were almost equally distributed in a collection of 485 wild and domesticated barley accessions. All domesticated barleys harboring the <jats:italic>Jek1</jats:italic> allele belong to single haplotype J1‐H1 indicating a genetic bottleneck during domestication. Domesticated barleys harboring the <jats:italic>Jek3</jats:italic> allele consisted of three haplotypes. <jats:italic>Jekyll</jats:italic>‐like sequences were found only in species of the closely related tribes Bromeae and Triticeae but not in other Poaceae. Non‐invasive magnetic resonance imaging revealed intrinsic grain structure in Triticeae and Bromeae, associated with the <jats:italic>Jekyll</jats:italic> function. The emergence of <jats:italic>Jekyll</jats:italic> suggests its role in the separation of the Bromeae and Triticeae lineages within the Poaceae and identifies the <jats:italic>Jekyll</jats:italic> genes as lineage‐specific.</jats:p>