Gradual genome size evolution and polyploidy in Allium from the Qinghai–Tibetan Plateau

Abstract

Abstract Background and Aims Genome size is an important plant trait, with substantial interspecies variation. The mechanisms and selective pressures underlying genome size evolution are importantly topics in evolutionary biology. There is considerable diversity in Allium from the Qinghai-Tibetan Plateau, where genome size variation and related evolutionary mechanisms are poorly understood. Methods We reconstructed the Allium phylogeny using DNA sequences from 71 species. We also estimated genome sizes of 62 species, and determined chromosome numbers in 65 species. We examined the phylogenetic signal associated with genome size variation, and tested how well the data fit different evolutionary models. The correlations between genome size variations and seed mass, altitude, and 19 bioclimatic factors were determined. Key Results Allium genome sizes differed substantially between species and within diploids, triploids, tetraploids, hexaploids, and octaploids. Size per monoploid genome (1Cx) tended to decrease with increasing ploidy levels. Allium polyploids tended to grow at a higher altitude than diploids. The phylogenetic tree was divided into three evolutionary branches. The genomes in Clade I were mostly close to the ancestral genome (18.781 pg), in Clades II and III tended to expand and contract, respectively. A weak phylogenetic signal was detected for Allium genome size. Furthermore, significant positive correlations were detected between genome size and seed mass, as well as between genome size and altitude. However, genome size was not correlated with 19 bioclimatic variables. Conclusions Allium genome size shows gradual evolution, followed by subsequent adaptive radiation. The three well-supported Allium clades are consistent with the previous studies. The evolutionary patterns in different Allium clades revealed genome contraction, expansion, and relative stasis. The Allium species in Clade II may follow adaptive radiation. The genome contraction in Clade III may be DNA loss after polyploidization. Allium genome size might be influenced by the selective pressure due to the conditions in the Qinghai–Tibetan Plateau (low temperature, high UV irradiation, and abundant phosphate in the soil).