DNA Remodeling by Strict Partial Endoreplication in Orchids, an Original Process in the Plant Kingdom

Abstract

DNA remodeling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analyzed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodeling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome 2C, plus 2–32 additional copies of a complementary part of the genome. The fixed proportion ranged from 89% of the genome in Vanilla mexicana down to 19% in V. pompona, the lowest value for all 148 orchids reported. Insterspecific hybridization did not suppress this phenomenon. Interestingly, this process was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of endocopies present, coherent with high transcription activity in endoreplicated nuclei. Our analyses suggest species-specific chromatin rearrangement. Towards understanding endoreplication, V. planifolia constitutes a tractable system for isolating the genomic sequences that confer an advantage via endoreplication from those that apparently suffice at diploid level.

Flow cytometry – a modern method for exploring genome size and nuclear DNA synthesis in horticultural and medicinal plant species

“…Analysing somaclonal variants of Phalaenopsis, Lee et al (2016) found that the degree of endoreduplication in the petals and flower stalks Mishiba and Mii, 2000 was higher in the variants than in control plants, and this corresponded with the diameter of the petal and the thickness of different organs, traits potentially desirable in orchid breeding. When applying FCM to analyse orchids, one must be aware, however, that in some Orchidaceae species partial endoreduplication occurs, which makes interpretation of the histograms challenging (Brown et al, 2017). One of the best recognized endoreduplication patterns in a fruit is that of S. lycopersicum (Pirrello et al, 2014, and references therein).…”

Flow cytometric seed screen data are consistent with models of chromosome inheritance in asymmetrically compensating allopolyploids

“…Overall, the potential of estimating flow cytometry DNA content in plant science has not been fully explored. Recent studies based on this method have revealed new phenomena in plant science (70)(71)(72) or new applications of the method (73). The present study highlights the use of FCM methodology, a powerful and precise tool for DNA content estimation, in plant reproduction biology.…”

“…Recent studies based on this method have revealed new phenomena in plant science (70)(71)(72) or new applications of the method (73). Overall, the potential of estimating flow cytometry DNA content in plant science has not been fully explored.…”

Flow cytometry as tool in plant sciences, with emphasis on genome size and ploidy level assessment

“…Cytometry data shows that endoreplication is not exponential but partial. In Vanilla planifolia, replication observed in each endocycle is not 2.00 but ~ 1.45, 1.6, 1.7, and 1.8 (Brown et al, 2017). The cumulative effect of this "strict partial endoreplication" leads to a loss of 41% of expected DNA content in 32C nuclei.…”

“…One way to obtain nuclei from different cell cycle phases, with a higher purity than chemical synchronisation, is to isolate them by chopping and sorting by cytometry. The yield will be lower but sufficient to do downstream molecular biology experiments (Pirrello et al, 2014) or imaging (Bourdon et al, 2012;Brown et al, 2017). Beyond nuclei, cytometry technology allows chromosome sorting.…”