Genome size and base composition variation in natural and experimental Narcissus (Amaryllidaceae) hybrids

Background and Aims

Although there is evidence that both allopolyploid and homoploid hybridization lead to rapid genomic changes, much less is known about hybrids from parents with different basic numbers without further chromosome doubling. Two natural hybrids, Narcissus × alentejanus (2n = 19) and N. × perezlarae (2n = 29), originated by one progenitor (N. cavanillesii, 2n = 28) and two others (N. serotinus, 2n = 10 and N. miniatus, 2n = 30, respectively) allow us to study how DNA content and composition varies in such hybrids.

Methods

Flow cytometry measurements with two staining techniques, PI and DAPI, were used to estimate 2C values and base composition (AT/GC ratio) in 390 samples from 54 wild populations of the two natural hybrids and their parental species. In addition, 20 synthetic F₁ hybrid individuals were also studied for comparison.

Key Results

Natural hybrids presented 2C values intermediate between those found in their parental species, although intra-population variance was very high in both hybrids, particularly for PI. Genome size estimated from DAPI was higher in synthetic hybrids than in hybrids from natural populations. In addition, differences for PI 2C values were detected between synthetic reciprocal crosses, attributable to maternal effects, as well as between natural hybrids and those synthetic F₁ hybrids in which N. cavanillesii acted as a mother.

Conclusions

Our results suggest that natural hybrid populations are composed of a mixture of markedly different hybrid genotypes produced either by structural chromosome changes, consistent with classic cytogenetic studies in Narcissus, or by transposon-mediated events.     

Cytogeography and genome size variation in the Claytonia perfoliata (Portulacaceae) polyploid complex

Background and Aims

Genome duplication is a central process in plant evolution and contributes to patterns of variation in genome size within and among lineages. Studies that combine cytogeography with genome size measurements contribute to our basic knowledge of cytotype distributions and their associations with variation in genome size.

Methods

Ploidy and genome size were assessed with direct chromosome counts and flow cytometry for 78 populations within the Claytonia perfoliata complex, comprised of three diploid taxa with numerous polyploids that range to the decaploid level. The relationship between genome size and temperature and precipitation was investigated within and across cytotypes to test for associations between environmental factors and nuclear DNA content.

Key Results

A euploid series (n = 6) of diploids to octoploids was documented through chromosome counts, and decaploids were suggested by flow cytometry. Increased variation in genome size among populations was found at higher ploidy levels, potentially associated with differential contributions of diploid parental genomes, variation in rates of genomic loss or gain, or undetected hybridization. Several accessions were detected with atypical genome sizes, including a diploid population of C. parviflora ssp. grandiflora with an 18 % smaller genome than typical, and hexaploids of C. perfoliata and C. parviflora with genomes 30 % larger than typical. There was a slight but significant association of larger genome sizes with colder winter temperature across the C. perfoliata complex as a whole, and a strong association between lower winter temperatures and large genome size for tetraploid C. parviflora.

Conclusions

The C. perfoliata complex is characterized by polyploids ranging from tetraploid to decaploid, with large magnitude variation in genome size at higher ploidy levels, associated in part with environmental variation in temperature.     

Genome size variation in Central European species of Cirsium (Compositae) and their natural hybrids

BACKGROUND AND AIMS: Nuclear DNA amounts of 12 diploid and one tetraploid taxa and 12 natural interspecific hybrids of Cirsium from 102 populations in the Czech Republic, Austria, Slovakia and Hungary were estimated. METHODS: DAPI and PI flow cytometry were used. KEY RESULTS: 2C-values of diploid (2n = 34) species varied from 2.14 pg in C. heterophyllum to 3.60 pg in C. eriophorum (1.68-fold difference); the 2C value for the tetraploid C. vulgare was estimated at 5.54 pg. The DNA contents of hybrids were located between the values of their putative parents, although usually closer to the species with the smaller genome. Biennial species of Cirsium possessed larger nuclear DNA amounts than their perennial relatives. Genome size was negatively correlated with Ellenberg's indicator values for continentality and moisture and with eastern limits of distribution. A negative relationship was also detected between the genome size and the tendency to form natural interspecific hybrids. On the contrary, C-values positively corresponded with the spinyness (degree of spinosity). AT frequency ranged from 48.38 % in C. eriophorum to 51.75 % in C. arvense. Significant intraspecific DNA content variation in DAPI sessions was detected in C. acaule (probably due to the presence of B-chromosomes), and in tetraploid C. vulgare. Only the diploid level was confirmed for the Pannonian C. brachycephalum, generally considered to be tetraploid. In addition, triploidy was discovered for the first time in C. rivulare. CONCLUSIONS: Considerable differences in nuclear DNA content exist among Central European species of Cirsium on the diploid level. Perennial soft spiny Cirsium species of wet habitats and continental distributions generally have smaller genomes. The hybrids of diploid species remain diploid, and their DNA content is smaller than the mean of the parents. Species with smaller genomes produce interspecific hybrids more frequently.     

Genome size variation and evolution in the grape family Vitaceae

Genome size variation is of fundamental biological importance and has been a longstanding puzzle in evolutionary biology. In the present study, the genome size of 61 accessions corresponding to 11 genera and 50 species of Vitaceae and Leeaceae is determined using flow cytometry. Phylogenetically based statistical analyses were used to infer ancestral character reconstructions of nuclear DNA contents. The DNA 1C‐values of 38 species are reported for the first time, with the largest genome (Cyphostemma humile (N. E. Br.) Desc. ex Wild & R. B. Drumm, 1C = 3.25 pg) roughly 10.48‐fold larger than the smallest (Vitis vulpina L., 1C = 0.31 pg). The large genomes are restricted to the tribe Cayratieae, and most other extant species in the family possess relatively small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor for the family had a relatively small genome (1C = 0.85 pg). Genome evolution in Vitaceae has been characterized by a trend towards genome size reduction, with just one episode of apparent DNA accumulation in the Cayratieae lineage. Such contrasting patterns of genome size evolution probably resulted from transposable elements and chromosome rearrangements, while neopolyploidization seems to contribute to recent genome increase in some species at the tips in the family tree.     

Genome size in Echinops L. and related genera (Asteraceae, Cardueae): karyological, ecological and phylogenetic implications

Genome size was assessed by flow cytometry in 33 species belonging to seven genera of the tribe Cardueae (Asteraceae), which can be grouped in three taxonomic complexes. 2C nuclear DNA content ranged from 1.49 to 16.98 pg, which is more than elevenfold variation. Genome size correlated well with some karyological traits. Nuclear DNA amount variations also have systematic and evolutionary implications and/or are linked to adaptations to ecological conditions.     

Genome size variation in Macaronesian angiosperms: forty percent of the Canarian endemic flora completed

Genome sizes for 127 Macaronesian endemic angiosperms from 69 genera and 32 families were estimated using propidium iodide flow cytometry. Only about 30-fold variation in 1C-values was found, ranging from 0.32 pg in Echium bonnetii to 9.52 pg in Scilla dasyantha. Taxa with very small DNA amounts (1C 1.4 pg) were the most dominant group (71.7%), whereas the frequency of other categories was much lower (18.9% and 9.4% in taxa with small (1.41–3.50 pg) and intermediate 1C-values (3.51–14.00 pg), respectively). Comparisons of average C- and Cx-values between Macaronesian endemics and non-Macaronesian representatives always revealed significantly smaller amounts in the former group at various taxonomic levels (genus, family, major phylogenetic lineage). Potential relationship between nuclear DNA content and insular burst of speciation is suggested owing to the marked prevalence of very small genomes among angiosperms that underwent rapid adaptive radiation. Merging all the genome size data on Macaronesian angiosperms available shows that this flora represents the best covered plant assemblage from the phytogeographic point of view.     

New data on genome size in 128 Asteraceae species and subspecies,with first assessments for 40 genera, 3 tribes and 2 subfamilies

The Asteraceae family has been broadly studied, but the values of genome size of only 3.5% of their species are known. To expand these data, we carried out a flow cytometric study of nuclear DNA content in a wide range of taxa of this family, filling gaps in some less studied groups. In addition, some chromosome counts have been performed (46 taxa, including the first one in two species and one subspecies). We provide genome size data for 167 taxa (184 accessions). Of these, data are new for 128 species and subspecies (141 accessions), 40 genera, three tribes (Barnadesieae, Gochnatieae and Nassauvieae) and two subfamilies (Barnadesioideae and Gochnatioideae). Most values (about 75%) are small or very small (1C ≤ 3.5 pg). The second reports on 17 species previously studied with other methods (i.e. first flow cytometric assessments) are also given. Finally, we contribute results for 22 species for which a first flow cytometric assessment has been published during the preparation of this article. The current data-set moves the percentage of coverage approximately from 3% to 4.7% at the specific level, from 6% to 11.6% at the generic level, from 34.9% to 41.9% at the tribal level and from 33% to 50% at the subfamily level.     

Genome evolution in the genus Sorghum (Poaceae)

BACKGROUND AND AIMS: The roles of variation in DNA content in plant evolution and adaptation remain a major biological enigma. Chromosome number and 2C DNA content were determined for 21 of the 25 species of the genus Sorghum and analysed from a phylogenetic perspective. METHODS: DNA content was determined by flow cytometry. A Sorghum phylogeny was constructed based on combined nuclear ITS and chloroplast ndhF DNA sequences. KEY RESULTS: Chromosome counts (2n = 10, 20, 30, 40) were, with few exceptions, concordant with published numbers. New chromosome numbers were obtained for S. amplum (2n = 30) and S. leiocladum (2n = 10). 2C DNA content varies 8.1-fold (1.27-10.30 pg) among the 21 Sorghum species. 2C DNA content varies 3.6-fold from 1.27 pg to 4.60 pg among the 2n = 10 species and 5.8-fold (1.52-8.79 pg) among the 2n = 20 species. The x = 5 genome size varies over an 8.8-fold range from 0.26 pg to 2.30 pg. The mean 2C DNA content of perennial species (6.20 pg) is significantly greater than the mean (2.92 pg) of the annuals. Among the 21 species studied, the mean x = 5 genome size of annuals (1.15 pg) and of perennials (1.29 pg) is not significantly different. Statistical analysis of Australian species showed: (a) mean 2C DNA content of annual (2.89 pg) and perennial (7.73 pg) species is significantly different; (b) mean x = 5 genome size of perennials (1.66 pg) is significantly greater than that of the annuals (1.09 pg); (c) the mean maximum latitude at which perennial species grow (-25.4 degrees) is significantly greater than the mean maximum latitude (-17.6) at which annual species grow. CONCLUSIONS: The DNA sequence phylogeny splits Sorghum into two lineages, one comprising the 2n = 10 species with large genomes and their polyploid relatives, and the other with the 2n = 20, 40 species with relatively small genomes. An apparent phylogenetic reduction in genome size has occurred in the 2n = 10 lineage. Genome size evolution in the genus Sorghum apparently did not involve a 'one way ticket to genomic obesity' as has been proposed for the grasses.     

Genome size variation in some representatives of the genus <Emphasis Type="Italic">Tripleurospermum</Emphasis>

Genome size has been estimated by flow cytometry in 14 populations belonging to eight taxa (seven species, one of them with two varieties) of the genus Tripleurospermum. 2C nuclear DNA amounts range from 4.87 to 9.22 pg, and nuclear DNA amounts per basic chromosome set from 1.99 to 2.75 pg. Statistically significant differences depending on ploidy level, life cycle or environmental factors such as altitude have been found. Also, genome size is positively correlated with total karyotype length. The presence of rhizome is related to nuclear DNA content in these species.This work was supported by project BOS2001-3041-C02-01 of the Spanish government, and one of the authors (S.G.) received a predoctoral grant from the Spanish government.     

Complex pattern of genome size variation in a polymorphic member of the Asteraceae

Aim  Although divergences in nuclear DNA content among different species within a genus are widely acknowledged, intraspecific variation is still a somewhat controversial issue. The aim of this study was to assess genome size variation in the polymorphic species Picris hieracioides L. (Asteraceae) and to search for potential interpretations of the size heterogeneity.
Location  Europe.
Methods  The genome sizes of 179 plants of P. hieracioides collected from 54 populations distributed across 10 European countries were determined by propidium iodide flow cytometry. Differences in nuclear DNA content were confirmed in simultaneous analyses.
Results  2C-values (population means) at the diploid level varied from 2.26 to 3.11 pg, spanning a 1.37-fold range. The variation persisted even after splitting the whole data set into two recently distinguished morphotypes (i.e. the 'Lower altitude' type and the 'Higher altitude' type) that possess significantly different nuclear DNA contents. Cluster analysis revealed the presence of three major groups according to genome size, which exhibited a particular geographical pattern. Generally, the genome size of both morphotypes increased significantly from south-west to north-east. A new cytotype, DNA triploid, was found for the first time.
Main conclusions  High intraspecific variation in the amount of nuclear DNA in P. hieracioides correlates with the extensive morphological variation found within the taxon. Despite the complex pattern that was presented, genome size variants were non-randomly distributed and reflected palaeovegetation history. We suggest that the complex evolutionary history of P. hieracioides (e.g. the existence of several cryptic lineages with different levels of cross-interactions) is the most plausible explanation for the observed heterogeneity in genome size.     

Nuclear DNA content and chromosome number in some diploid and tetraploid Centaurea (Asteraceae: Cardueae) from the Dalmatia region

Given the paucity of information about genome size in the genus Centaurea, nuclear DNA content of 15 Centaurea taxa, belonging to four subgenera and six different sections, has been investigated for the first time. The sample concerns 21 populations from the Dalmatia region of Croatia. The 2C DNA content and GC percentage were assessed by flow cytometry and chromosome number was determined using standard methods. Genome size of studied Centaurea ranged from 2C=1.67 to 3.72 pg. These results were in accordance with chromosome number and especially with ploidy level that varies throughout this group; 2C DNA values ranged from 1.67 to 3.43 pg for diploid, and from 3.19 to 3.72 for polyploid taxa. No significant intraspecific variations of DNA amount were found between two subspecies of C. visiani and C. ragusina, nor between two varieties of C. gloriosa. However, some populations of C. glaberrima and C. cuspidata showed a significant difference in DNA amount. Three different basic chromosome numbers were observed in studied species (x=9, 10, and 11). The most frequent basic number was x=9. C. rupestris, C. ragusina ssp. ragusina, and C. r. ssp. lungensis possessed x=10 and C. tuberosa x=11. The species with a basic chromosome number of x=9 had a small genome size and the smallest chromosomes (on average 0.09 to 0.12 pg/chromosome) but frequently present polyploidy. Centaurea ragusina ssp. ragusina and C. r. ssp. lungensis had a mean base composition 41.3% GC.     

Genome size in Bulgarian Centaurea s.l. (Asteraceae)

Thirty-nine species and subspecies of the genera Centaurea, Colymbada, Psephellus and Cyanus (all included in Centaurea s.l.) including many rare and endemic taxa of preponderantly Bulgarian distribution have been investigated with Feulgen DNA image densitometry for holoploid and monoploid genome size (C- and Cx-values). Cyanus varies gradually 2.17-fold between 0.74 pg and 1.56 pg (1Cx). In the remaining taxa two major genome size groups are found, which differ about 1.8-fold in Cx-value. Low values occur in Centaurea subgenera Acrolophus, Solstitiaria, Phalolepis (0.77 pg to 0.90 pg, 1Cx) and Jacea (0.95 pg to 1.09 pg, 1Cx), high values in the genera Colymbada (1.65 pg to 1.93 pg, 1Cx) and Psephellus (1.79 pg, 1Cx, in P. marschallianus). Cx-values support a distinction of Colymbada from Centaurea. Genome size variation is discussed with regard to phylogeny, life form (annual versus perennial), polyploidy, chromosome basic numbers, altitude of occurrence and climate, endemism, and rarity.     

Contribution to the genome size knowledge of New World species from the Heliantheae alliance (Asteraceae)

This article contributes first genome size assessments by flow cytometry for 16 species, 12 genera, and 3 tribes from family Asteraceae, mostly belonging to the Heliantheae alliance, an assembly of 13 tribes from subfamily Asteroideae with a large majority of its species in the New World. Most genome sizes are accompanied by their own chromosome counts, confirming in most cases, although not all, previous counts for the species, and revealing possible cases of unknown dysploidy or polyploidy for certain taxa. The data contribute to the pool of knowledge on genome size and chromosome numbers in the family Asteraceae and will further allow deeper studies and a better understanding on the role of dysploidy in the evolution of the Heliantheae alliance. However, we still lack data for tribes Chaenactideae, Neurolaeneae, Polymnieae, and Feddeeae (the latter, monospecific) to complete the alliance representation.     

Taxonomic implications of genome size for all species of the genus Gasteria Duval (Aloaceae)

Nuclear DNA content (2C) is used as a new criterion to investigate all species of the genus Gasteria Duval including the three recently described species Gasteria polita van Jaarsv., G. pendulifolia van Jaarsv. and G. glauca van Jaarsv.. The 122 accessions investigated have the same chromosome number (2n=2x=14), with exception of three tetraploid plants found. The nuclear DNA content of the diploids, as measured by flow cytometry with Propidium Iodide, is demonstrated to range from 32.8–43.2 pg. This implies that the largest genome contains roughly 10¹⁰ more base pairs than the smallest. Based on DNA content the species could be divided in five groups: G. rawlinsonii Oberm. with 32.8 pg, 13 mostly inland species with 34.3–36.0 pg, five coastal species with 36.5–39.0 pg and Gasteria batesiana Rowley with 43.2 pg. The thirteen species with 34.3–36.0 pg could be divided further, in a group of eight species occupying mainly very restricted areas with 34.3–35.1 pg and a second group of five species with 35.2–36.0 pg mainly occupying large areas. These five groups did not coincide very well with the two sections and four series of Gasteria based on a cladistic analysis by van Jaarsveld et al. (1994). Based on its long leafy branches, location in the centre of Gasteria species distribution and its by far lowest DNA content, G. rawlinsonii might be the most primitive member of the genus. Nuclear DNA content as measured by flow cytometry is shown to be relevant to provide additional information on the relationships between Gasteria species.     

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms

MethodsNuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes.ConclusionsGenlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.     

Genome size evolution and polyploidy in the Daphnia pulex complex (Cladocera: Daphniidae)

Genome size was estimated in 49 clones of the Daphnia pulex complex from temperate and subarctic locations using flow cytometry and microsatellite DNA analyses. Significant genome size differences were found in diploid species belonging to the two genetically distinct groups (the pulicaria and the tenebrosa groups), with clones from the tenebrosa group having genome sizes 22% larger than those in the pulicaria group. Combined flow cytometry and microsatellite DNA analyses revealed that nearly all polyploid clones in the D. pulex complex are triploid and not tetraploid, as was previously suggested. Sequencing analyses of the ND5 gene to position clones in their respective clades within the D. pulex complex have uncovered three triploid clones of Daphnia middendorffiana with a D. pulex maternal parent. This result was unexpected because Daphnia pulicaria has always been identified as the maternal parent of these hybrid polyploid clones. Triploid clones likely owe their origins to interactions between sexual and asexual populations. Further interactions in the tenebrosa group have generated tetraploid clones but these events have been rare.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 68–79.     

Pollen diversity in the genus Ptilostemon (Asteraceae,Cardueae) from Italy and its taxonomic and palynoecological implications

The results of a study on pollen morphology of the species of the genus Ptilostemon growing in Italy: Ptilostemon niveus, P. greuteri, P. gnaphaloides, P. casabonae, P. strictus, P. stellatus by light and scanning electron microscopy were presented and discussed including in relation to their taxonomic position. The exine shows two different ornamentation patterns: echinae and scabrae. This last ornamentation pattern together with other features was previously described in the genus Ptilostemon. Of 6 species analysed, P. stellatus is the only one that shows a scabrate ornamentation of exine. Two pollen types were recognized through the exine ornamentation, length of ectocolpus and polar outline: P. stellatus type and P. niveus type. A multivariate analysis (principal component analysis and linear discriminant analysis) was carried out with the aim of examining potential morphological characters which could be used to identify taxa. The data suggest that several characteristics can be used to delimit the species in particular the exine ornamentation. The results of our studies support the actually subgeneric classification, and several features of the pollen grains analysed seem to have a palynoecological role and an important taxonomic significance. A dichotomous key based on palynological data is also given.     

The considerable genome size variation of Hordeum species (poaceae) is linked to phylogeny, life form, ecology, and speciation rates

Genome size variation in plants is thought to be correlatedwith cytological, physiological, or ecological characters. However,conclusions drawn in several studies were often contradictory.To analyze nuclear genome size evolution in a phylogenetic framework,DNA contents of 134 accessions, representing all but one speciesof the barley genus Hordeum L., were measured by flow cytometry.The 2C DNA contents were in a range from 6.85 to 10.67 pg indiploids (2n = 14) and reached up to 29.85 pg in hexaploid species(2n = 42). The smallest genomes were found in taxa from theNew World, which became secondarily annual, whereas the largestdiploid genomes occur in Eurasian annuals. Genome sizes of polyploidtaxa equaled mostly the added sizes of their proposed progenitorsor were slightly (1% to 5%) smaller. The analysis of ancestralgenome sizes on the base of the phylogeny of the genus revealedlineages with decreasing and with increasing genome sizes. Correlationsof intraspecific genome size variation with the length of vegetationperiod were found in H. marinum populations from Western Europebut were not significant within two species from South America.On a higher taxonomical level (i.e., for species groups or theentire genus), environmental correlations were absent. Thiscould mostly be attributed to the superimposition of life-formchanges and phylogenetic constraints, which conceal ecogeographicalcorrelations.     

New chromosome counts in the genus Cousinia and the related genus Schmalhausenia (Asteraceae, Cardueae)

Twenty chromosome counts are reported in the genus Cousinia and the monotypic genus Schmalhausenia , which are part of the Arctium group, from Armenia, Iran, Kazakhstan and Uzbekistan. Twelve are new and eight provide confirmation of scarce or disputable previous data. The correlation between karyological data, pollen type and molecular phylogeny is very close, and on this basis two main groups can be defined. One is the arctioid group, which comprises the genera Arctium and Schmalhausenia , and a small part of the genus Cousinia , with x  = 18. The other is the genus Cousinia s.s. , with a dysploid series ranging from x  = 13–11. Some considerations on the chromosomal evolution in the group are made.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Socety , 2003, 143 , 411–418.     

2C DNA variation and relationships among New World species of the genus Lupinus (Fabaceae)

The 2C DNA values in 38 species and accessions of the genus Lupinus (Fabaceae) from the New World have been analysed using flow cytometry. They are representatives of North and South American species (the Atlantic and the Andean regions). Estimated 2C DNA values ranged from 1.08 pg in L. pusillus to 2.68 pg in L. albicaulis (both from North America), that is a variation of more than 2.5-fold. The variation for North American lupins was much higher than that for South American ones. Statistical analysis of the data resulted in a grouping that showed for North American lupins some correlation with the length of life cycle. Discussion concerns some aspects of the evolution of the genus.