Chromosome and genome size variation in Luzula (Juncaceae), a genus with holocentric chromosomes

The present study examines chromosome and genome size evolution in Luzula (woodrush; Juncaceae), a monocot genus with holocentric chromosomes. Detailed karyotypes and genome size estimates were obtained for seven Luzula spp., and these were combined with additional data from the literature to enable a comprehensive cytological analysis of the genus. So that the direction of karyotype and genome size changes could be determined, the cytological data were superimposed onto a phylogenetic tree based on the trnL‐F and internal transcribed spacer (ITS) DNA regions. Overall, Luzula shows considerable cytological variation both in terms of chromosome number (2n = 6–66) and genome size (15‐fold variation; 2C = 0.56–8.51 pg; 547.7–8322.8 Mb). In addition, there is considerable diversity in the genomic mechanisms responsible, with the range of karyotypes arising via agmatoploidy (chromosome fission), symploidy (chromosome fusion) and/or polyploidy accompanied, in some cases, by the amplification or elimination of DNA. Viewed in an evolutionary framework, no broad trend in karyotype or genome evolution was apparent across the genus; instead, different mechanisms of karyotype evolution appear to be operating in different clades. It is clear that Luzula exhibits considerable genomic flexibility and tolerance to large, genome‐scale changes. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 529–541.     

Karyological studies in Tripleurospermum (Asteraceae, Anthemideae) from north-east Anatolia

Chromosome number and morphology in 14 taxa belonging to 19 populations of Tripleurospermum Sch. Bip. were studied using karyological and numerical taxonomical techniques. Data on chromosome measurements were analysed using cluster analysis. Chromosome numbers of these taxa are 2 n  = 2 x  = 18, 4 x  = 36 and 5 x  = 42–48. Seven records are new, two are not consistent with previous counts, and the remainder confirm the very limited previous data (one to three records). A new ploidy level (pentaploidy) is reported for the first time for the genus. Some correlations between ploidy levels and morphological characters are noted and several systematic and evolutionary aspects of the genus are discussed in the light of karyological data.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 146 , 427–438.     

The dynamic ups and downs of genome size evolution in Brassicaceae

Crucifers (Brassicaceae, Cruciferae) are a large family comprisingsome 338 genera and c. 3,700 species. The family includes importantcrops as well as several model species in various fields ofplant research. This paper reports new genome size (GS) datafor more than 100 cruciferous species in addition to previouslypublished C-values (the DNA amount in the unreplicated gameticnuclei) to give a data set comprising 185 Brassicaceae taxa,including all but 1 of the 25 tribes currently recognized. Evolutionof GS was analyzed within a phylogenetic framework based ongene trees built from five data sets (matK, chs, adh, trnLF,and ITS). Despite the 16.2-fold variation across the family,most Brassicaceae species are characterized by very small genomeswith a mean 1C-value of 0.63 pg. The ancestral genome size (ancGS)for Brassicaceae was reconstructed as ^anc1C = 0.50 pg. Approximately50% of crucifer taxa analyzed showed a decrease in GS comparedwith the ancGS. The remaining species showed an increase inGS although this was generally moderate, with significant increasesin C-value found only in the tribes Anchonieae and Physarieae.Using statistical approaches to analyze GS, evolutionary gainsor losses in GS were seen to have accumulated disproportionatelyfaster within longer branches. However, we also found that GShas not changed substantially through time and most likely evolvespassively (i.e., a tempo that cannot be distinguished betweenneutral evolution and weak forms of selection). The data revealan apparent paradox between the narrow range of small GSs overlong evolutionary time periods despite evidence of dynamic genomicprocesses that have the potential to lead to genome obesity(e.g., transposable element amplification and polyploidy). Toresolve this, it is suggested that mechanisms to suppress amplificationand to eliminate amplified DNA must be active in Brassicaceaealthough their control and mode of operation are still poorlyunderstood.     

Role of adaptive and non-adaptive mechanisms forming complex patterns of genome size variation in six cytotypes of polyploid Allium oleraceum (Amaryllidaceae) on a continental scale

Background and Aims

Although the large variation in genome size among different species is widely acknowledged, the occurrence and extent of variation below the species level are still controversial and have not yet been satisfactorily analysed. The aim of this study was to assess genome size variation in six ploidy levels (2n = 3x–8x) of the polyploid Allium oleraceum over a large geographical gradient and to search for potential interpretations of the size variation.

Methods

The genome sizes of 407 individuals of A. oleraceum collected from 114 populations across Europe were determined by flow cytometry using propidium iodide staining. The genome size variation was correlated with spatial, climatic and habitat variables.

Key Results

The mean holoploid genome size (2C DNA) was 42·49, 52·14, 63·34, 71·94, 85·51 and 92·12 pg at the tri-, tetra-, penta-, hexa-, hepta- and octoploid levels, respectively. Genome size varied from a minimum of 2·3 % in the octoploids to a maximum of 18·3 % in the tetraploids. Spatial structuring of genome size was observed within the tetra- and pentaploids, where 2C DNA significantly increased with both latitude and longitude, and correlated with several climatic variables, suggesting a gradient of continentality. Genome size in hexaploids showed low variation, weak correlation with climatic variables and no spatial structuring. Downsizing in monoploid genome size was observed between all cytotypes except for heptaploids. Splitting populations into western and eastern European groups resulted in strong differences in monoploid genome size between groups in tetra- and pentaploids but not in hexaploids. The monoploid genome sizes of the cytotypes were similar in the western group but diverged in the eastern group.

Conclusions

Complex patterns of holoploid and monoploid genome size variation found both within and between A. oleraceum cytotypes are most likely the result of several interacting factors, including different evolutionary origins of cytotypes via hybridization of parental combinations with different genome sizes in the south-western and south-eastern part of Europe, introgression between cytotypes, and antropic dispersal. The role of broad-scale and fine-scale environmental variables in shaping genome size is probably of minor importance in A. oleraceum.     

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.     

Genetic diversity of Allium munzii (Amaryllidaceae), a rare southern California species and implication for its conservation

An understanding of genetic diversity within and among populations of rare plant species is a prerequisite to develop effective conservation management strategies and reintroduction programs. Allium munzii is a narrow endemic species distributed in western Riverside County, California, USA and known from 18 extant element occurrences. We sampled 119 individuals from 11 element occurrences and investigated within and among population genetic diversity using two variable chloroplast markers (rpL32–trnL intergenic spacer and rpoC1 intron). Of the total genetic variation detected in A. munzii, 87.65% was due to differences among occurrences. Furthermore, our results revealed that most of the element occurrences are strongly genetically differentiated. There are low levels of gene flow between occurrences, not due to isolation by distance but possibly resulting from habitat fragmentation. Non-significant values of Tajima's D and Fu's Fs were found in all occurrences suggesting no demographic expansion in A. munzii. Ex situ seed and bulb conservation is recommended to enable introduction of individuals to occurrences with low abundance and genetic diversity.     

Genome size and karyotype evolution in the slipper orchids (Cypripedioideae: Orchidaceae)

Nuclear DNA contents (4C) were estimated by Feulgen microdensitometry in 27 species of slipper orchids. These data and recent information concerning the molecular systematics of Cypripedioideae allow an interesting re-evaluation of karyotype and genome size variation among slipper orchids in a phylogenetic context. DNA amounts differed 5.7-fold, from 24.4 pg in Phragmipedium longifolium to 138.1 pg in Paphiopedilum wardii. The most derived clades of the conduplicate-leaved slipper orchids have undergone a radical process of genome fragmentation that is most parsimoniously explained by Robertsonian changes involving centric fission. This process seems to have occurred independently of genome size variation. However, it may reflect environmental or selective pressures favoring higher numbers of linkage groups in the karyotype.     

A karyological study of Asphodelus L. (Asphodelaceae) from the Western Mediterranean

The following aspects of Asphodelus karyology are analysed: base number, polyploidy, chromosome size, chromosome morphology, satellited chromosomes, structural heteromorphism, karyotype asymmetry and karyotype evolution. The base number 0 ×= 14 is common to all species except for A. refractus , which has the derived ×= 13. Three ploidy levels occur, often in the same species; diploid, tetraploid and hexaploid, with 2n = 28, 56 and 84. Chromosomes are generally small to medium-small, with the occasional presence of medium-large chromosomes. The most frequent chromosome types are metacentric of type m and submetacentric. Metacentric chromosomes of type M occur only in sections. Verineopsis, Verinea and Plagiasphodelus ; subtelocentric chromosomes occur only in sections Asphodelus and Plagiasphodelus. There is a wide variability in relation to the number of satellited chromosomes, relative to ploidy level. There are usually two to four in diploids, four to eight in tetraploids and usually six, exceptionally up to 12, in the hexaploid. Satellites are present on the shortest arm, exceptionally on the longest arm. There is a high degree of structural heteromorphism in practically all the species which affects satellited and non satellited chromosomes. Karyotype asymmetry is generally of type 2B. Inter-and intra-chromosomal differences are estimated by the A1 and A2 indexes. Both indices vary in the karyotype evolution of the genus, with a decrease of A1 and an increase of A2. The role of polyploidy, hybridization, asymmetry and decrease of chromosome size in the evolution of Asphodelus is discussed.     

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.     

A novel indicator of karyotype evolution in the tribe Leucocoryneae (Allioideae,Amaryllidaceae)

Journal of Plant Research - The tribe Leucocoryneae is taxonomically and cytogenetically complex, mainly due to its extraordinary morphological and karyological variation. Robertsonian...     

Chromosome evolution in the genus Mikania (Compositae)

Karyotypic analysis of ten species of the genus Mikania was carried out using Feulgen staining. Species belonging to the following sections were analyzed: Section Thyrsigerae containing M. additicia (2n = 34), M. hemisphaerica, M. lanuginosa, and M. punctata (2n = 36), and Mikania sericea (2n = 42), which adds a new basic chromosome number (x = 21) to the genus and to the tribe Eupatorieae; Section Corymbosae with M. hastato-cordata (2n = 34) and M. involucrata and M. microptera with 2n = 36 chromosomes; Section Spicato-Racemosae with M. sessilifolia, with 2n = 108 chromosomes. One unidentified species with 2n = 34 chromosomes was also analyzed. All the species studied show one large pair of chromosomes with a secondary constriction in the middle region of the long arm. The morphology of this chromosome suggests that it can be considered as a cytological marker for the genus. Because of the distinctive inflorescence types found in the genus Mikania and the high frequency of species with x = 18, a correlation between morphological and chromosomal evolution is discussed. The present study suggests that the basic original chromosome number for the genus is x = 18, from which the others (x = 17, 19, 20, 21) have been derived by aneuploidy to form the observed aneuploid series.     

Bulb tunic anatomy and its taxonomic implication in Allium L. (Amaryllidaceae: Allioideae)

Abstract

Allium is taxonomically a difficult genus with blurred taxonomic borders at all taxonomic ranks. In this research, anatomy and morphology of bulb tunics in 42 species of the genus representing its 16 currently recognized sections and 6 subgenera (Allium, Cepa, Reticulatobulbosa, Amerallium, Polyprason and Melanocrommyum) were investigated. Our results indicated the following characters to be most informative at sectional and subgeneric levels: features of calcium oxalate crystals and subepidermal cell layer of the outermost bulb tunic, type of tracheids, and bulbils presence. Three main types of crystals, i.e. prismatic, sand and druses, were fairly common among the investigated species except for the members of A. sect. Acanthoprason (A. subg. Melanocrommyum) that often lack crystals. The subepidermal layers of outer tunics were mostly composed of hexagonal, rectangular, or elongated cells but A. paradoxum (A. subg. Amerallium, sect. Briseis) showed the pentagonal type and A. longisepalum (A. subg. Amerallium, sect. Molium) the elliptic type of subepidermal cells. The members of A. sub. Melanocrommyum showed various types of tunic cells and crystals.     

Evolution of genome space occupation in ferns: linking genome diversity and species richness

Background and AimsThe dynamics of genome evolution caused by whole genome duplications and other processes are hypothesized to shape the diversification of plants and thus contribute to the astonishing variation in species richness among the main lineages of land plants. Ferns, the second most species-rich lineage of land plants, are highly suitable to test this hypothesis because of several unique features that distinguish fern genomes from those of seed plants. In this study, we tested the hypothesis that genome diversity and disparity shape fern species diversity by recording several parameters related to genome size and chromosome number.MethodsWe conducted de novo measurement of DNA C-values across the fern phylogeny to reconstruct the phylogenetic history of the genome space occupation in ferns by integrating genomic parameters such as genome size, chromosome number and average DNA amount per chromosome into a time-scaled phylogenetic framework. Using phylogenetic generalized least square methods, we determined correlations between chromosome number and genome size, species diversity and evolutionary rates of their transformation.Key ResultsThe measurements of DNA C-values for 233 species more than doubled the taxon coverage from ~2.2 % in previous studies to 5.3 % of extant diversity. The dataset not only documented substantial differences in the accumulation of genomic diversity and disparity among the major lineages of ferns but also supported the predicted correlation between species diversity and the dynamics of genome evolution.ConclusionsOur results demonstrated substantial genome disparity among different groups of ferns and supported the prediction that alterations of reproductive modes alter trends of genome evolution. Finally, we recovered evidence for a close link between the dynamics of genome evolution and species diversity in ferns for the first time.     

Satellite DNA and chromosomes in Neotropical fishes: methods,applications and perspectives

Constitutive heterochromatin represents a substantial portion of the eukaryote genome, and it is mainly composed of tandemly repeated DNA sequences, such as satellite DNAs, which are also enriched by other dispersed repeated elements, including transposons. Studies on the organization, structure, composition and in situ localization of satellite DNAs have led to consistent advances in the understanding of the genome evolution of species, with a particular focus on heterochromatic domains, the diversification of heteromorphic sex chromosomes and the origin and maintenance of B chromosomes. Satellite DNAs can be chromosome specific or species specific, or they can characterize different species from a genus, family or even representatives of a given order. In some cases, the presence of these repeated elements in members of a single clade has enabled inferences of a phylogenetic nature. Genomic DNA restriction, using specific enzymes, is the most frequently used method for isolating satellite DNAs. Recent methods such as C₀t–1 DNA and chromosome microdissection, however, have proven to be efficient alternatives for the study of this class of DNA. Neotropical ichthyofauna is extremely rich and diverse enabling multiple approaches with regard to the differentiation and evolution of the genome. Genome components of some species and genera have been isolated, mapped and correlated with possible functions and structures of the chromosomes. The 5SHindIII‐DNA satellite DNA, which is specific to Hoplias malabaricus of the Erythrinidae family, has an exclusively centromeric location. The As51 satellite DNA, which is closely correlated with the genome diversification of some species from the genus Astyanax, has also been used to infer relationships between species. In the Prochilodontidae family, two repetitive DNA sequences were mapped on the chromosomes, and the SATH 1 satellite DNA is associated with the origin of heterochromatic B chromosomes in Prochilodus lineatus. Among species of the genus Characidium and the Parodontidae family, amplifications of satellite DNAs have demonstrated that these sequences are related to the differentiation of heteromorphic sex chromosomes. The possible elimination of satellite DNA units could explain the genome compaction that occurs among some species of Neotropical Tetraodontiformes. These topics are discussed in the present review, showing the importance of satellite DNA analysis in the differentiation and karyotype evolution of Actinopterygii.     

Karyotype evolution and cytotaxonomy in Brazilian species of Rhynchospora Vahl (Cyperaceae)

Karyotypes were analysed in 113 populations of 34 species of Rhynchospora (Cyperaceae). They showed typical holocentric chromosomes lacking primary constrictions. Nucleolar constrictions were observed in the terminal regions of a few chromosomes (except in R. nanuzae , in which they were interstitial). The chromosome numbers varied between 2 = 4 and 2n = 50. The primary base number seems to be x = 5; x = 6 and x = 9 are secondary. Dysploidy occurred at low frequency, whereas polyploidy seemed to be the predominant event in the karyotype evolution of the genus. Karyotypic differences were found in R. consanguinea var. speciosa and R. consanguinea var. rigida and the closely related R. emaciata, R. riparia and R. tenuis from section Tenues. On the other hand, karyotypic similarities occurred among sections Valderugosae, Marisculae, Stenophylku and Cemuae.     

Chromosome studies in Hippeastrum (Amaryllidaceae): variation in genome size

This paper presents the karyotype and DNA content of 12 diploid species of Hippeastrum from South America. The variation in genome size is compared with the karyotype and DNA content of Amaryllis belladonna from South Africa. The Hippeastrum species present a uniform and bimodal basic karyotype formula, but significant differences are found in the total chromosome volume (TCV) and nuclear DNA content. A positive correlation between the DNA content and TCV is also observed. The karyotype's constancy is a product of changes in DNA content occurring in the whole chromosome complement. The DNA addition to the long and short sets of chromosomes varies independently. In species with higher DNA contents, the short chromosomes add equal DNA amounts to both arms, maintaining their metacentric morphology, whereas the long chromosomes add DNA only to the short arm, increasing the chromosome symmetry. These data show that the evolutionary changes in DNA amount are proportional to chromosome length, maintaining the karyotypic uniformity. A. belladonna has a larger DNA content and possesses a karyotype different from that of Hippeastrum spp., supporting the distinction between the two genera and upholding the name Amaryllis for the South African entity against Hippeastrum for the South American genus.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 171–178.