Flow cytometry protocols, relative genome size and ploidy levels for 1104 species of non-apomictic angiosperms from the Eastern Alps - a community resource based on the screening of 45,000 samples

Abstract

Flow cytometry provides a reliable and fast method for estimating genome size and ploidy levels in plants. Until recently, most studies employed fresh tissues, which limits the use of the method with samples from remote areas or when an extremely high number of samples needs to be processed in a short time. Although there is growing evidence that silica-dried material can be used for ploidy estimation in some taxa, no flora-wide study has been available so far. Here, we provide methodological aspects of an unprecedented study exploring ploidy variation of non-apomictic angiosperms in the Eastern Alps. We have analysed ca. 45,000 silica-dried samples of 1135 species using flow cytometry with DAPI as stain. We were able to obtain ploidy level information from 1104 (97%) of species. The unsuccessful species included succulent plants of the family Crassulaceae (genera Jovibarba, Rhodiola, Sedum, Sempervivum), the achlorophyllous parasitic or mycoheterotrophic genera Orobanche and Hypopitis, and a handful of others. About 80% of samples were successfully analysed using a single universal protocol and leaf tissue, while in the remaining species the use of alternative tissues (such as petioles or flowers) and/or protocol modifications were needed (targeting composition of buffers, duration of fixation or staining time or use of alternative buffers). A total of 377 species (34%) included polyploid cytotypes and 179 (16%) species were ploidy-variable. As a community resource, we provide relative genome sizes and ploidy assignments of 1332 cytotypes retrieved from 1104 species along with methodological details (e.g. buffers, standards, analysed plant organs, histogram quality). We believe that this dataset will facilitate future research in particular species as well as in flora-wide investigations of ploidy level variation of the Central European flora in general. We are confident that novel cytotypes of many species will be discovered in other geographic areas, and we would be delighted if the present dataset could serve the botanical community for comparison.

Plant phenotyping relevance

植物のゲノムサイズ・倍数性を推定するフローサイトメトリー法の大規模な適用と、組織・バッファー・固定・染色条件の改良を中心に扱い、再利用可能なデータセットも提供しているため。

Code and data availability

The paper's core outputs (Supplementary Tables S1–S3 with RGS values, ploidy assignments, protocol details, and orchid P estimates) are the paper-specific assets, but no public deposit URL for them is provided in the supplied blocks. The URLs mentioned (Chrobase, Senckenberg, InfoFlora, chromosomes.sav.sk, Pladias) are

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