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Physical mapping of genome and epigenome marks of orchidaceous plants using visualization technology: understanding genomic orientation and implications

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Abstract

The Orchidaceae is one of the largest families of angiosperms, comprising more than 26,000 species in ca. 800 genera. Orchids species have relatively stable genomes with only 38 or 40 chromosomes, but individual phenotypes are extremely diverse. Since interspecific/intergeneric hybridization and polyploid production by artificial crossing are relatively easy, many cultivars have been bred to realize high commercial value in this group of plants. Such hybrids envisage genomic flexibility and intergenomic orientation. In order to elucidate the mechanisms of genomic flexibility, we have studied the genomes and epigenome marks of native Asian orchids, namely Vanda, Phalaenopsis, Cymbidium, and Dendrobium, using modern molecular cytogenetic techniques that facilitate physical visualization. Whereas, conventional meiotic analysis remains an important resource to understand genomic affinities based on chromosome pairing during meiosis, but the orchid taxa per se are not so well amenable for cytological observation, thus limiting the availability of information for genome analysis. Therefore, we developed a multi-color GISH method that can visualize genomes and reveal genome-donor species and hybridization history in artificial hybrids. We also focused our studies on epigenetic changes in the genome to elucidate the factors responsible thereof. The findings presented here provide information on physical visualization of genome(s), chromosomal distribution patterns of chromatin modifications with special emphasis on histone methylation, acetylation, phosphorylation, and centromere-specific histone marks in orchids using immuno-FISH. The novel findings emanating from this study are: (i) the dual modified histone H3S10phK14ac, which targets the peri-centromeric position of chromosomes may serve as a novel cytological marker to centromere, (ii) there is differential response to chromosomal DNA methylation among species and ploidy variants as discerned from 5mC distribution; larger chromosome size and elevated ploidy level exhibit enhanced methylation, (iii) in artificial intergenomic hybrids, genomes with large chromosomes and chromosomes located in the periphery of the nucleus tend to have more 5mC epigenetic changes, (iv) when identified in GISH experiments, the larger chromosome genome was found to exhibit more similarity to hybrid phenotypes. It is underpinned that to understand the flexibility of orchid genomes, it is important to grasp the entire genome through visualization techniques rather than fragmentary information at the molecular or cellular level.

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Acknowledgements

Sincere thanks are also due to Dr. SK Sharma, Dr. Go Suzuki, and all students of Plant Molecular Genetics Laboratory, OsakaKyoiku University, Osaka, Japan who were involved during the orchid project from 2010 to 2015, for their constant help and support. Figs. 9 and 14 reproduced in this article are from authors own publication, for which they hold author copyright.

Funding

This work was supported in part by Grants-in-Aidfor Scientific Research (C) (No. 22580004 to YM) from the JapanSociety for Promotion of Science (JSPS), Japan.

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Authors and Affiliations

  1. Kansai University of Welfare Sciences, Kashiwara, Osaka, 582-0026, Japan

    Maki Yamamoto

  2. Osaka Kyoiku University, Kashiwara, Osaka, 582-8582, Japan

    Yasuhiko Mukai

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  1. Maki Yamamoto
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YM conceived the idea, MY and YM contributed in planning/execution of research, and writing of the manuscript. Both the authorrs have read and consented to publish.

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Correspondence to Yasuhiko Mukai.

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Yamamoto, M., Mukai, Y. Physical mapping of genome and epigenome marks of orchidaceous plants using visualization technology: understanding genomic orientation and implications. Nucleus 66, 289–304 (2023). https://doi.org/10.1007/s13237-023-00448-0

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