Satellite DNA probes of Alstroemeria longistaminea (Alstroemeriaceae) paint the heterochromatin and the B chromosome, reveal a G-like banding pattern, and point to a strong structural karyotype conservation

Differential Repeat Accumulation in the Bimodal Karyotype of Agave L

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.

CMA/DAPI Banding of Plant Chromosomes

Chromosome banding based on base-specific fluorochromes, mainly double staining with chromomycin A₃ (CMA) and 4'-6-diamidino-2-phenylindole (DAPI), has been widely used since the 1970s. This technique allows the differential staining of distinct types of heterochromatin. Afterward, the fluorochromes can be easily removed and leave the preparation ready for sequential procedures such as FISH or immunodetection. Interpretations of similar bands obtained with different techniques, however, merit certain caution. Here we present a detailed protocol for CMA/DAPI staining optimized for plant cytogenetics and call attention to the most common sources of misinterpretation of DAPI bands.