Shrinking genomes? Evidence from genome size variation in Crepis (Compositae)

Large-scale surveys of genome size evolution in angiosperms show that the ancestral genome was most likely small, with a tendency towards an increase in DNA content during evolution. Due to polyploidisation and self-replicating DNA elements, angiosperm genomes were considered to have a 'one-way ticket to obesity' (Bennetzen & Kellogg 1997). New findings on how organisms can lose DNA challenged the hypotheses of unidirectional evolution of genome size. The present study is based on the classical work of Babcock (1947a) on karyotype evolution within Crepis and analyses karyotypic diversification within the genus in a phylogenetic context. Genome size of 21 Crepis species was estimated using flow cytometry. Additional data of 17 further species were taken from the literature. Within 30 diploid Crepis species there is a striking trend towards genome contraction. The direction of genome size evolution was analysed by reconstructing ancestral character states on a molecular phylogeny based on ITS sequence data. DNA content is correlated to distributional aspects as well as life form. Genome size is significantly higher in perennials than in annuals. Within sampled species, very small genomes are only present in Mediterranean or European species, whereas their Central and East Asian relatives have larger 1C values.     

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.     

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 evolution in Sapindaceae at subfamily level: a case study of independence in relation to karyological and palynological traits

Sapindaceae s.l. is a moderately large family of trees, shrubs and lianas. Current knowledge on genome size and how it varies in this family is scarce. This research aims to characterize the DNA content in 39 species of Sapindaceae, mainly in tribe Paullinieae s.s., by the analysis of the variation in genome size relative to karyotypic and palynological features. Nuclear DNA amount was measured by flow cytometry, and linear regression analyses were conducted to analyse the relationship between genome size variation and various karyotypic and palynological features. Genome size varied nine‐fold among species, ranging from 1C = 0.305 pg (Lophostigma plumosum) to 2.710 pg (Cardiospermum heringeri). The low regression coefficients obtained suggest that genome size mainly varies independently of karyotypic and palynological features. With regard to karyotype evolution, the constant chromosome number but variable genome size in Houssayanthus, Paullinia and Serjania suggest that structural changes mainly caused by changes in the amounts of repetitive DNA are more important than numerical change. In contrast, in Cardiospermum and Urvillea, variation in chromosome number and genome size supports the suggestion that numerical and structural changes are important in the karyotype evolution of these genera. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 589–600.     

Punctuated genome size evolution in Liliaceae

Most angiosperms possess small genomes (mode 1C = 0.6 pg, median 1C = 2.9 pg). Those with truly enormous genomes (i.e. > or = 35 pg) are phylogenetically restricted to a few families and include Liliaceae - with species possessing some of the largest genomes so far reported for any plant as well as including species with much smaller genomes. To gain insights into when and where genome size expansion took place during the evolution of Liliaceae and the mode and tempo of this change, data for 78 species were superimposed onto a phylogenetic tree and analysed. Results suggest that genome size in Liliaceae followed a punctuated rather than gradual mode of evolution and that most of the diversification evolved recently rather than early in the evolution of the family. We consider that the large genome sizes of Liliaceae may have emerged passively rather than being driven primarily by selection.     

Nuclear DNA amounts in pacific Crustacea

Nuclear DNA amounts have been determined for 42 species of crustaceans bringing the total number of species with known nuclear DNA content to over 70. Genome size in Crustacea varies over a 25-fold range with a modal value of 2 to 3 pg haploid being common in many groups. Both average genome size and the amount of variability among species are characteristic for certain groups. A trend towards small genomes is evident in advanced and specialized crustacean groups. Somatic polyploidy is a very pronounced feature of the Crustacea. The data suggest that evolution by polyploidy may be more common in crustaceans than earlier data had indicated. These features and the presence of very characteristic satellite fractions in the nuclear DNA recommend the Crustacea for further studies in evolutionary genetics.     

Genomic diversity in two related plant species with and without sex chromosomes--Silene latifolia and S. vulgaris

Background

Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood.

Methodology/Principal Findings

We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family.

Conclusions/Significance

Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.     

不同生活型被子植物功能性状与基因组大小的关系

基因组大小在被子植物物种之间存在着巨大的变异, 但目前对不同生活型被子植物功能性状与基因组大小的关系缺乏统一的认识。本研究基于被子植物245科2,226属11,215个物种的基因组大小数据, 探讨了不同生活型物种种子重量、最大植株高度和叶片氮、磷含量4个功能性状与基因组大小之间的关系。结果表明, 被子植物最大植株高度和种子重量与基因组大小间的关系在草本和木本植物中存在显著差异。草本植物最大植株高度与基因组大小的关系不显著, 但种子重量与其呈极显著的正相关关系。木本植物最大植株高度与基因组大小显著负相关, 但种子重量与其关系不显著。木本植物叶片氮含量与基因组大小呈显著正相关, 但其他生活型植物的叶片氮、磷含量与基因组大小均无显著相关性。本研究表明被子植物功能性状与基因组大小的相关性在不同生活型间存在差异, 这为深入研究植物多种功能性状和植物生活型与基因组大小的权衡关系在植物演化和生态适应中的作用提供了重要依据。     

Genome sizes of cyclopoid copepods (Crustacea): evidence of evolutionary constraint

Genome sizes for 36 species of cyclopoid copepods were determined by DNA-Feulgen cytophotometry of nuclei from adults collected from diverse habitats and locales in North America, South America, Europe, and Asia. Genome sizes are small, show a 20-fold range ( C  = 0.10–2.02 pg DNA), and vary in a discontinuous fashion. The genomes of cyclopoid copepods are remarkably small and constant within each species, unlike the large and variable genomes of marine calanoid species. These differences may reflect the evolutionary antiquity of marine copepods in relation to marine, brackish, and freshwater copepods, as well as differences in mechanisms used to modulate genome size. The small genome sizes of contemporary cyclopoids provide substantive evidence of evolutionary constraint, possibly favouring small genomes, rapid replication rates and accelerated development as adaptive strategies for survival in often fragmented, stressful, and changing habitats. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 625–635.     

Geographical gradients in the genome size variation of wild coffee trees (Coffea) native to Africa and Indian Ocean islands

The genus Coffea, mainly native to Africa and to the Indian Ocean islands (Mascarocoffea), accounts for 124 species. Genome size data are available for 23 African species. The aim of this study was to assess the genome size of 44 Mascarocoffea species and to investigate possible association with species geographic distribution, stomata traits, and species relationships. 2?C values were measured using flow cytometry. A lyophilization procedure for leaves was tested. The 2?C nuclear DNA content of Mascarocoffea species ranged from 0.96 to 1.41?pg. Coffea mauritiana and Coffea humblotiana have the smallest genomes and Coffea millotii has the largest. Mean 2?C DNA for Mascarocoffea and Africa is 1.19 and 1.43?pg, respectively. The overall DNA values corresponded to two partially overlapped normal distributions: one harboring species from east Africa Mascarocoffea, the other harboring species from west/central Africa. Plotted on a geographical map according to the native origin of species, these values showed a gradient in Madagascar and Africa. Genome sizes increased following a north to southeast gradient in Madagascar and an east to west gradient in Africa. None, or only weak correlations were noted between genome size and stomata parameters. Genetically close species could be highly distinctive in their genome size while divergent species could be similarly sized. The non-random geographic distribution and habitat of species, and the absence of correlation between genome size and genetic relationships, suggest that during Coffea genome evolution, both DNA content increase and/or decrease occurred independently in Africa and in the Indian Ocean Islands.     

Large genomes among caridean shrimp.

Recent genome size estimates for Arctic amphipods have revealed the largest genomes known in the Crustacea. Here we provide additional data for 7 species of caridean shrimp collected from the Canadian Arctic and the Gulf of St. Lawrence. Genome sizes were estimated by flow cytometry and haploid C-values ranged from 8.53 +/- 0.30 pg in Pandalus montagui (Pandalidae) to 40.89 +/- 1.23 pg in Sclerocrangon ferox (Crangonidae). The value for S. ferox represents the largest decapod genome yet recorded and indicates a 38-fold variation in genome size within this order. These data suggest that large genomes may be relatively common in Arctic crustaceans, and underline the need for further comparative studies.     

Genome size diversity in orchids: consequences and evolution

Background

The amount of DNA comprising the genome of an organism (its genome size) varies a remarkable 40 000-fold across eukaryotes, yet most groups are characterized by much narrower ranges (e.g. 14-fold in gymnosperms, 3- to 4-fold in mammals). Angiosperms stand out as one of the most variable groups with genome sizes varying nearly 2000-fold. Nevertheless within angiosperms the majority of families are characterized by genomes which are small and vary little. Species with large genomes are mostly restricted to a few monocots families including Orchidaceae.

Scope

A survey of the literature revealed that genome size data for Orchidaceae are comparatively rare representing just 327 species. Nevertheless they reveal that Orchidaceae are currently the most variable angiosperm family with genome sizes ranging 168-fold (1C = 0·33–55·4 pg). Analysing the data provided insights into the distribution, evolution and possible consequences to the plant of this genome size diversity.

Conclusions

Superimposing the data onto the increasingly robust phylogenetic tree of Orchidaceae revealed how different subfamilies were characterized by distinct genome size profiles. Epidendroideae possessed the greatest range of genome sizes, although the majority of species had small genomes. In contrast, the largest genomes were found in subfamilies Cypripedioideae and Vanilloideae. Genome size evolution within this subfamily was analysed as this is the only one with reasonable representation of data. This approach highlighted striking differences in genome size and karyotype evolution between the closely related Cypripedium, Paphiopedilum and Phragmipedium. As to the consequences of genome size diversity, various studies revealed that this has both practical (e.g. application of genetic fingerprinting techniques) and biological consequences (e.g. affecting where and when an orchid may grow) and emphasizes the importance of obtaining further genome size data given the considerable phylogenetic gaps which have been highlighted by the current study.Key words: AFLP, C-value, chromosome, evolution, genome size, guard cell size, Orchidaceae, Robertsonian fission, Robertsonian fusion     

Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids

Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2–5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12–90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.     

Polyploidy does not control all: Lineage‐specific average chromosome length constrains genome size evolution in ferns

Recent studies investigating the evolution of genome size diversity in ferns have shown that they have a distinctive genome profile compared with other land plants. Ferns are typically characterized by possessing medium‐sized genomes, although a few lineages have evolved very large genomes. Ferns are different from other vascular plant lineages as they are the only group to show evidence for a correlation between genome size and chromosome number. In this study, we aim to explore whether the evolution of fern genome sizes is not only shaped by chromosome number changes arising from polyploidy but also by constraints on the average amount of DNA per chromosome. We selected the genus Asplenium L. as a model genus to study the question because of the unique combination of a highly conserved base chromosome number and a high frequency of polyploidy. New genome size data for Asplenium taxa were combined with existing data and analyzed within a phylogenetic framework. Genome size varied substantially between diploid species, resulting in overlapping genome sizes among diploid and tetraploid spleenworts. The observed additive pattern indicates the absence of genome downsizing following polyploidy. The genome size of diploids varied non‐randomly and we found evidence for clade‐specific trends towards larger or smaller genomes. The 578‐fold range of fern genome sizes have arisen not only from repeated cycles of polyploidy but also through clade‐specific constraints governing accumulation and/or elimination of DNA.     

SYMBIODINIUM (PYRRHOPHYTA) GENOME SIZES (DNA CONTENT) ARE SMALLEST AMONG DINOFLAGELLATES1

Using flow cytometric analysis of fluorescence, we measured the genome sizes of 18 cultured “free‐living” species and 29 Symbiodinium spp. isolates cultured from stony corals, gorgonians, anemones, jellyfish, and giant clams. Genome size directly correlated with cell size, as documented previously for most eukaryotic cell lines. Among the smallest of dinoflagellates, Symbiodinium spp. (6–15 μm) possessed the lowest DNA content that we measured (1.5–4.8 pg·cell^?1). Bloom‐forming or potentially harmful species in the genera Alexandrium, Karenia, Pfiesteria, and Prorocentrum possessed genomes approximately 2 to 50 times larger in size. A phylogenetic analysis indicated that genome/cell size has apparently increased and decreased repeatedly during the evolution of dinoflagellates. In contrast, genome sizes were relatively consistent across distantly and closely related Symbiodinium spp. This may be the product of intracellular host habitats imposing strong selective pressures that have restricted symbiont size.     

Nuclear DNA content of Vitis species,cultivars, and other genera of the Vitaceae

The nuclear DNA content was analyzed in Vitis species, hybrid cultivars, and genera of the Vitaceae using flow cytometry. Significant variation was found among Vitis species, hybrids, and other genera of the Vitaceae (Ampelopsis and Parthenocissus). DNA content was estimated to range from 0.98 to 1.05 pg/2C within V. labrusca (ns) and 0.86 to 1.00 pg/2C within V. vinifera (ns). Genotypes from Vitis and Parthenocissus were similar in nuclear DNA content (approximately 1.00 pg/2C) whereas they differed significantly from Ampelopsis (1.39 pg/2C). No correlation between DNA content and the center of origin of genotypes of the Vitaceae was noted. Based on the present study, the Vitis genome size is 475 Mbp, 96% of which is non-coding. Knowledge of DNA content is useful in order to understand the complexity of the Vitis genome and to establish a relationship between the genetic and physical map for map-based cloning.     

Is genome size of Lepidoptera linked to host plant range?

Genome size varies considerably among organisms, largely as the result of differences in the content of non‐coding and/or repetitive DNA, such as introns, pseudogenes, or transposable elements, as well as whole‐genome duplications. Genome size is known to correlate with metabolic rates. Because polyphagy also affects the metabolism, a correlation between diet specialization and genome size can be expected. To test this hypothesis, a study was undertaken with five closely related species of stem borers which are easy to rear under artificial conditions, namely Busseola fusca (Fuller), Busseola segeta (Bowden), Busseola nairobica Le Ru, Sesamia calamistis Hampson, and Sesamia nonagrioides Lefebvre (all Lepidoptera: Noctuidae). However, as the number of species was too low for correlating diet with genome size in Lepidoptera in general, literature data from 16 Lepidoptera species were used in addition. The results pointed to a relationship between genome size and the insect's host plant range in Lepidoptera, but below the family level only, with larger genomes in polyphagous compared to specialist species. In addition, the genome size appeared to be influenced not only by host plant range but also by environmental/climatic conditions. Studies to test this hypothesis should be done strictly below the family level.     

Conifer genome sizes of 172 species,covering 64 of 67 genera,range from 8 to 72 picogram

Nuclear genome size of conifers as measured by flow cytometry with propidium iodide was investigated, striving to collect at least a single species from each genus. 64 out of 67 genera and 172 species were measured. Of the 67 genera, 21 are reported here for the first time and the same is true for 76 species. This nearly doubles the number of measured genera and adds 50% to the number of analyzed species. Conifers have chromosome numbers in the range of n = (7)10–12(19). However, the nuclear DNA content (2C‐value) is shown here to range from 8.3 to 71.6 picogram. The largest genome contains roughly 6 × 10¹⁰ more base pairs than the smallest genome. Genome sizes are evaluated and compared with available taxonomic treatments. For the mainly (sub)tropical Podocarpaceae small genome sizes were found with a 2C‐value of only 8–28 pg, with 13.5 pg on average. For the Taxaceae 2C‐values from 23–60 pg were determined. Not surprisingly, the genus Pinus with 97 species (39 species measured here) has a broad range with 2C = 38–72 pg. A factor of 2 difference is also found in the Cupressaceae (136 species) with nuclear DNA contents in the range 18–35 pg. Apart from the allohexaploid Sequoia, ploidy plays a role only in Juniperus and some new polyploids are found. The data on genome size support conclusions on phylogenetic relationships obtained by DNA sequencing. Flow cytometry is applicable even to young plants or seeds for the monitoring of trade in endangered species.     

Sauropod dinosaurs evolved moderately sized genomes unrelated to body size

Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77–2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97–2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05–5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.     

Chromosome numbers and DNA content in Bromeliaceae: additional data and critical review

For the large Neotropical plant family Bromeliaceae, we provide new data on chromosome numbers, cytological features and genome size estimations, and combine them with data available in the literature. Root‐tip chromosome counts for 46 species representing four subfamilies and a literature review of previously published data were carried out. Propidium iodide staining and flow cytometry were used to estimate absolute genome sizes in five subfamilies of Bromeliaceae, sampling 28 species. Most species were diploid with 2n = 50 in Bromelioideae, Puyoideae and Pitcairnioideae, followed by 2n = 48 observed mainly in Tillandsioideae. Individual chromosome sizes varied more than tenfold, with the largest chromosomes observed in Tillandsioideae and the smallest in Bromelioideae. Genome sizes (2C‐values) varied from 0.85 to 2.23 pg, with the largest genomes in Tillandsioideae. Genome evolution in Bromeliaceae relies on two main mechanisms: polyploidy and dysploidy. With the exception of Tillandsioideae, polyploidy is positively correlated with genome size. Dysploidy is suggested as the mechanism responsible for the generation of the derived chromosome numbers, such as 2n = 32/34 or 2n = 48. The occurrence of B chromosomes in the dysploid genus Cryptanthus suggests ongoing speciation processes closely associated with chromosome rearrangements. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 349–368.