Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life‐history traits and climatic conditions

Abstract

In angiosperms, genome size and nucleobase composition (GC content) exhibit pronounced variation with possible adaptive consequences. The hyperdiverse orchid family possessing the unique phenomenon of partial endoreplication (PE) provides a great opportunity to search for interactions of both genomic traits with the evolutionary history of the family.Using flow cytometry, we report values of both genomic traits and the type of endoreplication for 149 orchid species and compare these with a suite of life-history traits and climatic niche data using phylogeny-based statistics. The evolution of genomic traits was further studied using the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to access their adaptive potential.Pronounced variation in genome size (341-54 878 Mb), and especially in GC content (23.9-50.5%), was detected among orchids. Diversity in both genomic traits was closely related to the type of endoreplication, plant growth form and climatic conditions. GC content was also associated with the type of dormancy. In all tested scenarios, OU models always outperformed BM models.Unparalleled GC content variation was discovered in orchids, setting new limits for plants. Our study indicates that diversity in both genome size and GC content has adaptive consequences and is tightly linked with evolutionary transitions to PE. † Research 1647Range-wide climatic variation represented by either standard deviations (SD) or median values (med.) of particular Bioclim variables.

Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

“…Most plants fully replicate their genome during endocycles [70], although there are a few exceptions (e.g. various orchid species; [21,22]). We found very little evidence for over-or under-replication occurring in endocycling maize root cells, unlike the distinctive over-and under-replication found in Drosophila endocycles (reviewed in [17] and references therein).…”

“…Even though endopolyploidy is common in plants, there are very few reports of over-or under-replication of specific sequences. Some orchids exhibit a phenomenon in which only a fraction of the genome is endoreplicated [21,22], but in most cases, endopolyploid cells have DNA contents that are multiples of the 2C value. Both highly repetitive heterochromatic regions and highly expressed genes are extensively endoreduplicated in maize endosperm nuclei, as would be expected for uniform replication of the entire genome [23].…”

Evolutionary dynamics of neutral phenotypes under DNA substitution models

“…We note that in practice even neutral evolution of GC content may still be problematic if analyzed with the standard OU process models[41] because the rate of increase of variance depends on the number of loci (See Appendix). Thus, although for a fixed sequence size GC content appears to evolve according to an OU process, for real sequences (that change in length over the phylogeny) although the variance in GC content is expected to increase approximately linearly for reasonably short evolutionary times, it will increase at a slower rate for longer sequences.…”

Early Diverging and Core Bromelioideae (Bromeliaceae) Reveal Contrasting Patterns of Genome Size Evolution and Polyploidy

“…Diaphoranthema ( Till, 1992 ). Moreover, the GC content was considered to have an adaptive role due to differences in the physical properties of GC and AT base pairs ( Šmarda and Bureš, 2012 ) and/or due to mode of endoreplication ( Trávníček et al, 2019 ). In monocots, it has been demonstrated that higher GC contents are favored in cold and dry climates ( Šmarda et al, 2014 ).…”

“…By adding substantial new data, we aim here 1) to analyze the distribution and potential evolutionary consequences of genome size and GC content variation as well as of the occurrence of polyploidy in the subfamily Bromelioideae. More specifically, using previously published phylogenetic framework combined with multiple regression analyses of genomic and climatic variables and model tests of genomic character evolution, we would like to examine whether 2a) previously confirmed fast radiation in the core tank-forming Bromelioideae ( Silvestro et al, 2014 ) could be coupled with polyploidy and genomic rearrangements (assessed by divergent GC content and monoploid genome size (Cx); Trávníček et al, 2019 ) or, alternatively 2b) if the higher extinction rate in early diverging tank-less Bromelioideae is associated with these processes.…”