Ty1-Copia retrotransposons are heterogeneous, extremely high copy number and are major players in the genome organization and evolution of Agave tequilana

Agave tequilana is native to Mexico and is famous for its use in the production of the alcoholic beverage tequila. The crop is extremely prone to insects and diseases, and a breeding programme for selection and conservation is required. Moreover, poorly understood classification of agave varieties and the limited availability of molecular data represent a big hurdle in its genetic research and improvement. Retrotransposons are mobile genetic elements that can occupy large proportions of plant genomes and play a vital role in their organisation and evolution. They can be used as genetic tools to address the challenges faced by A. tequilana. Ty1-Copia retrotransposons were isolated and characterised, and their copy number in the genome of A. tequilana was estimated. The phylogenetic analysis of isolated reverse transcriptase sequences showed that A. tequilana contains a large population of Ty1-Copia retrotransposons. They occur in the form of groups of closely related heterogeneous elements. The copy number estimates revealed that they are extremely abundant in A. tequilana. The characterisation of the Ty1-Copia population suggests that they are a major component of the agave genome and might have played a vital role in its genome organisation and evolution.