Differential Repeat Accumulation in the Bimodal Karyotype of Agave L

Abstract

The genus Agave presents a bimodal karyotype with x = 30 (5L, large, +25S, small chromosomes). Bimodality within this genus is generally attributed to allopolyploidy in the ancestral form of Agavoideae. However, alternative mechanisms, such as the preferential accumulation of repetitive elements at the macrochromosomes, could also be important. Aiming to understand the role of repetitive DNA within the bimodal karyotype of Agave, genomic DNA from the commercial hybrid 11648 (2n = 2x = 60, 6.31 Gbp) was sequenced at low coverage, and the repetitive fraction was characterized. In silico analysis showed that ~67.6% of the genome is mainly composed of different LTR retrotransposon lineages and one satellite DNA family (AgSAT171). The satellite DNA localized at the centromeric regions of all chromosomes; however, stronger signals were observed for 20 of the macro- and microchromosomes. All transposable elements showed a dispersed distribution, but not uniform across the length of the chromosomes. Different distribution patterns were observed for different TE lineages, with larger accumulation at the macrochromosomes. The data indicate the differential accumulation of LTR retrotransposon lineages at the macrochromosomes, probably contributing to the bimodality. Nevertheless, the differential accumulation of the satDNA in one group of macro- and microchromosomes possibly reflects the hybrid origin of this Agave accession.

Keywords: bimodality; centromeric satellite; hybrid; macro- and microchromosomes; repetitive DNA; satellite DNA; sisal; transposable elements.

Figure 1

Distribution of the most abundant LTR retrotransposons (in red) in the mitotic chromosomes of hybrid Agave 11648 (DAPI in grey) after FISH, showing the differential chromosome patterns and accumulation at the macrochromosome pairs. (A–C), Ty3/gypsy Athila; (D–F), Ty3/gypsy Chromovirus; (G–I), Ty3/gypsy Ogre; (J–L), Ty1/copia SIRE; (M–O), Ty1/copia TAR; (P–R), Ty1/copia Tork. Insets show one macrochromosome of the same cell at higher magnification.

Figure 2

Distribution of tandem repeats and heterochromatin on chromosomes of Agave hybrid H11648. (A) DAPI (in grey); (B) AgSAT171 probe (in red) showing strong or weak signals in all chromosomes; (C) overlay of AgSAT171 (red) and 35S rDNA site (green, arrowheads) showing 20 chromosomes with stronger signals and heteromorphism for the chromosome pair bearing the rDNA site; (D) consensus sequence logo of AgSAT171 (black arrows signalized the primer positions); (E) CMA⁺/DAPI⁻ heterochromatic bands (yellow); 5S (red) and 35S ribosomal DNA (in green, insets), with the 35S colocalizing with CMA⁺ bands (arrowheads). Arrows indicate the difference in AgSAT171 signal intensity between chromosomes of the large pair that harbours the 35S rDNA site (in C) or the second CMA⁺ block that does not colocalize with the rDNA (in E).