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

Abstract

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.

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

“…Retrotransposons (Copia-type) are common in the plant kingdom, and often contain a percentage of DNA that may play a role in genome organization and evolution of plants (Stergiou et al, 2002;Khaliq et al, 2012).The SCoT13 250 showed high percentage of identity and query coverage with two sequences of copia-type retrotransposons of two different olive sequences (94595-B and 58259-G) (Fig. 9) along with unannotated sequences belonging to Vitis vinifera and different plant species.…”

Review Article: ISTR, a Retrotransposons-Based Marker to Assess Plant Genome Variability with Special Emphasis in the Genera <i>Zea</i> and <i>Agave</i>

“…Variation between initial agave explants and their micropropagated plants were detected. The differences between adult plants and off-shoots and among micropropagated plants [26][27][28] were detected, as well as the location of Ty1-copia retrotransposons in the A. tequilana genome [29,30]. The implications of detect such differences impacts the quality of tequila, because A. tequilana Weber var.…”

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“…Globally this virus is found in six genotypes having numerous subtypes [7]. Variations among different genotypes of HCV are about 1/3.…”