New estimates and synthesis of chromosome number, ploidy level and genome size variation in Allium sect. Codonoprasum: a step towards understanding the hitherto unresolved diversification and evolution of the section

Background The genus Allium is known for its high chromosomal variability, but most chromosome counts are based on a few individuals and genome size (GS) reports are limited in certain taxonomic groups. This is evident in the Allium sect. Codonoprasum , a species-rich (> 150 species) and taxonomically complex section with weak morphological differences between taxa, the presence of polyploidy and frequent misidentification of taxa. Consequently, a significant proportion of older karyological reports may be unreliable and GS data are lacking for the majority of species within the section. This study, using chromosome counting and flow cytometry (FCM), provides the first complex and detailed insight into variation in chromosome number, polyploid frequency and distribution, and GS in section members, a step towards understanding the section's unresolved diversification and evolution. Results We analysed 1,582 individuals from 311 populations of 25 taxa and reported DNA ploidy levels and their GS, with calibration from chromosome counts in 21 taxa. Five taxa had multiple ploidy levels. GS estimates for 16 taxa are primary estimates. A comprehensive review of chromosome number and DNA-ploidy levels in 128 taxa of the section revealed that all taxa had x = 8, except A. rupestre with two polyploid series (x = 8, descending dysploidy x = 7), unique for this section. Diploid taxa dominated (71.1%), while di-/polyploid (12.5%) and pure polyploid (16.4%) taxa were less common. Ploidy diversity showed that diploid taxa were dominant in the eastern Mediterranean (> 85%), decreasing towards the west and north, with only polyploid taxa present in northern and northwestern Europe. A 4.1-fold variation in GS was observed across 33 taxa (2C = 22.3–92.1 pg), mainly due to polyploidy, with GS downsizing observed in taxa with multiple ploidy levels. Intra-sectional GS variation suggests evolutionary relationships, and intraspecific GS variation within some taxa may indicate taxonomic heterogeneity and/or historical migration patterns. Conclusions Our study showed advantages of FCM as an effective tool for detecting ploidy levels and determining GS within the section. GS could be an additional character in understanding evolution and phylogenetic relationships within the section.