Identification and characterization of a new satellite-like DNA family in three Agave species

Abstract

Repeated DNA analysis was conducted in three Agave species (A. angustifolia Haworth, A. tequilana Weber and A. fourcroydes Lemaire). Self-priming PCR was initially used to generate repeated PCR products and their sequence information was then used to build different primers sets. The ATsat102-113 primer set was able to amplify repeated PCR products, including probably multimers without becoming a typical ladder profile, in all Agave accessions analyzed. Sequence analysis of these amplifications identified two subfamilies of repeated DNA which share six conserved short motifs but exhibit a high genetic distance and different sequence traits between them. Consensus monomers obtained have a length higher than 100 bp and are rich in Adenine/Thymine percentage, as many satellites of plants. A representative probe of these consensus monomers was able to hybridize in some PCR amplified products and the more frequent short motif 1 (CTYRAGTTSG) also exhibits probably multimers without becoming a typical ladder profile. These Agave satellite-like subfamilies have different homogenization rates and the subfamily 2 is more conserved. These satellite-like monomers are transcribed and exhibited a strong relation with transposable element signatures of the LTR/Gypsy families and with A. tequilana TSA sequences, some which exhibits transposon-related domains in different locations to the satellite-like sequences identified. FISH analysis of these satellites-like subfamilies only may be reliable determined in the diploid (A. angustifolia Haworth var. Marginata and A. tequilana Weber ‘Azul’) accessions. In these generally showed a subtelomeric hybridization with less interstitial signals.