Characterization of repetitive sequences in Dendrobium officinale and comparative chromosomal structures in Dendrobium species using FISH

Tandem repeats are one of the most conserved features in the eukaryote genomes. Dendrobium is the third largest genus in family Orchidaceae compromising over 1,200 species. However, the organization of repetitive se-quences in Dendrobium species remains unclear. In this study, we performed the identification and character-ization of the tandem repeats in D. officinale genome using graph-based clustering and Fluorescence in situ hybridization (FISH). Six major clusters including five satellite DNAs (DofSat1-5) and one 5S rDNA repeat (Dof5S) were identified as tandem repeats. The tandem organization of DofSat5 was verified by PCR amplifi-cation and southern blotting. The chromosomal locations of the repetitive DNAs in D. officinale were investigated by FISH using the tandem repeats and oligos probes. The results showed that each of the DofSat5, 5S and 45S rDNA had one pair of strong signals on D. officinale chromosomes. The distribution of repetitive DNAs along chromosomes was also investigated based on genomic in situ hybridization (GISH) among four Dendrobium species. The results suggested complex chromosomal fusion/segmentation and rearrangements during the evo-lution of Dendrobium species. In conclusion, the present study provides new landmarks for unequival differen-tiation of the Dendrobium chromosomes and facilitate the understanding the chromosome evolution in Dendrobium speceis.

Automated summary

This study identified and characterized the tandem repeats in the genome of Dendrobium officinale using graph-based clustering and FISH. Six major clusters, including satellite DNAs and a rDNA repeat, were identified as tandem repeats. The organization of one cluster was confirmed using PCR amplification and southern blotting. The chromosomal locations and distribution of the repetitive DNAs were investigated, revealing complex chromosomal fusion/segmentation and rearrangements during the evolution of Dendrobium species. This study provides new insights into the differentiation of Dendrobium chromosomes and the chromosome evolution in Dendrobium species.