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

The ecological adaptation of the unparalleled plastome character evolution in slipper orchids

Plastomes may have undergone adaptive evolution in the process of plant adaptation to diverse environments, whereby species may differ in plastome characters. Cypripedioideae successfully colonized distinct environments and could be an ideal group for studying the interspecific variation and adaptive evolution of plastomes. Comparative study of plastomes, ancestral state reconstruction, phylogenetic-based analysis, ecological niche modelling, and selective pressure analysis were conducted to reveal the evolutionary patterns of plastomes in Cypripedioideae and their relationship with environmental factors. The plastomes of the three evolved genera had reduced plastome size, increased GC content, and compacted gene content compared to the basal group. Variations in plastome size and GC content are proved to have clear relationships with climate regions. Furthermore, ecological niche modelling revealed that temperature and water factors are important climatic factors contributing to the distributional difference which is directly correlated with the climate regions. The temperature-sensitive genes ndh genes, infA, and rpl20 were found to be either lost/pseudogenized or under positive selection in the evolved groups. Unparalleled plastome character variations were discovered in slipper orchids. Our study indicates that variations in plastome characters have adaptive consequences and that temperature and water factors are important climatic factors that affect plastome evolution. This research highlights the expectation that plants can facilitate adaptation to different environmental conditions with the changes in plastome and has added critical insight for understanding the process of plastome evolution in plants.

Comparative Analyses of Chloroplast Genomes Provide Comprehensive Insights into the Adaptive Evolution of Paphiopedilum (Orchidaceae)

An elucidation of how the selection pressures caused by habitat environments affect plant plastid genomes and lead to the adaptive evolution of plants, is a very intense area of research in evolutionary biology. The genus Paphiopedilum is a predominant group of orchids that includes over 66 species with high horticultural and ornamental value. However, owing to the destructive exploitation and habitat deterioration of wild germplasm resources of Paphiopedilum, it needs more molecular genetic resources and studies on this genus. The chloroplast is cytoplasmically inherited and often used in evolutionary studies. Thus, for this study, we newly sequenced, assembled and annotated five chloroplast genomes of the Paphiopedilum species. The size of these genomes ranged from 155,886 bp (P. henryanum) to 160,503 bp (P. ‘GZSLKY’ Youyou) and they contained 121–122 genes, which consisted of 76 protein coding genes, eight ribosomal RNAs, and 37–38 transfer RNAs. Combined with the other 14 Paphiopedilum species, the characteristics of the repeat sequences, divergent hotspot regions, and the condo usage bias were evaluated and identified, respectively. The gene transfer analysis showed that some fragments of the ndh and ycf gene families were shared by both the chloroplast and nucleus. Although the genomic structure and gene content was conserved, there was a significant boundary shift caused by the inverted repeat (IR) expansion and small single copy (SSC) contraction. The lower GC content and loss of ndh genes could be the result of adaptive evolutionary responses to its unique habitats. The genes under positive selection, including accD, matK, psbM, rpl20, rps12, ycf1, and ycf2 might be regarded as potential candidate genes for further study, which significantly contribute to the adaptive evolution of Paphiopedilum.

Genome Size and Labellum Epidermal Cell Size Are Evolutionarily Correlated With Floral Longevity in Paphiopedilum Species

Genome size is known to influence phenotypic traits in leaves and seeds. Although genome size is closely related to cellular and developmental traits across biological kingdoms, floral longevity is a floral trait with important fitness consequence, but less is known about the link between floral longevity and sizes of genomes and cells. In this study, we examined evolutionary coordination between genome size, floral longevity, and epidermal cell size in flowers and leaves in 13 Paphiopedilum species. We found that, across all the study species, the genome size was positively correlated with floral longevity but negatively associated with labellum epidermal cell size, and a negative relationship was found between floral longevity and labellum epidermal cell size. This suggested that genome size is potentially correlated with floral longevity, and genome size has an important impact on life-history trait. In addition, genome size was positively correlated with leaf epidermal cell size, which was different from the relationship in flower due to different selective pressures they experienced or different functions they performed. Therefore, genome size constraints floral longevity, and it is a strong predictor of cell size. The impact of genome size on reproduction might have more implications for the evolution of flowering plants and pollination ecology.

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

Changes in chromosome number and karyotype evolution are important to plant diversification, as they are both major drivers of speciation processes. Herein, chromosome number, karyotype, and genome size of the Korean lady's slipper orchid Cypripedium japonicum Thunb., an endangered species, were investigated in natural populations. Furthermore, all cytological data from this species are reported herein for the first time. The chromosome number of all investigated C. japonicum plants was diploid (2n = 2x = 22), with x = 11 as base chromosome number, whereby the species can now be clearly distinguished from the Japanese lady's slipper orchid. The karyotypes of all studied individuals were of similar length, symmetrical, and rather unimodal. Flow cytometry of the C. japonicum revealed that the genome size ranged from 28.38 to 30.14 pg/1C. Data on chromosome number and karyotypes were largely consistent with previous results indicating that Korean (x = 11) populations of C. japonicum are more closely related to Chinese populations (x = 11) compared to Japanese (x = 10) populations. These comprehensive cytological results will benefit the efforts to discriminate the geographically isolated and endangered Eastern Asian (China, Japan, and Korea) lady's slipper orchid species.

Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability

Angraecoid orchids present a remarkable diversity of chromosome numbers, which makes them a highly suitable system for exploring the impact of karyotypic changes on cladogenesis, diversification and morphological differentiation. We compiled an annotated cytotaxonomic checklist for 126 species of Angraecinae, which was utilised to reconstruct chromosomal evolution using a newly-produced, near-comprehensive phylogenetic tree that includes 245 angraecoid taxa. In tandem with this improved phylogenetic framework, using combined Bayesian, maximum likelihood and parsimony approaches on ITS-1 and five plastid markers, we propose a new cladistic nomenclature for the angraecoids, and we estimate a new timeframe for angraecoid radiation based on a secondary calibration, and calculate diversification rates using a Bayesian approach. Coincident divergence dates between clades with identical geographical distributions in the angraecoids and the pantropical orchid genus Bulbophyllum suggest that the same events may have intervened in the dispersal of these two epiphytic groups between Asia, continental Africa, Madagascar and the Neotropics. The major angraecoid lineages probably began to differentiate in the Middle Miocene, and most genera and species emerged respectively around the Late Miocene-Pliocene boundary and the Pleistocene. Ancestral state reconstruction using maximum likelihood estimation revealed an eventful karyotypic history dominated by descending dysploidy. Karyotypic shifts seem to have paralleled cladogenesis in continental tropical Africa, where approximately 90% of the species have descended from at least one inferred transition from n = 17-18 to n = 25 during the Middle Miocene Climatic Transition, followed by some clade-specific descending and ascending dysploidy from the Late Miocene to the Pleistocene. Conversely, detected polyploidy is restricted to a few species lineages mostly originating during the Pleistocene. No increases in net diversification could be related to chromosome number changes, and the apparent net diversification was found to be highest in Madagascar, where karyotypic stasis predominates. Finally, shifts in chromosome number appear to have paralleled the evolution of rostellum structure, leaflessness, and conspicuous changes in floral colour.

Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization

BACKGROUND

Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA.

RESULTS

SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific.

CONCLUSIONS

We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.

Post-polyploid diploidization and diversification through dysploid changes

Whole-genome duplications are widespread across land plant phylogenies and particularly frequent in ferns and angiosperms. Genome duplications spurred the evolution of key innovations associated with diversification in many angiosperm clades and lineages. Such diversifications are not initiated by genome doubling per se. Rather, differentiation of the primary polyploid populations through a range of processes results in post-polyploid genome diploidization. Structural diploidization gradually reverts the polyploid genome to one functionally diploid-like through chromosomal rearrangements which frequently result in dysploid changes. Dysploidies may lead to reproductive isolation among post-polyploid offspring and significantly contribute to speciation and cladogenetic events.

Taxonomic placement of Paphiopedilum rungsuriyanum (Cypripedioideae; Orchidaceae) based on morphological, cytological and molecular analyses

BACKGROUND

Paphiopedilum rungsuriyanum from Northern Laos was discovered and described in 2014. It is characterized by having miniature tessellated leaves, a flower having a helmet shaped lip with a V-shaped neckline, and a semi-lunate, 3-dentate staminode with an umbo. These morphological features distinguish P. rungsuriyanum from the other known sections/subgenera of Paphiopedilum, making it difficult to group with existing infrageneric units.

RESULTS

Paphiopedilum rungsuriyanum has chromosome number of 2n = 26. Fluorescence in situ hybridization study demonstrates that there are two 45S rDNA signals in the telomeric region of chromosomes, and more than 20 5S rDNA signals dispersed signals in the pericentromeric and centromeric regions. Phylogenetic analyses based on four nuclear (i.e. ITS, ACO, DEF4 and RAD51) and four plastid (i.e. atpI-atpH, matK, trnS-trnfM and ycf1) gene regions indicate that P. rungsuriyanum is nested in subgenus Paphiopedilum and is a sister to section Paphiopedilum.

CONCLUSIONS

The results in combination with karyomorphological, rDNA FISH patterns, morphological and phylogenetic analyses suggest a new section Laosianum to accommodate this species in the current sectional circumscription of subgenus Paphiopedilum.

Detecting Mechanisms of Karyotype Evolution in Heterotaxis (Orchidaceae)

The karyotype is shaped by different chromosome rearrangements during species evolution. However, determining which rearrangements are responsible for karyotype changes is a challenging task and the combination of a robust phylogeny with refined karyotype characterization, GS measurements and bioinformatic modelling is necessary. Here, this approach was applied in Heterotaxis to determine what chromosome rearrangements were responsible for the dysploidy variation. We used two datasets (nrDNA and cpDNA, both under MP and BI) to infer the phylogenetic relationships among Heterotaxis species and the closely related genera Nitidobulbon and Ornithidium. Such phylogenies were used as framework to infer how karyotype evolution occurred using statistical methods. The nrDNA recovered Ornithidium, Nitidobulbon and Heterotaxis as monophyletic under both MP and BI; while cpDNA could not completely separate the three genera under both methods. Based on the GS, we recovered two groups within Heterotaxis: (1) "small GS", corresponding to the Sessilis grade, composed of plants with smaller genomes and smaller morphological structure, and (2) "large GS", corresponding to the Discolor clade, composed of plants with large genomes and robust morphological structures. The robust karyotype modeling, using both nrDNA phylogenies, allowed us to infer that the ancestral Heterotaxis karyotype presented 2n = 40, probably with a proximal 45S rDNA on a metacentric chromosome pair. The chromosome number variation was caused by ascending dysploidy (chromosome fission involving the proximal 45S rDNA site resulting in two acrocentric chromosome pairs holding a terminal 45S rDNA), with subsequent descending dysploidy (fusion) in two species, H. maleolens and H. sessilis. However, besides dysploidy, our analysis detected another important chromosome rearrangement in the Orchidaceae: chromosome inversion, that promoted 5S rDNA site duplication and relocation.

Genomic organization of repetitive DNAs highlights chromosomal evolution in the genus Clarias (Clariidae, Siluriformes)

BACKGROUND

The genus Clarias (Clariidae, Siluriformes) contains at least 61 species naturally spread over vast regions of Asia, India and Africa. However, Clarias species have also been introduced in many different countries and represent the most widespread catfishes in the world. These fishes are also known as "walking catfishes" due to their ability to move over land. A large degree of chromosomal variation has been previously found in this family, mainly using conventional cytogenetic investigations, with diploid chromosome numbers ranging between 48 and 100. In this study, we analyzed the karyotype structure and distribution of four repetitive DNA sequences (5S and 18S rDNAs and (CA)15 and (GA)15 microsatellites) in three Clarias species (C. batrachus, C. gariepinus, C. macrocephalus), as well as in a probable natural hybrid of the two latter species from different Thailand river basins.

RESULTS

Clarias gariepinus and C. macrocephalus had 2n = 56 and 2n = 54, respectively, as well as karyotypes composed mainly by metacentric and submetacentric chromosomes. Their karyotypes differed in the number and location of 5S and 18S rDNA sites and in the degree of microsatellite accumulation. An intermediate chromosomal pattern incorporating those of the parental species was found in the probable hybrid, confirming its interspecific origin. Clarias batrachus had 2n = 104 chromosomes and its karyotype was dominated by mainly acrocentric elements, indicating that unusual multiple centric fissions were involved in its karyotype differentiation. The karyotype of this species presented an unexpected dispersion of ribosomal DNAs, possessing 54 and 12 sites of 5S and 18S rDNAs, respectively, as well as a high accumulation and differential distribution of both microsatellite repeats, representing 'hot spots' for chromosomal rearrangement.

CONCLUSION

Both conventional and molecular cytogenetic markers were useful tools for demonstrating remarkable evolutionary dynamism and highlighting multiple chromosomal rearrangements and hybridization events correlated with the notable karyotypic diversity of these walking catfishes.

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.

Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes

Chromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we have used comparative chromosome painting (CCP) to reconstruct the pathways of descending and ascending dysploidy in the genus Boechera (tribe Boechereae, Brassicaceae). We describe the origin and structure of three Boechera genomes and establish the origin of the previously described aberrant Het and Del chromosomes found in Boechera apomicts with euploid (2n = 14) and aneuploid (2n = 15) chromosome number. CCP analysis allowed us to reconstruct the origin of seven chromosomes in sexual B. stricta and apomictic B. divaricarpa from the ancestral karyotype (n = 8) of Brassicaceae lineage I. Whereas three chromosomes (BS4, BS6, and BS7) retained their ancestral structure, five chromosomes were reshuffled by reciprocal translocations to form chromosomes BS1-BS3 and BS5. The reduction of the chromosome number (from x = 8 to x = 7) was accomplished through the inactivation of a paleocentromere on chromosome BS5. In apomictic 2n = 14 plants, CCP identifies the largely heterochromatic chromosome (Het) being one of the BS1 homologues with the expansion of pericentromeric heterochromatin. In apomictic B. polyantha (2n = 15), the Het has undergone a centric fission resulting in two smaller chromosomes - the submetacentric Het' and telocentric Del. Here we show that new chromosomes can be formed by a centric fission and can be fixed in populations due to the apomictic mode of reproduction.

Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in South-East Asia

South-East Asia covers four of the world's biodiversity hotspots, showing high species diversity and endemism. Owing to the successive expansion and contraction of distribution and the fragmentation by geographical barriers, the tropical flora greatly diversified in this region during the Tertiary, but the evolutionary tempo and mode of species diversity remain poorly investigated. Paphiopedilum, the largest genus of slipper orchids comprising nearly 100 species, is mainly distributed in South-East Asia, providing an ideal system for exploring how plant species diversity was shaped in this region. Here, we investigated the evolutionary history of this genus with eight cpDNA regions and four low-copy nuclear genes. Discordance between gene trees and network analysis indicates that reticulate evolution occurred in the genus. Ancestral area reconstruction suggests that vicariance and long-distance dispersal together led to its current distribution. Diversification rate variation was detected and strongly correlated with the species diversity in subg. Paphiopedilum (~80 species). The shift of speciation rate in subg. Paphiopedilum was coincident with sea-level fluctuations in the late Cenozoic, which could have provided ecological opportunities for speciation and created bridges or barriers for gene flow. Moreover, some other factors (e.g. sympatric distribution, incomplete reproductive barriers and clonal propagation) might also be advantageous for the formation and reproduction of hybrid species. In conclusion, our study suggests that the interplay of reticulate evolution and sea-level fluctuations has promoted the diversification of the genus Paphiopedilum and sheds light into the evolution of Orchidaceae and the historical processes of plant species diversification in South-East Asia.

Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae)

Changes in chromosome number and structure are important contributors to adaptation, speciation and macroevolution. In flowering plants, polyploidy and subsequent reductions in chromosome number by fusion are major sources of chromosomal evolution, but chromosome number increase by fission has been relatively unexplored. Here, we use comparative linkage mapping with gene-based markers to reconstruct chromosomal synteny within the model flowering plant genus Mimulus (monkeyflowers). Two sections of the genus with haploid numbers ≥ 14 have been inferred to be relatively recent polyploids because they are phylogenetically nested within numerous taxa with low base numbers (n=8-10). We combined multiple data sets to build integrated genetic maps of the M. guttatus species complex (section Simiolus, n=14) and the M. lewisii group (section Erythranthe; n=8), and then aligned the two integrated maps using >100 shared markers. We observed strong segmental synteny between M. lewisii and M. guttatus maps, with essentially 1-to-1 correspondence across each of 16 chromosomal blocks. Assuming that the M. lewisii (and widespread) base number of 8 is ancestral, reconstruction of 14 M. guttatus chromosomes requires at least eight fission events (likely shared by Simiolus and sister section Paradanthus (n=16)), plus two fusion events. This apparent burst of fission in the yellow monkeyflower lineages raises new questions about mechanisms and consequences of chromosomal fission in plants. Our comparative maps also provide insight into the origins of a chromosome exhibiting centromere-associated female meiotic drive and create a framework for transferring M. guttatus genome resources across the entire genus.

Insights into the dynamics of genome size and chromosome evolution in the early diverging angiosperm lineage Nymphaeales (water lilies)

Nymphaeales are the most species-rich lineage of the earliest diverging angiosperms known as the ANA grade (Amborellales, Nymphaeales, Austrobaileyales), and they have received considerable attention from morphological, physiological, and ecological perspectives. Although phylogenetic relationships between these three lineages of angiosperms are mainly well resolved, insights at the whole genome level are still limited because of a dearth of information. To address this, genome sizes and chromosome numbers in 34 taxa, comprising 28 species were estimated and analysed together with previously published data to provide an overview of genome size and chromosome diversity in Nymphaeales. Overall, genome sizes were shown to vary 10-fold and chromosome numbers and ploidy levels ranged from 2n = 2x = 18 to 2n = 16x = ∼224. Distinct patterns of genome diversity were apparent, reflecting the differential incidence of polyploidy, changes in repetitive DNA content, and chromosome rearrangements within and between genera. Using model-based approaches, ancestral genome size and basic chromosome numbers were reconstructed to provide insights into the dynamics of genome size and chromosome number evolution. Finally, by combining additional data from Amborellales and Austrobaileyales, a comprehensive overview of genome sizes and chromosome numbers in these early diverging angiosperms is presented.

Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid

Background

Paphiopedilum is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence In Situ Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within Paphiopedilum. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity.

Results

5S and 25S rDNA loci among Paphiopedilum species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity.

Conclusions

Paphiopedilum species display many chromosomal rearrangements - for example, duplications, translocations, and inversions - but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus a model system for the study of complex chromosomal evolution in plants.

Chromosome pairing affinities in interspecific hybrids reflect phylogenetic distances among lady's slipper orchids (Paphiopedilum)

BACKGROUND AND AIMS

Lady's slipper orchids (Paphiopedilum) are of high value in floriculture, and interspecific hybridization has long been used for breeding improved cultivars; however, information regarding the genome affinities of species and chromosome pairing behaviour of the hybrids remains almost unknown. The present work analyses the meiotic behaviour of interspecific hybrids by genomic in situ hybridization and cytologically evaluates the genomic relationships among parental species.

METHODS

Eight interspecific F(1) hybrids of Paphiopedilum species in various subgenera or sections were investigated in this study. The chromosome behaviour in meiosis of these interspecific hybrids was analysed and subjected to genomic in situ hybridization and fluorescent in situ hybridization.

KEY RESULTS

Genomic in situ hybridization was demonstrated as an efficient method to differentiate between Paphiopedilum genomes and to visualize the chromosome pairing affinities in interspecific F(1) hybrids, clarifying the phylogenetic distances among these species. Comparatively regular chromosome pairing observed in the hybrids of P. delenatii × P. bellatulum, P. delenatii × P. rothschildianum and P. rothschildianum × P. bellatulum suggested high genomic affinities and close relationships between parents of each hybrid. In contrast, irregular chromosome associations, such as univalents, trivalents and quadrivalents occurred frequently in the hybrids derived from distant parents with divergent karyotypes, such as P. delenatii × P. callosum, P. delenatii × P. glaucophyllum, P. rothschildianum × P. micranthum and P. rothschildianum × P. moquetteanum. The existence of multivalents and autosyndesis demonstrated by genomic in situ hybridization in this study indicates that some micro-rearrangements and other structural alterations may also play a part in differentiating Paphiopedilum species at chromosomal level, demonstrated as different chromosome pairing affinities in interspecific hybrids.

CONCLUSIONS

The results indicate that genome homology and the interaction of genetic factors, but not chromosome number nor karyotype similarity, determine the chromosome pairing behaviour in Paphiopedilum hybrids.

Dynamics of chromosome number and genome size variation in a cytogenetically variable sedge (Carex scoparia var. scoparia, Cyperaceae)

PREMISE OF THE STUDY

High intraspecific cytogenetic variation in the sedge genus Carex (Cyperaceae) is hypothesized to be due to the "diffuse" or non-localized centromeres, which facilitate chromosome fission and fusion. If chromosome number changes are dominated by fission and fusion, then chromosome evolution will result primarily in changes in the potential for recombination among populations. Chromosome duplications, on the other hand, entail consequent opportunities for divergent evolution of paralogs. In this study, we evaluate whether genome size and chromosome number covary within species.

METHODS

We used flow cytometry to estimate genome sizes in Carex scoparia var. scoparia, sampling 99 plants (23 populations) in the Chicago region, and we used meiotic chromosome observations to document chromosome numbers and chromosome pairing relations.

KEY RESULTS

Chromosome numbers range from 2n = 62 to 2n = 68, and nuclear DNA 1C content from 0.342 to 0.361 pg DNA. Regressions of DNA content on chromosome number are nonsignificant for data analyzed by individual or population, and a regression model that excludes slope is favored over a model in which chromosome number predicts genome size.

CONCLUSIONS

Chromosome rearrangements within cytogenetically variable Carex species are more likely a consequence of fission and fusion than of duplication and deletion. Moreover, neither genome size nor chromosome number is spatially autocorrelated, which suggests the potential for rapid chromosome evolution by fission and fusion at a relatively fine geographic scale (<350 km). These findings have important implications for ecological restoration and speciation within the largest angiosperm genus of the temperate zone.

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.

Chromosome diversity and evolution in Liliaceae

BACKGROUND AND AIMS

There is an extensive literature on the diversity of karyotypes found in genera within Liliaceae, but there has been no attempt to analyse these data within a robust phylogenetic framework. In part this has been due to a lack of consensus on which genera comprise Liliaceae and the relationships between them. Recently, however, this changed with the proposal for a relatively broad circumscription of Liliaceae comprising 15 genera and an improved understanding of the evolutionary relationships between them. Thus there is now the opportunity to examine patterns and trends in chromosome evolution across the family as a whole.

METHODS

Based on an extensive literature survey, karyo-morphometric features for 217 species belonging to all genera in Liliaceae sensu the APG (Angiosperm Phylogeny Group) were obtained. Included in the data set were basic chromosome number, ploidy, chromosome total haploid length (THL) and 13 different measures of karyotype asymmetry. In addition, genome size estimates for all species studied were inferred from THLs using a power regression model constructed from the data set. Trends in karyotype evolution were analysed by superimposing the karyological data onto a phylogenetic framework for Liliaceae.

KEY RESULTS AND CONCLUSIONS

Combining the large amount of data enabled mean karyotypes to be produced, highlighting marked differences in karyotype structure between the 15 genera. Further differences were noted when various parameters for analysing karyotype asymmetry were assessed. By examining the effects of increasing genome size on karyotype asymmetry, it was shown that in many but not all (e.g. Fritillaria and all of Tulipeae) species, the additional DNA was added preferentially to the long arms of the shorter chromosomes rather than being distributed across the whole karyotype. This unequal pattern of DNA addition is novel, contrasting with the equal and proportional patterns of DNA increase previously reported. Overall, the large-scale analyses of karyotype features within a well-supported phylogenetic framework enabled the most likely patterns of chromosome evolution in Liliaceae to be reconstructed, highlighting diverse modes of karyotype evolution, even within this comparatively small monocot family.

The dynamic ups and downs of genome size evolution in Brassicaceae

Crucifers (Brassicaceae, Cruciferae) are a large family comprising some 338 genera and c. 3,700 species. The family includes important crops as well as several model species in various fields of plant research. This paper reports new genome size (GS) data for more than 100 cruciferous species in addition to previously published C-values (the DNA amount in the unreplicated gametic nuclei) to give a data set comprising 185 Brassicaceae taxa, including all but 1 of the 25 tribes currently recognized. Evolution of GS was analyzed within a phylogenetic framework based on gene 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 genomes with a mean 1C-value of 0.63 pg. The ancestral genome size (ancGS) for Brassicaceae was reconstructed as (anc)1C=0.50 pg. Approximately 50% of crucifer taxa analyzed showed a decrease in GS compared with the ancGS. The remaining species showed an increase in GS although this was generally moderate, with significant increases in C-value found only in the tribes Anchonieae and Physarieae. Using statistical approaches to analyze GS, evolutionary gains or losses in GS were seen to have accumulated disproportionately faster within longer branches. However, we also found that GS has not changed substantially through time and most likely evolves passively (i.e., a tempo that cannot be distinguished between neutral evolution and weak forms of selection). The data reveal an apparent paradox between the narrow range of small GSs over long evolutionary time periods despite evidence of dynamic genomic processes that have the potential to lead to genome obesity (e.g., transposable element amplification and polyploidy). To resolve this, it is suggested that mechanisms to suppress amplification and to eliminate amplified DNA must be active in Brassicaceae although their control and mode of operation are still poorly understood.

Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution

BACKGROUND AND AIMS

Species' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species' identification.

METHODS

Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes.

KEY RESULTS

Six of 21 currently accepted species were recovered. The results also support recognition of the 'C. pumila' clade as a single species. Molecular phylogenetic relationships within the 'C. acicularis-C. madida' and 'C. ferdinandiana-C. neowiedii' species' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands.

CONCLUSIONS

The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic data proved to be a valuable source of information to understand evolutionary patterns within Maxillariinae orchids.

Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes

Chromosomal change is one of the more hotly debated potential mechanisms of speciation. It has long been argued over whether--and to what degree--changes in chromosome structure contribute to reproductive isolation and, ultimately, speciation. In this review we do not aim to completely analyze accumulated data about chromosomal speciation but wish to draw attention to several critical points of speciation-related chromosomal change, namely: (a) interrelations between chromosomal rearrangements and repetitive DNA fraction; (b) mobility of ribosomal DNA clusters; and (c) rDNA and transposable elements as perpetual generators of genome instability.

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 correlated with 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 species of 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 in diploids (2n = 14) and reached up to 29.85 pg in hexaploid species (2n = 42). The smallest genomes were found in taxa from the New World, which became secondarily annual, whereas the largest diploid genomes occur in Eurasian annuals. Genome sizes of polyploid taxa equaled mostly the added sizes of their proposed progenitors or were slightly (1% to 5%) smaller. The analysis of ancestral genome sizes on the base of the phylogeny of the genus revealed lineages with decreasing and with increasing genome sizes. Correlations of intraspecific genome size variation with the length of vegetation period were found in H. marinum populations from Western Europe but were not significant within two species from South America. On a higher taxonomical level (i.e., for species groups or the entire genus), environmental correlations were absent. This could mostly be attributed to the superimposition of life-form changes and phylogenetic constraints, which conceal ecogeographical correlations.

Evolution of genome size in the angiosperms

Genome size varies extensively across the flowering plants, which has stimulated speculation regarding the ancestral genome size of these plants and trends in genome evolution. We investigated the evolution of C-values across the angiosperms using a molecular phylogenetic framework and C-values not previously available for crucial basal angiosperms, including Amborella, Illiciaceae, and Austrobaileya. Reconstructions of genome size across the angiosperms and extant gymnosperms indicate that the ancestral genome size for angiosperms is very small (1C ≤ 1.4 pg), in agreement with an earlier analysis of Leitch et al. (1998). Furthermore, a very small genome size (1C ≤ 1.4 pg) is ancestral not only for the angiosperms in general, but also for most major clades of flowering plants, including the monocots and the eudicots. The ancestral genome of core eudicots may also have been very small given that very low 1C-values appear to be ancestral for major clades of core eudicots, such as Caryophyllales, Saxifragales, and asterids. Very large genomes occur in clades that occupy derived positions within the monocots and Santalales.