Institute of Horticulture Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Gene. 2022 Dec 20;846:146869. doi: 10.1016/j.gene.2022.146869. Epub 2022 Sep 6.
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 sequences in Dendrobium species remains unclear. In this study, we performed the identification and characterization 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 amplification 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 evolution of Dendrobium species. In conclusion, the present study provides new landmarks for unequival differentiation of the Dendrobium chromosomes and facilitate the understanding the chromosome evolution in Dendrobium speceis.
串联重复是真核生物基因组中最保守的特征之一。石斛属是兰科植物中第三大属，包含超过 1200 个种。然而，石斛属物种中重复序列的组织仍然不清楚。在这项研究中，我们使用基于图的聚类和荧光原位杂交（FISH）方法，对铁皮石斛基因组中的串联重复进行了鉴定和特征分析。确定了六个主要的聚类，包括五个卫星 DNA（DofSat1-5）和一个 5S rDNA 重复（Dof5S），它们被鉴定为串联重复。通过 PCR 扩增和 Southern blot 验证了 DofSat5 的串联组织。使用串联重复和寡核苷酸探针进行 FISH，研究了铁皮石斛中重复 DNA 的染色体位置。结果表明，DofSat5、5S 和 45S rDNA 中的每一个都在铁皮石斛染色体上有一对强信号。基于四个石斛属物种之间的基因组原位杂交（GISH），还研究了重复 DNA 在染色体上的分布。结果表明，在石斛属物种的进化过程中，发生了复杂的染色体融合/断裂和重排。总之，本研究为铁皮石斛染色体的不均等分化提供了新的标记，并有助于理解石斛属物种的染色体进化。
