Genome Size Variation across a Cypriot Fabeae Tribe Germplasm Collection

Abstract

DNA content is an important trait linked to the evolutionary routes of taxa and often connected to speciation. In the present study, we studied C-values variation across the Cypriot Fabeae gene pool. Several hundred plants (Vicia spp., Lens spp., Pisum spp.) were sampled across Cyprus. Accurate estimates were established by flow cytometry and propidium iodine staining for 155 discrete populations/accessions. A ten-fold variation was detected across lineages with 1C DNA content varying from 1.584 pg for V. cretica (ARI02420) to 13.983 pg for V. faba (ARI00187). In general, flow cytometry was precise for the characterization of species, even though there were instances of genome overlapping across taxa. Most analyses in the current work refer to species that have not been characterized before by flow cytometry (or any other DNA content estimation method). Still, a correlation to C-values previously reported in Kew Plant DNA C-values database was attempted. A high degree of correlation except for V. dalmatica was established. The evaluation of genome size trait in relation with the Fabeae phylogeny, revealed that Pisum and Lens genera were rather homogenous, but an astonishing fluctuation was shown for Vicia spp. Moreover, it was established that genome up- or down-scaling was not directly linked to speciation drivers. The genomic size measurements presented here could deliver extra quality control for the identification and characterization of taxa in germplasm collections, particularly in cases where species share morphological characters.

Keywords: C-value; DNA content; flow cytometry; genetic resources; legumes.

Figure 1

Distribution of sampling sites across Cypriot regions. In total, 155 Fabeae populations (belonging to 29 species) were collected.

Figure 2

Illustration of floral diversity in the Fabeae tribe. (A) V. lunata; (B) V. cypria; (C) V. laxiflora; (D) V. Villosa; (E) V. angustifolia; (F) V. bithynica; (G) V. narbonensis; (H) V. faba; (I) V. hybrida; (J) V. lathyroides; (K) V. sativa subsp. sativa; (L) V. sativa subsp. sativa; (M) V. peregrina; (N) V. amphicarpa; (O) V. lutea; (P) V. palaestina; (Q) P. fulvum; (R) P. sativum subsp. biflorum; (S) P. sativum subsp. sativum; (T) P. sativum subsp. sativum. scale bar: 1 cm (all pictures © Angelos kyratzis).

Figure 3

(A) FL2-A fluorescence histograms of Zea mays cv. CE-777 (red peaks) and Pisum sativum subsp. sativum ARI00308 (yellow peaks) with diploid (2C) and tetraploid (4C) nuclei. (B) FL2-A fluorescence histograms of Zea mays cv. CE-777 (yellow peaks) and Vicia lunata ARI01343 (red peaks) PI-stained nuclei. Besides diploid (2C) and tetraploid (4C) cells, nuclei with a higher ploidy level (8C) were also detected.

Figure 4

Box plots of mean 1C-values (logarithmic scale) within species. Horizontal lines depict the median value. Boxes below and above the mean line designate quartiles. Lines at the whiskers’ margins (vertically) identify extreme data points, and circles indicate the outliers.

Figure 5

C-values correlation across the 20 common taxa analyzed in the current study that are also presented in the Kew Plant C-values database (https://cvalues.science.kew.org/ (accessed on 3 March 2023)). Data were highly correlated (R² ≈ 0.95) across species. A notable departure was found merely for Vicia dalmatica (depicted as a red circle).

Figure 6

Discrete parsimony optimization of C-values (Mbp) in the Cypriot Fabeae tribe analyzed with the mesquite software. Reconstruction of ancestral states for C-values on an ITS1-5.8S-ITS2-based phylogenetic tree. Blue and cyan branches symbolize moderately small genome DNA content while green, orange, and red designate, respectively, medium-sized and larger genomes. NCBI nucleotide accessions correspond to the following taxa: JX506157.1; L. culinaris, MT002742.1; L. ervoides, JX506158.1; L. nigricans, JN966984.1; L. orientalis, KU678816.1; P. fulvum, KU678853.1; P. sativum subsp. biflorum, AY143482.1; P. sativum subsp. sativum, HM470604.1; V. amphicarpa, KJ787206.1; V. angustifolia, HM470596.1; V. bithynica, JX506196.1; V. cassia, JX506205.1; V. cretica, JX506208.1; V. cypria, HM470636.1; V. dalmatica, HM470634.1; V. ervilia, MW843838.1; V. faba, HM470625.1; V. hybrida, HM470597.1; V. johannis, HM470610.1; V. lathyroides, JX506301.1; V. parviflora, JX506244.1; V. lutea, HM470591.1; V. narbonensis, MN736419.1; V. palaestina, HM470631.1; V. peregrina, JX506278.1; V. pubescens, HM470602.1; V. sativa subsp. sativa, HM470615.1; V. villosa subsp. eriocarpa.