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.     

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.     

Nuclear DNA content of the Solanum spp. in the series Etuberosa as determined by laser flow cytometry

Nuclear DNA content was determined in three accessions of Solanum brevidens, three accessions of S. etuberosum, and one accession of S. fernandezianum, which are diploid (2n = 2×= 24), closely related, non tuber-bearing wild potato species belonging to the series Etuberosa (Solanaceae). The plants were grown in vitro at 18°C or at 25°/22°C (day/night). S. brevidens was also grown in soil in the glasshouse at 25°/19°C (day/night), and in growth chambers at 18°C or 32°C. Leaf nuclei were isolated using a chopping method and stained with propidium iodide. Chicken red blood cells (CRBC; 2.33 pg) were added to the samples of nuclei as internal standards. The fluorescence of plant nuclei relative to CRBC was measured with an EPICS PROFILE flow cytometer. The 2C values of in vitro-grown S. brevidens and S. etuberosum were similar (1.48–1.54 pg, depending on the accession), but they were smaller than the 2C value of S. fernandezianum (1.63 pg). The 2C values of S. brevidens and S. etuberosum were generally smaller than those of the diploid species S. berthaultii (1.60–1.61 pg) and the diploid clones of S. tuberosum (1.60–1.72 pg). A similar relative difference of nuclear DNA content was found also between tetraploid S. brevidens and tetraploid S. tuberosum (2C = 3.15–3.16 pg and 3.50–3.62 pg, respectively). High (32°C) and low (18°C) growth temperatures caused abnormal changes in morphology and reduced fertility in S. brevidens in the growth chamber. The 2C values of S. brevidens grown at 25°/19°C (day/night) or at 32°C were similar, whereas the 2C values were c. 10% lower at 18°C.     

基于流式细胞术的乌饭树核DNA含量(2C-值)测定

核DNA含量(2C-值)是描述植物生物多样性的一个重要特征参数。该研究利用流式细胞仪检测越橘属植物乌饭树核DNA含量,建立了适合乌饭树的流式细胞术测定方法:以野生乌饭树的嫩叶为材料,以已知核DNA含量的水稻品种‘日本晴’为内标,采用GPB解离液,细胞核悬液加入50μL獉mL-1碘化丙啶染色5 min即可上机检测。结果表明:(1) 9个乌饭树单株的核DNA含量平均值为(1.22±0.03) pg,最小值为1.18 pg,最大值为1.27 pg。(2)检测结果与已知的越橘属二倍体植株的2C-值含量相似,且不同地理来源的单株DNA含量没有显著差异(P>0.05),推测这9个单株为二倍体植株。(3)测定的乌饭树核DNA含量(2C-值)可丰富越橘属植物的C-值库;基于流式细胞术建立的乌饭树核DNA含量测定方法可为该属其他植物的相关研究提供借鉴。     

Nuclear DNA content of Solanum species grown in vitro, as determined by flow cytometry

The DNA relative content in nuclei from several Solanum species, which were used as partners for somatic hybridization, were determined using a flow cytometry method. The nuclei were isolated mechanically or via protoplasts from leaves of in vitro grown plants. In the case of S. nigrum as well as S. tuberosum cv. Bzura and dihaploid clone H8105, the nuclei were also obtained from suspension cultured cells by lysis of protoplasts. The source and the method of nuclei isolation affected the pattern of nuclear DNA in the genotypes studied. The mesophyll nuclei showed two distinct peaks on the DNA histograms, whereas the DNA peaks produced by cell suspension nuclei were broad and less distinct. The DNA content in the nuclei, calculated from the DNA histograms of the samples and a DNA standard historgam (Trout Red Blood Cells, having DNA content of 5.05 pg per nucleus), were much lower in mesophyll nuclei than in those obtained from the cell suspension for the same genotypes. The results are discussed in respect of the genetic instability of Solanum genotypes. The usefulness of a flow cytometry approach in somatic hybridization research is also discussed.     

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.     

Quantitation of spermatogenesis by DNA flow cytometry: Comparative study among six species of mammals

Suspensions of testicular germ cells from six species of mammals were prepared and stained for the DNA content with a fluorochrome (ethidium bromide) adopting a common technique and subjected to DNA flow cytometry. While uniform staining of the germ cells of the mouse, hamster, rat and monkey could be obtained by treating with 0.5% pepsin for 60 min followed by staining with ethidium bromide for 30 min, that of the guinea pig and rabbit required for optimal staining pepsinization for 90 min and treatment with ethidium bromide for 60 min. The procedure adopted here provided a uniform recovery of over 80% of germ cells with each one of the species tested and the cell population distributed itself according to the DNA content (expressed as C values) into 5 major classes-spermatogonia (2C), cells in S-phase, primary spermatocytes (4C), round spermatids (1C), and elongating/elongated spermatids (HC). Comparison of the DNA distribution pattern of the germ cell populations between species revealed little variation in the relative quantities of cells with 2C (8–11%), S-phase (6–9%), and 4C (6–9%) amount of DNA. Though the spermatid cell populations exhibited variations (1C:31–46%, HCl:7–20% and and HC2:11–25%) they represented the bulk of germ cells (70–80%). The overall conversion of 2C to 1C (1C:2C ratio) and meiotic transformation of 4C cells to 1C (1C:4C ratio) kinetics were relatively constant between the species studied. The present study clearly demonstrates that DNA flow cytometry can be adopted with ease and assurance to quantify germ cell transformation and as such spermatogenesis by analysing a large number of samples with consistency both within and across the species barrier. Any variation from the norms in germ cell proportions observed following treatment, fore.g. hormonal stimulation or deprivation can then be ascribed due to a specific effect of the hormone/drug on single/multiple steps in germ cell transformation     

Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species

Background and Aims: After the initial boom in the application of flow cytometryin plant sciences in the late 1980s and early 1990s, which wasaccompanied by development of many nuclear isolation buffers,only a few efforts were made to develop new buffer formulas.In this work, recent data on the performance of nuclear isolationbuffers are utilized in order to develop new buffers, generalpurpose buffer (GPB) and woody plant buffer (WPB), for plantDNA flow cytometry. Methods: GPB and WPB were used to prepare samples for flow cytometricanalysis of nuclear DNA content in a set of 37 plant speciesthat included herbaceous and woody taxa with leaf tissues differingin structure and chemical composition. The following parametersof isolated nuclei were assessed: forward and side light scatter,propidium iodide fluorescence, coefficient of variation of DNApeaks, quantity of debris background, and the number of particlesreleased from sample tissue. The nuclear genome size of 30 selectedspecies was also estimated using the buffer that performed betterfor a given species. Key Results: In unproblematic species, the use of both buffers resulted inhigh quality samples. The analysis of samples obtained withGPB usually resulted in histograms of DNA content with higheror similar resolution than those prepared with the WPB. In morerecalcitrant tissues, such as those from woody plants, WPB performedbetter and GPB failed to provide acceptable results in somecases. Improved resolution of DNA content histograms in comparisonwith previously published buffers was achieved in most of thespecies analysed. Conclusions: WPB is a reliable buffer which is also suitable for the analysisof problematic tissues/species. Although GPB failed with someplant species, it provided high-quality DNA histograms in speciesfrom which nuclear suspensions are easy to prepare. The resultsindicate that even with a broad range of species, either GPBor WPB is suitable for preparation of high-quality suspensionsof intact nuclei suitable for DNA flow cytometry.     

Nuclear DNA amounts in Macaronesian angiosperms

Nuclear DNA contents for 104 Macaronesian angiosperms, with particular attention on Canary Islands endemics, were analysed using propidium iodide flow cytometry. Prime estimates for more than one-sixth of the whole Canarian endemic flora (including representatives of 11 endemic genera) were obtained. The resulting 1C DNA values ranged from 0.19 to 7.21 pg for Descurainia bourgeauana and Argyranthemum frutescens, respectively (about 38-fold difference). The majority of species, however, possessed (very) small genomes, with C-values <1.6 pg. The tendency towards small nuclear DNA contents and genome sizes was confirmed by comparing average values for Macaronesian and non-Macaronesian representatives of individual families, genera and major phylogenetic lineages. Our data support the hypothesis that the insular selection pressures in Macaronesia favour small C-values and genome sizes. Both positive and negative correlations between infrageneric nuclear DNA amount variation and environmental conditions on Tenerife were also found in several genera.     

Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species

Hybridization and polyploidy can induce rapid genomic changes, including the gain or loss of DNA, but the magnitude and timing of such changes are not well understood. The homoploid hybrid system in Helianthus (three hybrid-derived species and their two parents) provides an opportunity to examine the link between hybridization and genome size changes in a replicated fashion. Flow cytometry was used to estimate the nuclear DNA content in multiple populations of three homoploid hybrid Helianthus species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus), the parental species (Helianthus annuus and Helianthus petiolaris), synthetic hybrids, and natural hybrid-zone populations. Results confirm that hybrid-derived species have 50% more nuclear DNA than the parental species. Despite multiple origins, hybrid species were largely consistent in their DNA content across populations, although H. deserticola showed significant interpopulation differences. First- and sixth-generation synthetic hybrids and hybrid-zone plants did not show an increase from parental DNA content. First-generation hybrids differed in DNA content according to the maternal parent. In summary, hybridization by itself does not lead to increased nuclear DNA content in Helianthus, and the evolutionary forces responsible for the repeated increases in DNA content seen in the hybrid-derived species remain mysterious.     

Plant morphology,genome size,and SSR markers differentiate five distinct taxonomic groups among accessions in the genus Miscanthus

Information on genome size, ploidy level, and genomic polymorphisms among accessions of the genus Miscanthus can assist in taxonomic studies, help understand the evolution of the genus, and provide valuable information to biomass crop improvement programs. Taxonomic investigation combining variation in plant morphology, genome size, chromosome numbers, and simple sequence repeat (SSR) marker polymorphisms were applied to characterize 101 Miscanthus accessions. A total of 258 amplicons generated from 17 informative SSR primer pairs was subjected to cluster and principal coordinate analysis and used to characterize genetic variation and relationships among 31 Miscanthus accessions, including four interspecific Miscanthus hybrids created from controlled pollinations, and four Saccharum, six Erianthus, and one Sorghum bicolor accessions. Miscanthus accessions were distinct from accessions in the genera Erianthus and Saccharum. Miscanthus accessions fell into five taxonomic groups, including the existing taxonomic section Miscanthus, diploid and tetraploid Miscanthus sacchariflorus, and a fourth (M. × giganteus) and fifth group (Miscanthus ‘purpurascens’); the last two being intermediate forms. In contrast to previous work, our findings suggest diploid and tetraploid M. sacchariflorus are taxonomically different, the latter more closely related to M. sacchariflorus var lutarioriparius. We also suggest that Miscanthus ‘purpurascens’ accessions are interspecific hybrids between Miscanthus sinensis and diploid M. sacchariflorus based on DNA content and SSR polymorphisms. The evolution of Miscanthus and related genera is discussed based on combined analysis and geographical origin.     

A rapid means of sex identification inSilene latifolia by use of flow cytometry

Sex identification in dioecious plants using nonflowering material would have broad applications in both basic and applied research. We present a method using flow cytometry for diagnosing the sex of the dioecious speciesSilene latifolia Poiret (Caryophyllaceae) by means of sexual differences in nuclear DNA content and base-pair composition. Males have a significantly larger genome, attributable to the known sex-chromosome heteromorphism. Males and females also differ in the AT/GC composition, attributable to differences in non-recombining portions of the sex chromosomes. The two measures enable assignment of individuals to sex with a combined error rate of 9%. These results forS. latifolia indicate useful directions for future research into sex diagnostics for other dioecious species.     

Comparisons with Caenorhabditis (approximately 100 Mb) and Drosophila (approximately 175 Mb) using flow cytometry show genome size in Arabidopsis to be approximately 157 Mb and thus approximately 25% larger than the Arabidopsis genome initiative estimate of approximately 125 Mb

Recent genome sequencing papers have given genome sizes of 180 Mb for Drosophila melanogaster Iso-1 and 125 Mb for Arabidopsis thaliana Columbia. The former agrees with early cytochemical estimates, but numerous cytometric estimates of around 170 Mb imply that a genome size of 125 Mb for arabidopsis is an underestimate. In this study, nuclei of species pairs were compared directly using flow cytometry. Co-run Columbia and Iso-1 female gave a 2C peak for arabidopsis only approx. 15 % below that for drosophila, and 16C endopolyploid Columbia nuclei had approx. 15 % more DNA than 2C chicken nuclei (with >2280 Mb). Caenorhabditis elegans Bristol N2 (genome size approx. 100 Mb) co-run with Columbia or Iso-1 gave a 2C peak for drosophila approx. 75 % above that for 2C C. elegans, and a 2C peak for arabidopsis approx. 57 % above that for C. elegans. This confirms that 1C in drosophila is approx. 175 Mb and, combined with other evidence, leads us to conclude that the genome size of arabidopsis is not approx. 125 Mb, but probably approx. 157 Mb. It is likely that the discrepancy represents extra repeated sequences in unsequenced gaps in heterochromatic regions. Complete sequencing of the arabidopsis genome until no gaps remain at telomeres, nucleolar organizing regions or centromeres is still needed to provide the first precise angiosperm C-value as a benchmark calibration standard for plant genomes, and to ensure that no genes have been missed in arabidopsis, especially in centromeric regions, which are clearly larger than once imagined.     

Nuclear DNA content in allopolyploid species and synthetic hybrids in the grass genus Paspalum

DNA content was estimated by flow cytometry in seventeen taxa from the Dilatata, Quadrifaria and Paniculata groups of Paspalum and five synthetic hybrids. Results were compared to known genome constitutions and phylogenetic relationships. DNA 2C-values ranged from 1.24 pg in diploid P. juergensii to 3.79 pg in a hexaploid biotype of P. dilatatum. The I genome of three Quadrifaria diploids is 1.2 to 1.5-fold larger than the J genome of P. juergensii (Paniculata). The 2C-values of the IIJJ tetraploids of the Dilatata group are lower than expected based on putative genome donors. Reduction of genome sizes could have occurred after the formation of the allopolyploids of the Dilatata group. The DNA content of all synthetic hybrids is in accordance with the sum of parental C-values. The interactions driving genome downsizing may operate differently during the transition from diploidy to polyploidy than on subsequent increases in ploidy level.     

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.     

Genome size estimations on Ulmus minor Mill., Ulmus glabra Huds., and Celtis australis L. using flow cytometry

The Ulmaceae family is composed of nearly 2000 species widely distributed in the northern hemisphere. Despite their wide distribution area, there are only four native species in the Iberian Peninsula. In this work the genome size of three of those species (ULMUS MINOR, U. GLABRA, and CELTIS AUSTRALIS) was estimated using flow cytometry. The nuclear DNA content of C. AUSTRALIS was estimated as 2.46 +/- 0.061 pg/2C, of U. MINOR as 4.25 +/- 0.158 pg/2C, and of U. GLABRA as 4.37 +/- 0.103 pg/2C of DNA. No statistically significant differences were detected among individuals of the same species. These species revealed to be problematic for flow cytometric analyses, due to the release of mucilaginous compounds into the nuclear suspension. Despite that, the modified protocol here presented ensured high quality analyses (low coefficient of variation and background debris and nuclear fluorescence stability), opening good perspectives on its application to estimate the genome size of species with similar problems.     

Ploidal levels in the arctic-alpine polyploid Draba lactea (Brassicaceae) and its low-ploid relatives

Ploidal level information is of particular importance in intricate polyploid complexes such as in arctic-alpine Draba . Relative DNA content is reported for the tetra- and hexaploid D. lactea and seven of its low-ploid relatives. Flow cytometry was used to study 200 plants from 93 populations, the screening based on relative fluorescence. Absolute DNA content was determined by Feulgen densitometry for 13 plants from seven species, and reference chromosome numbers were determined in 12 plants (1–3 per species) representing six species. The plants grouped into diploids (2 n  = 16), tetraploids (2 n  = 32), hexaploids (2 n  = 48), and two triploids. Each ploidal level showed a linear increase in relative DNA content, pointing to a relatively recent polyploid origin. The diploid level was confirmed in D. nivalis, D. subcapitata, D. fladnizensis , and D. lonchocarpa. Draba palanderiana , reported previously as di-, tetra- and octoploid, was diploid in all investigated accessions. Hexa- and tetraploids were observed in D. lactea , in approximately the same ratio (8 : 1) as reported previously. The ploidal levels of the Central Asian D. altaica and D. turczaninovii are reported here for the first time as diploid and tetraploid, respectively.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 333–347.     

Evaluation of the effects of cryopreservation of isolated erythrocytes and leukocytes of largemouth bass by flow cytometry

We examined the effects of separation and freezing on fish leukocyte and erythrocyte morphology by light microscopy and on DNA content as measured by flow cytometry (FCM). Leukocytes and erythrocytes of largemouth bass Micropterus salmoides were isolated by density gradient centrifugation of whole blood, and frozen in liquid nitrogen in a buffer containing DMSO as a cryopreservative. The coefficient of variation (CV) of the G₀/G₁ peak of the cells was used to assess variation in nuclear DNA content within cell populations before and after separation and freezing treatments. In erythrocytes, the CV did not change significantly (P>0.05) when nuclei were isolated and stained without freezing or when erythrocytes were frozen prior to nuclear isolation and staining. In leukocytes, freezing and thawing prior to isolation and staining of nuclei significantly increased the CV (P<0.05), and produced hyperdiploid shoulders of the G₀/G₁ peak. However, the CV of leukocyte nuclei that were isolated and stained prior to freezing and the CV of non-frozen leukocyte nuclei did not differ (P>0.05). Microscopy showed that the freezing protocol had little effect on erythrocyte morphology, but caused irregular swelling in leukocytes. Freezing intact leukocytes also significantly (p<0.05) altered the apparent distribution of cells among the phases of the cell cycle as measured by FCM. The distributions of leukocyte nuclei that were isolated and stained prior to freezing were not different to non-frozen leukocytes. DNA measurements of nucleated blood cells are widely used in physiological, genetic and toxicological studies. Our results suggest that whole blood and erythrocytes for use in such studies can be frozen whole using a simple protocol, but leukocyte nuclei must be isolated and stained before freezing to avoid serious artifacts.     

Inter-simple sequence repeat markers and flow cytometry for the characterization of closely related Citrus limon germplasms

The genetic relationship among commercial cultivars of Citrus limon (lemon) was analysed by inter-simple sequence repeats (ISSR) and flow cytometry techniques. Two cultivars with a close germplasm were distinguished by screening 10 SSR primers and by measuring DNA content of prestained nuclei.     

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.