Variation in genome size in the Valeriana officinalis complex resulting from multiple chromosomal evolutionary processes

Abstract

Polyploidy, aneuploidy and change in DNA content of monoploid genomes or chromosomes are the principal causes of the variation in genome size. We studied these phenomena in central-European populations of the Valeriana officinalis complex in order to identify mechanisms or forces driving its evolution. The complex comprises di-, tetra-and octoploid morphologically defined so-called taxonomic "types". Within the study area there are also intermediate "transitional types" the existence of which hampers the application of traditional taxonomic concepts. We thus chose AFLP genotyping and admixture analyses to identify the genetic structuring of the material studied. Di-(2x), tetra-(4x) and octoploidy (8x) were confirmed as major ploidy levels. Major genetic clusters roughly corresponded to these ploidy levels (for K = 2: 2x-and 8x-clusters, for K = 4 with nearly identical probability: 2x-, 4x-, 8x-and unspecific clusters were identified), which further more significantly differed from each other in monoploid absolute genome size (mean 1Cx for 2x = 1.48 pg, 4x 1.29 pg, 8x 1.10 pg). Several individuals of all ploidy levels were admixed, particularly tetraploids. Relative genome size (the sample: standard DAPI fluorescence) was positively correlated with the proportion of the diploid genetic cluster shared by the tetraploids, indicating that hybridization caused the variation in genome size. This result is in accordance with the significant negative correlation of the genome size of tetraploids with their geographic distance to the diploids. However, remarkable intra-ploidy variation in relative genome size was recorded for all ploidy levels (1.14-fold in diploids, 1.28-fold in tetraploids, 1.19-fold in octoploids). We identified aneuploidy as an additional source of variation in genome size in the di-and tetraploids. The contribution of extra chromosomes to absolute genome size exceeded the observed variation within euploids in the diploids, whereas it was included in the regular variability in genome size recorded for the eutetraploids. Variation in monoploid genome size was recorded in polyploids but not in diploids, indicating that polyploids experienced higher dynamics in the evolution of their genomes. Finally, 38.0-63.2% of the total intra-ploidy variation in relative genome size occurred within populations. In conclusion, the Valeriana officinalis complex provides an example of variation in genome size due to four principal evolutionary forces: polyploidization, change in chromosome number and in DNA content of chromosomes and (secondarily) hybridization, but their relative importance differed among ploidy levels. Although the stability in the size of the monoploid genome in species is considered to be the standard case, we found great variability within populations suggesting that genome size is variable even within narrowly defined taxa.

Cytotype variation, cryptic diversity and hybridization in Ranunculus sect. Batrachium revealed by flow cytometry and chromosome numbers

“…In an attempt to change this disappointing state of knowledge, we decided to analyse the variation in ploidy level and genome size in an extensive set of Batrachium populations using flow cytometry (FCM), which (i) is an efficient tool for analysing a large number of individuals rapidly, allowing to reveal the structure of populations and to detect rare cytotypes and hybrids, (ii) is frequently used in studies of evolutionarily and taxonomically intricate groups of plants, including polyploid and hybridogenous complexes (e.g. Suda et al 2010, Trávníček et al 2011a, Chumová et al 2015, Flatscher et al 2015, Lepší et al 2015, Bressler et al 2017, Feulner et al 2017 and homoploid plants (Loureiro et al 2010, Prančl et al 2014, (iii) has been successfully used as a basic method for taxonomic determination and delimitation of other complex aquatic taxa, such as Callitriche (Prančl et al 2014) and Nymphaea (Volkova et al 2010, Kabátová et al 2014, and (iv) has never been used to investigate Batrachium, with the exception of a single R. trichophyllus population (Hidalgo et al 2015). We used flow cytometry combined with chromosome counting to improve our understanding and identification of water-crowfoots in central Europe.…”

Genome-wide characterization of genetic diversity and population structure of Valeriana officinalis L.

“…In the above-mentioned cereals studies the PIC value was significantly higher and amounted to 0.302 and 0.265 in wheat and 0.37 and 0.22 in rye for SNPs and silicoDArTs, respectively [36,38]. However, it should be noted that the genome of V. officinalis is more than 2.5 times smaller than the genome of Secale cerale L. and more than 4 times smaller than the genome of T. durum [23,39,40]. On the other hand, similar to the our (~ 0.18) PIC values were obtained in the study of Ctenophorus caudicinctus, Litoria ewingii and Litoria paraewingi the Australian lizard and frogs [35].…”

“…Previous studies concerned mainly the content and specification of active compounds and their use for therapeutic purposes [1,[19][20][21][22]. Several studies using molecular markers, such as Amplified Fragment Length Polymorphism (AFLP) or Random Amplification of Polymorphic DNA (RAPD) were performed for this species, but none of them concerned the intraspecies diversity analysis [23][24][25]. In this context, Valeriana wallichii DC (syn.…”

Quality Control of Valerianae Radix by Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) Spectroscopy

“…Sample/standard DAPI fluorescence ratios (henceforth relative genome size) were calculated from the means of fluorescence histograms. DNA ploidies were inferred by comparison of the relative genome size of unknown samples with those of karyotyped (i.e., chromosome counted) individuals [18].…”