Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata, a keystone species of western North America

PREMISE

Polyploidization is often followed by diploidization. Diploidization is generally studied using synthetic polyploid lines and/or crop plants, but rarely using extant diploids or nonmodel plants such as Artemisia tridentata. This threatened western North American keystone species has a large genome compared to congeneric Artemisia species; dominated by diploid and tetraploid cytotypes, with multiple origins of tetraploids with genome size reduction.

METHODS

The genome of an A. tridentata sample was resequenced to study genome evolution and compared to that of A. annua, a diploid congener. Three diploid genomes of A. tridentata were compared to test for multiple diploidization events.

RESULTS

The A. tridentata genome had many chromosomal rearrangements relative to that of A. annua, while large-scale synteny of A. tridentata chromosome 3 and A. annua chromosome 4 was conserved. The three A. tridentata genomes had similar sizes (4.19-4.2 Gbp), heterozygosity (2.24-2.25%), and sequence (98.73-99.15% similarity) across scaffolds, and in k-mer analyses, similar patterns of diploid heterozygous k-mers (AB = 41%, 47%, and 47%), triploid heterozygous k-mers (AAB = 18-21%), and tetraploid k-mers (AABB = 13-17%). Biallelic SNPs were evenly distributed across scaffolds for all individuals. Comparisons of transposable element (TE) content revealed differential enrichment of TE clades.

CONCLUSIONS

Our findings suggest population-level TE differentiation after a shared polyploidization-to-diploidization event(s) and exemplify the complex processes of genome evolution. This research approached provides new resources for exploration of abiotic stress response, especially the roles of TEs in response pathways.

Small genome size and variation in ploidy levels support the naturalization of vascular plants but constrain their invasive spread

Karyological characteristics are among the traits underpinning the invasion success of vascular plants. Using 11 049 species, we tested the effects of genome size and ploidy levels on plant naturalization (species forming self-sustaining populations where they are not native) and invasion (naturalized species spreading rapidly and having environmental impact). The probability that a species naturalized anywhere in the world decreased with increasing monoploid genome size (DNA content of a single chromosome set). Naturalized or invasive species with intermediate monoploid genomes were reported from many regions, but those with either small or large genomes occurred in fewer regions. By contrast, large holoploid genome sizes (DNA content of the unreplicated gametic nucleus) constrained naturalization but favoured invasion. We suggest that a small genome is an advantage during naturalization, being linked to traits favouring adaptation to local conditions, but for invasive spread, traits associated with a large holoploid genome, where the impact of polyploidy may act, facilitate long-distance dispersal and competition with other species.

Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species (Artemisia tridentata)

Current and past climatic changes can shift plant climatic niches, which may cause spatial overlap or separation between related taxa. The former often leads to hybridization and introgression, which may generate novel variation and influence the adaptive capacity of plants. An additional mechanism facilitating adaptations to novel environments and an important evolutionary driver in plants is polyploidy as the result of whole genome duplication. Artemisia tridentata (big sagebrush) is a landscape-dominating foundational shrub in the western United States which occupies distinct ecological niches, exhibiting diploid and tetraploid cytotypes. Tetraploids have a large impact on the species' landscape dominance as they occupy a preponderance of the arid spectrum of A. tridentata range. Three distinct subspecies are recognized, which co-occur in ecotones - the transition zone between two or more distinct ecological niches - allowing for hybridization and introgression. Here we assess the genomic distinctiveness and extent of hybridization among subspecies at different ploidies under both contemporary and predicted future climates. We sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Population genomic analyses revealed distinct diploid subspecies and at least two distinct tetraploid gene pools, indicating independent origins of the tetraploid populations. We detected low levels of hybridization (2.5%) between the diploid subspecies, while we found evidence for increased admixture between ploidy levels (18%), indicating hybridization has an important role in the formation of tetraploids. Our analyses highlight the importance of subspecies co-occurrence within these ecotones to maintain gene exchange and potential formation of tetraploid populations. Genomic confirmations of subspecies in the ecotones support the subspecies overlap predicted by the contemporary climate niche models. However, future mid-century projections of subspecies niches predict a substantial loss in range and subspecies overlap. Thus, reductions in hybridization potential could affect new recruitment of genetically variable tetraploids that are vital to this species' ecological role. Our results underscore the importance of ecotone conservation and restoration.

Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

Artemisia Linn. is a large genus within the family Asteraceae that includes several important medicinal plants. Because of their similar morphology and chemical composition, traditional identification methods often fail to distinguish them. Therefore, developing an effective identification method for Artemisia species is an urgent requirement. In this study, we analyzed 15 chloroplast (cp) genomes, including 12 newly sequenced genomes, from 5 Artemisia species. The cp genomes from the five Artemisia species had a typical quadripartite structure and were highly conserved across species. They had varying lengths of 151,132-151,178 bp, and their gene content and codon preferences were similar. Mutation hotspot analysis identified four highly variable regions, which can potentially be used as molecular markers to identify Artemisia species. Phylogenetic analysis showed that the five Artemisia species investigated in this study were sister branches to each other, and individuals of each species formed a monophyletic clade. This study shows that the cp genome can provide distinguishing features to help identify closely related Artemisia species and has the potential to serve as a universal super barcode for plant identification.

A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands

Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2-Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research.

A draft genome provides hypotheses on drought tolerance in a keystone plant species in Western North America threatened by climate change

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty-one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates of A. tridentata subsp. tridentata AQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with nondrought-tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome-to-phenome work.

Primeras medidas del tamaño del genoma en Carduncellusy los géneros afines Femeniasia y Phonus (Asteraceae, Cardueae), con datos para 21 táxones

El tamaño del genoma de 18 especies del género Carduncellus, dos especies de los géneros relacionados, Phonus y el género monotípico Femeniasia (F. balearica) ha sido medido por primera vez mediante citometría de flujo. Los niveles de ploidía se asignaron utilizando datos de tamaño del genoma junto con los recuentos de cromosomas previamente reportados. Se construyó un marco filogenético para visualizar la distribución de las características citogenéticas de los táxones. Los resultados confirmaron tres niveles de ploidía (2x, 4x y 6x), con un predominio de los táxones diploides. Los valores de 2C oscilaron entre 3,24 pg en Carduncellus calvus y 11,16 pg en C. eriocephalus, mientras que el tamaño del genoma monoploide (1Cx) osciló entre 1,29 pg en C. duvauxii (4x) y 2,30 pg en Phonus rhiphaeus (2x). La media de los valores 1Cx para los tetraploides fue menor que para los diploides. Los valores de tamaño del genoma de Carduncellus, Femeniasia y Phonus fueron más elevados que los de Carthamus dentro del mismo nivel de ploidía. Este resultado concuerda con una tendencia frecuentemente observada en plantas en la que los táxones con ciclos de vida largos presentan tamaños del genoma más elevados que los táxones relacionados que poseen ciclos de vida cortos.

Development of an In Vitro Method of Propagation for Artemisia tridentata subsp. tridentata to Support Genome Sequencing and Genotype-by-Environment Research

Basin big sagebrush (Artemisia tridentata subsp. tridentata) is a keystone species of the sagebrush steppe, a widespread ecosystem of western North America threatened by climate change. The study’s goal was to develop an in vitro method of propagation for this taxon to support genome sequencing and genotype-by-environment research on drought tolerance. Such research may ultimately facilitate the reintroduction of big sagebrush in degraded habitats. Seedlings were generated from two diploid mother plants (2n = 2x = 18) collected in environments with contrasting precipitation regimes. The effects of IBA and NAA on rooting of shoot tips were tested on 45 individuals and 15 shoot tips per individual. Growth regulator and individual-seedling effects on percent rooting and roots per shoot tip were evaluated using statistical and clustering analyses. Furthermore, rooted shoot tips were transferred into new media to ascertain their continued growth in vitro. The results suggest that A. tridentata is an outbred species, as shown by individuals’ effect on rooting and growth. IBA addition was the most effective method for promoting adventitious rooting, especially in top-performing individuals. These individuals also have high survival and growth rates upon transferring to new media, making them suitable candidates for generating biomass for genome sequencing and producing clones for genotype-by-environment research.

Comparative chloroplast genome analysis of Artemisia (Asteraceae) in East Asia: insights into evolutionary divergence and phylogenomic implications

BACKGROUND

Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge.

RESULTS

To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power.

CONCLUSIONS

The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.

Competition among native and invasive Phragmites australis populations: An experimental test of the effects of invasion status, genome size, and ploidy level

Among the traits whose relevance for plant invasions has recently been suggested are genome size (the amount of nuclear DNA) and ploidy level. So far, research on the role of genome size in invasiveness has been mostly based on indirect evidence by comparing species with different genome sizes, but how karyological traits influence competition at the intraspecific level remains unknown. We addressed these questions in a common-garden experiment evaluating the outcome of direct intraspecific competition among 20 populations of Phragmites australis, represented by clones collected in North America and Europe, and differing in their status (native and invasive), genome size (small and large), and ploidy levels (tetraploid, hexaploid, or octoploid). Each clone was planted in competition with one of the others in all possible combinations with three replicates in 45-L pots. Upon harvest, the identity of 21 shoots sampled per pot was revealed by flow cytometry and DNA analysis. Differences in performance were examined using relative proportions of shoots of each clone, ratios of their aboveground biomass, and relative yield total (RYT). The performance of the clones in competition primarily depended on the clone status (native vs. invasive). Measured in terms of shoot number or aboveground biomass, the strongest signal observed was that North American native clones always lost in competition to the other two groups. In addition, North American native clones were suppressed by European natives to a similar degree as by North American invasives. North American invasive clones had the largest average shoot biomass, but only by a limited, nonsignificant difference due to genome size. There was no effect of ploidy on competition. Since the North American invaders of European origin are able to outcompete the native North American clones, we suggest that their high competitiveness acts as an important driver in the early stages of their invasion.

Dissimilar molecular and morphological patterns in an introgressed peripheral population of a sand dune species (Armeria pungens, Plumbaginaceae)

Introgression is a poorly understood evolutionary outcome of hybridisation because it may remain largely undetected whenever it involves the transfer of small parts of the genome from one species to another. Aiming to understand the early stages of this process, a putative case from the southernmost border of the Armeria pungens range from its congener A. macrophylla is revisited following the discovery of a subpopulation that does not show phenotypic signs of introgression and resembles typical A. pungens. We analysed morphometrics, nuclear ribosomal DNA ITS and plastid DNA (trnL-trnF) sequences, genome size, 45S and 5S rDNA loci-FISH data and nrDNA IGS sequences. Within the study site, most individuals match morphologies of either of the two hybridising species, particularly the new subpopulation, with intermediate phenotypes being scarce. This pattern does not fully fit molecular evidence revealing two ITS ribotypes co-occurring intragenomically in most plants from the study site and one single plastid haplotype. Genome size and structural features of the IGS sequences both indicate that A. pungens from the study site is genetically more similar to its sympatric congener than to the remainder of its conspecifics. Introgression of A. macrophylla into A. pungens and plastid capture explain all the evidence analysed. However, important features to understand the origin and fate of the introgressed population, such as the degree and direction of introgression, which are important for understanding early stages of hybridisation in plants with low reproductive barriers, should be addressed with new data.

Small genome separates native and invasive populations in an ecologically important cosmopolitan grass

The literature suggests that small genomes promote invasion in plants, but little is known about the interaction of genome size with other traits or about the role of genome size during different phases of the invasion process. By intercontinental comparison of native and invasive populations of the common reed Phragmites australis, we revealed a distinct relationship between genome size and invasiveness at the intraspecific level. Monoploid genome size was the only significant variable that clearly separated the North American native plants from those of European origin. The mean Cx value (the amount of DNA in one chromosome set) for source European native populations was 0.490 ± 0.007 (mean ± SD), for North American invasive 0.506 ± 0.020, and for North American native 0.543 ± 0.021. Relative to native populations, the European populations that successfully invaded North America had a smaller genome that was associated with plant traits favoring invasiveness (long rhizomes, early emerging abundant shoots, resistance to aphid attack, and low C:N ratio). The knowledge that invasive populations within species can be identified based on genome size can be applied to screen potentially invasive populations of Phragmites in other parts of the world where they could grow in mixed stands with native plants, as well as to other plant species with intraspecific variation in invasion potential. Moreover, as small genomes are better equipped to respond to extreme environmental conditions such as drought, the mechanism reported here may represent an emerging driver for future invasions and range expansions.

Progress in the study of genome size evolution in Asteraceae: analysis of the last update

The Genome Size in Asteraceae Database (GSAD, http://www.asteraceaegenomesize.com) has been recently updated, with data from papers published or in press until July 2018. This constitutes the third release of GSAD, currently containing 4350 data entries for 1496 species, which represent a growth of 22.52% in the number of species with available genome size data compared with the previous release, and a growth of 57.72% in terms of entries. Approximately 6% of Asteraceae species are covered in terms of known genome sizes. The number of source papers included in this release (198) means a 48.87% increase with respect to release 2.0. The significant data increase was exploited to study the genome size evolution in the family from a phylogenetic perspective. Our results suggest that the role of chromosome number in genome size diversity within Asteraceae is basically associated to polyploidy, while dysploidy would only cause minor variation in the DNA amount along the family. Among diploid taxa, we found that the evolution of genome size shows a strong phylogenetic signal. However, this trait does not seem to evolve evenly across the phylogeny, but there could be significant scale and clade-dependent patterns. Our analyses indicate that the phylogenetic signal is stronger at low taxonomic levels, with certain tribes standing out as hotspots of autocorrelation between genome size and phylogeny. Finally, we also observe meaningful associations among nuclear DNA content on Asteraceae species and other phenotypical and ecological traits (i.e. plant habit and invasion ability). Overall, this study emphasizes the need to continue generating and analysing genome size data in order to puzzle out the evolution of this parameter and its many biological correlates.

Artemisia campestris L.: review on taxonomical aspects, cytogeography, biological activities and bioactive compounds

Artemisia campestris L. (Asteraceae) is a polymorphic species that consists of many subspecies and varieties. It is known for its medicinal, pharmacological, and culinary properties. This review is undertaken with the aim to highlight some aspects of this plant, specifically the taxonomy, the cytogeography, the phytochemistry with an emphasis on the structure-activity relationship (SAR) of the main bioactive compounds of A. campestris L. in addition to its biological properties and the food control properties. The bibliographic data compiled in this review allowed the revision of 146 papers, by using different databases and scientific engines, such as Scopus, ScienceDirect, Pubmed, and google scholar. The taxonomic analysis has embedded A. campestris L. in the tribe Anthemideae, and the genus Artemisia L. Also many subtaxa have been identified, and a subspecific classification of this species has been established on the basis of its botanical characters. The cytogenetic findings evidenced that A.campestris L. is prevailed by the chromosome number x = 9, with a polyploidization degree ranging from diploidy to hexaploidy according to the geographical distribution of the plant populations, while the genome size seems to be proportional to the ploidy level, suggesting an adaptive trait of the cytotypes to new environments. This plant is rich in polyphenols, flavonoids, and terpenic compounds, which substantiate the bioactivities attributed to its extracts and essential oil. Hence, the SAR of the main bioactive compounds of A. campestris L., mainly the prominent flavonoids, phenolic acids, and terpenes revealed a tight link between specific chemical entities of the bioactive compound and the respective biological activity. Many biological activities were approached in this review, mainly the antioxidant, antivenom, antidiabetic, antihyperlipidemic, anti-inflammatory, antihypertensive, anti-leishmaniasis, antinociceptive, wound healing, and analgesic activities in addition to the hepatoprotective, nephroprotective, neuroprotective, and gastroprotective actions. Finally, the food preservative ability of the extracts and essential oil obtained from A.campestris L. have been fully discussed. The present review contributes to the literature, by bringing more clarifications about the different aspects of A.campestris L., like taxonomy, cytogeography and biological interests of this species. The SAR approach of some constituents that occur in A.campestris L., gives a solid support that can be used to explore the bioactivity of components isolated from this species, while the preservative properties of this plant can be usefully exploited for the agrifood sector.

A genome size and phylogenetic survey of Mediterranean Tripleurospermum and Matricaria (Anthemideae, Asteraceae)

The study of genome size variation can contribute valuable information on species relationships as well as correlate to several morphological or ecological features, among others. Here we provide an extensive report on genome sizes on genus Tripleurospermum and its closely related genus Matricaria, which are two typically Mediterranean genera particularly widespread and diverse in Turkey, the origin of most of the populations here studied. We analyse and discuss genome size variation in the first relatively complete molecular phylogenetic framework of Tripleurospermum (based on ITS and ETS ribosomal DNA-rDNA-regions). We find cases of intraspecific genome size variation, which could be taxonomically significant. Genome downsizing is also detected as the typical response to polyploidisation in Tripleurospermum taxa, being most conspicuous at the tetraploid level. Several positive correlations with genome size, including those with pollen and stomatal size or cypsela length, among others, are also found. Remarkably, taxa presenting rhizomes tend to present higher genome sizes, confirming a trend to accumulate nuclear DNA in such species, which could be explained by the nutrient reserves availability in their storage organs, allowing genome expansion, or by the lower rates of sexual reproduction in rhizomatous taxa.

Contrasting growth phenology of native and invasive forest shrubs mediated by genome size

Examination of the significance of genome size to plant invasions has been largely restricted to its association with growth rate. We investigated the novel hypothesis that genome size is related to forest invasions through its association with growth phenology, as a result of the ability of large-genome species to grow more effectively through cell expansion at cool temperatures. We monitored the spring leaf phenology of 54 species of eastern USA deciduous forests, including native and invasive shrubs of six common genera. We used new measurements of genome size to evaluate its association with spring budbreak, cell size, summer leaf production rate, and photosynthetic capacity. In a phylogenetic hierarchical model that differentiated native and invasive species as a function of summer growth rate and spring budbreak timing, species with smaller genomes exhibited both faster growth and delayed budbreak compared with those with larger nuclear DNA content. Growth rate, but not budbreak timing, was associated with whether a species was native or invasive. Our results support genome size as a broad indicator of the growth behavior of woody species. Surprisingly, invaders of deciduous forests show the same small-genome tendencies of invaders of more open habitats, supporting genome size as a robust indicator of invasiveness.

The striking and unexpected cytogenetic diversity of genus Tanacetum L. (Asteraceae): a cytometric and fluorescent in situ hybridisation study of Iranian taxa

BACKGROUND

Although karyologically well studied, the genus Tanacetum (Asteraceae) is poorly known from the perspective of molecular cytogenetics. The prevalence of polyploidy, including odd ploidy warranted an extensive cytogenetic study. We studied several species native to Iran, one of the most important centres of diversity of the genus. We aimed to characterise Tanacetum genomes through fluorochrome banding, fluorescent in situ hybridisation (FISH) of rRNA genes and the assessment of genome size by flow cytometry. We appraise the effect of polyploidy and evaluate the existence of intraspecific variation based on the number and distribution of GC-rich bands and rDNA loci. Finally, we infer ancestral genome size and other cytogenetic traits considering phylogenetic relationships within the genus.

RESULTS

We report first genome size (2C) estimates ranging from 3.84 to 24.87 pg representing about 11 % of those recognised for the genus. We found striking cytogenetic diversity both in the number of GC-rich bands and rDNA loci. There is variation even at the population level and some species have undergone massive heterochromatic or rDNA amplification. Certain morphometric data, such as pollen size or inflorescence architecture, bear some relationship with genome size. Reconstruction of ancestral genome size, number of CMA+ bands and number of rDNA loci show that ups and downs have occurred during the evolution of these traits, although genome size has mostly increased and the number of CMA+ bands and rDNA loci have decreased in present-day taxa compared with ancestral values.

CONCLUSIONS

Tanacetum genomes are highly unstable in the number of GC-rich bands and rDNA loci, although some patterns can be established at the diploid and tetraploid levels. In particular, aneuploid taxa and some odd ploidy species show greater cytogenetic instability than the rest of the genus. We have also confirmed a linked rDNA arrangement for all the studied Tanacetum species. The labile scenario found in Tanacetum proves that some cytogenetic features previously regarded as relatively constant, or even diagnostic, can display high variability, which is better interpreted within a phylogenetic context.

The hidden side of plant invasions: the role of genome size

The ecological role of genome size in plant biology, biogeography, and morphology has garnered increasing attention as the methods and technology associated with measuring cytological characteristics have become more reliable and accessible. However, how plant genome size influences plant invasions and at what stage in the invasion this influence occurs have been little explored. Several large-scale analyses of published data have yielded valuable interspecific comparisons, but experimental studies that manipulate environmental factors are needed, particularly below the species level, to fully understand the role that genome size plays in plant invasion. In this review, we summarize the available knowledge, discuss the integration of genome size data into invasion research, and suggest how it can be applied to detect and manage invasive species. We also explore how global climate change could exert selective pressures on plant populations with varying genome sizes, thereby increasing the distribution range and invasiveness of some populations while decreasing others. Finally, we outline avenues for future research, including considerations of large-scale studies of intraspecific variation in genome size of invasive populations, testing the interaction of genome size with other factors in macroecological analyses of invasions, as well as the role this trait may play in plant-enemy interactions.

North American Artemisia species from the subgenus Tridentatae (Sagebrush): a phytochemical, botanical and pharmacological review

The genus Artemisia consists of between 350 and 500 species with most of the North American endemic Artemisia species contained within the subgenus Tridentatae (Sagebrush). The reported uses of these species by Native American and First Nations peoples include analgesic, antiinflammatory, antiseptic, immunostimulation activity, as well as the treatment of afflictions from spiritual origins. Taxonomic revision for North American Sagebrush has created a number of synonyms that confuse the literature. The phytochemical diversity of the Tridentatae includes at least 220 distinct and important specialized metabolites. This manuscript reviews the current phytochemical, botanical and pharmacological understanding for the subgenus Tridentatae, and provides a foundation for future studies of the metabolomes of the Tridentatae. Modern approaches to phytochemical analysis and drug discovery are likely to provide interesting lead compounds in the near future.

Recent updates and developments to plant genome size databases

Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols.

Karyotype evolution and phylogenetic analyses in the genus Cardiospermum L. (Paullinieae, Sapindaceae)

Cardiospermum L. belongs to the Paullinieae tribe (Sapindaceae) and comprises 16 species. Of these, 12 species are present in South America and all occur in Brazil. Cardiospermum shows the most variable chromosome number of the tribe. Phylogenetic relationships within the genus Cardiospermum, especially with other species of the tribe, are poorly understood. This research focuses on characterisation of the karyotypic features of Cardiospermum using conventional cytogenetic methods, CMA/DAPI chromosome banding and fluorescence in situ hybridisation (FISH). To elucidate the phylogeny of the genus, the nuclear markers ITS1 and ITS2 were sequenced and analysed using maximum parsimony and Bayesian inference. Cardiospermum shows important diversity in basic numbers, with x = 7, 9, 10, 11 and 12. All species studied have metacentric and submetacentric chromosomes, some species have subtelocentric chromosomes, while telocentric chromosomes are absent. The interphase nuclei differentiate the Cardiospermum species into two groups. The CMA(3) /DAPI chromosome banding revealed the presence of an AT-rich terminal region in C. corindum, C. grandiflorum and C. urvilleoides, whereas GC-rich regions were found in C. grandiflorum, C. halicacabum var. halicacabum, C. halicacabum var. microcarpum, C. heringeri and C. integerrimum. FISH revealed syntenic and non-syntenic distribution of the 18-5.8-26S and 5S rDNA. The syntenic distribution always occurred in the short arms of the same chromosome in all of the species. The phylogenetic relationships reveal, in part, the taxonomic arrangement of the genus Cardiospermum.

The genus Artemisia (Asteraceae: Anthemideae) at a continental crossroads: molecular insights into migrations, disjunctions, and reticulations among Old and New World species from a Beringian perspective

Artemisia is the largest genus (ca. 350-500+ spp.) in the tribe Anthemideae and is composed of ecologically, morphologically, and chemically diverse species that are found primarily throughout the Northern Hemisphere. Two major centers of diversity for the genus are located in Eurasia and western North America, but phytogeographic links connecting these two regions are observed all across the North Pacific Rim and adjacent areas in the Arctic, including many islands and archipelagos. Previous phylogenetic studies have helped to clarify major lineages and identify likely sister relationships, but many questions remain unanswered regarding the relationships and migration history of New and Old World species. Here we investigate the phylogenetics of Artemisia within a biogeographic context centered in the Beringian Region and offer new hypotheses concerning species relationships, migration history, and the likely role of reticulate evolution in the genus. Our sampling included many new taxa and emphasized multiple accessions of widespread species, species from proposed refugia, and species with disjunct/vicariant distributions. The ITS phylogeny contained 173 accessions (94 new and 79 from GenBank) and indicated that Artemisia is paraphyletic by the exclusion of several small Asian genera and the North American genus Sphaeromeria. Following a survey of thirteen chloroplast loci, phylogenies based on two plastid markers (psbA-trnH and rpl32-trnL spacers) were constructed with a reduced data set, and though largely consistent with the ITS topology, revealed several cases of possible introgression among New World and Beringian species. Our analysis reveals that North American Artemisia species have multiple origins, and that western North America has served as a source for some colonizing elements in eastern Asia and South America.

Intraspecific cytotypic variation and complicated genetic structure in the Phlox amabilis-P. woodhousei (Polemoniaceae) complex

PREMISE OF THE STUDY

Polyploidy is widely recognized as an important process in the evolution of plants, but less attention has been paid to the study of intraspecific polyploidy, including its prevalence, formation, taxonomic implications, and effect on genetic diversity, structure, and gene flow within and among individuals and populations. Here we studied intraspecific ploidy level variation in the Phlox amabilis-P. woodhousei complex to determine the amount and distribution of cytotypic and genetic variation present and measure the extent of gene flow among species, cytotypes, and populations.

METHODS

Flow cytometry and microsatellite analyses were used to ascertain cytotypic variation, genetic diversity, and population structure within and among eight populations of P. amabilis and 10 populations of P. woodhousei from Arizona and New Mexico.

KEY RESULTS

Our analyses support the recognition of P. amabilis and P. woodhousei as two distinct species. Both species exhibit cytotypic variation with geographically structured diploid, tetraploid, and hexaploid populations, and genetic analyses suggest a combination of auto- and allopolyploidy in their formation. Diploid, tetraploid, and most hexaploid populations within species share much of their genetic variation, while some hexaploid populations are genetically distinct. All populations maintain moderately high genetic diversity and connectivity, and genetic structure is strongly influenced by geography.

CONCLUSIONS

This study highlights the potential for complicated patterns of genetic variation relative to cytotypic variation and provides evidence for the role of cytotypic variation and geographic isolation in shaping diversity, differentiation, and potentially speciation in the P. amabilis-P. woodhousei complex.

The more the better? The role of polyploidy in facilitating plant invasions

BACKGROUND

Biological invasions are a major ecological and socio-economic problem in many parts of the world. Despite an explosion of research in recent decades, much remains to be understood about why some species become invasive whereas others do not. Recently, polyploidy (whole genome duplication) has been proposed as an important determinant of invasiveness in plants. Genome duplication has played a major role in plant evolution and can drastically alter a plant's genetic make-up, morphology, physiology and ecology within only one or a few generations. This may allow some polyploids to succeed in strongly fluctuating environments and/or effectively colonize new habitats and, thus, increase their potential to be invasive.

SCOPE

We synthesize current knowledge on the importance of polyploidy for the invasion (i.e. spread) of introduced plants. We first aim to elucidate general mechanisms that are involved in the success of polyploid plants and translate this to that of plant invaders. Secondly, we provide an overview of ploidal levels in selected invasive alien plants and explain how ploidy might have contributed to their success.

CONCLUSIONS

Polyploidy can be an important factor in species invasion success through a combination of (1) 'pre-adaptation', whereby polyploid lineages are predisposed to conditions in the new range and, therefore, have higher survival rates and fitness in the earliest establishment phase; and (2) the possibility for subsequent adaptation due to a larger genetic diversity that may assist the 'evolution of invasiveness'. Alternatively, polyploidization may play an important role by (3) restoring sexual reproduction following hybridization or, conversely, (4) asexual reproduction in the absence of suitable mates. We, therefore, encourage invasion biologists to incorporate assessments of ploidy in their studies of invasive alien species.

A molecular phylogenetic approach to western North America endemic Artemisia and allies (Asteraceae): untangling the sagebrushes

PREMISE OF THE STUDY

Artemisia subgenus Tridentatae plants characterize the North American Intermountain West. These are landscape-dominant constituents of important ecological communities and habitats for endemic wildlife. Together with allied species and genera (Picrothamnus and Sphaeromeria), they make up an intricate series of taxa whose limits are uncertain, likely the result of reticulate evolution. The objectives of this study were to resolve relations among Tridentatae species and their near relatives by delimiting the phylogenetic positions of subgenus Tridentatae species with particular reference to its New World geographic placement and to provide explanations for the relations of allied species and genera with the subgenus with an assessment of their current taxonomic placement.

METHODS

Bayesian inference and maximum parsimony analysis were based on 168 newly generated sequences (including the nuclear ITS and ETS and the plastid trnS(UGA)-trnfM(CAU) and trnS(GCU)-trnC(GCA)) and 338 previously published sequences (ITS and ETS). Genome size by flow cytometry of species from Sphaeromeria was also determined.

KEY RESULTS

The results support an expanded concept and reconfiguration of Tridentatae to accommodate additional endemic North American Artemisia species. The monotypic Picrothamnus and all Sphaeromeria species appear nested within subgenus Tridentatae clade.

CONCLUSIONS

A redefinition of subgenus Tridentatae to include other western North American endemics is supported. We propose a new circumscription of the subgenus and divide it into three sections: Tridentatae, Filifoliae, and Nebulosae. The position of the circumboreal and other North American species suggests that subgenus Artemisia is the ancestral stock for the New World endemics, including those native to South America.

Methodology significantly affects genome size estimates: quantitative evidence using bryophytes

Flow cytometry (FCM) is commonly used to determine plant genome size estimates. Methodology has improved and changed during the past three decades, and researchers are encouraged to optimize protocols for their specific application. However, this step is typically omitted or undescribed in the current plant genome size literature, and this omission could have serious consequences for the genome size estimates obtained. Using four bryophyte species (Brachythecium velutinum, Fissidens taxifolius, Hedwigia ciliata, and Thuidium minutulum), three methodological approaches to the use of FCM in plant genome size estimation were tested. These included nine different buffers (Baranyi's, de Laat's, Galbraith's, General Purpose, LB01, MgSO(4), Otto's, Tris.MgCl(2), and Woody Plant), seven propidium iodide (PI) staining periods (5, 10, 15, 20, 45, 60, and 120 min), and six PI concentrations (10, 25, 50, 100, 150, and 200 microg ml(-1)). Buffer, staining period and staining concentration all had a statistically significant effect (P = 0.05) on the genome size estimates obtained for all four species. Buffer choice and PI concentration had the greatest effect, altering the 1C-values by as much as 8% and 14%, respectively. As well, the quality of the data varied with the different methodology used. Using the methodology determined to be the most accurate in this study (LB01 buffer and PI staining for 20 min at 150 microg ml(-1)), three new genome size estimates were obtained: B. velutinum: 0.46 pg, H. ciliata: 0.30 pg, and T. minutulum: 0.46 pg. While the peak quality of flow cytometry histograms is important, researchers must consider that changes in methodology can also affect the relative peak positions and therefore the genome size estimates obtained for plants using FCM.

Genome size dynamics in Artemisia L. (Asteraceae): following the track of polyploidy

Polyploidy is a key factor in the evolution of higher plants and plays an important role in the variation of plant genomes, leading to speciation in some cases. During polyploidisation, different balancing processes take place at the genomic level that can promote variation in nuclear DNA content. We estimated genome size using flow cytometry in 84 populations of 67 Artemisia species and one population of Crossostephium chinense. A total of 73 sequences of nrDNA ITS and 3'-ETS were newly generated and analysed, together with previously published sequences, to address the evolution of genome size in a phylogenetic framework. Differences in 2C values were detected among some lineages, as well as an increase of genome size heterogeneity in subgenera whose phylogenetic relationships are still unclear. We confirmed that the increase in 2C values in Artemisia polyploids was not proportional to ploidy level, but 1Cx genome size tended to decrease significantly when high ploidy levels were reached. The results lead us to hypothesise that genome size in polyploids tends to a maximum as it follows saturation behaviour, in agreement with the Michaelis-Menten model. We tested different arithmetic functions with our dataset that corroborated a non-linear relationship of genome size increase in polyploids, allowing us to suggest a theoretical upper limit for the DNA content of this genus.

Genome Size Study in the Valerianaceae: First Results and New Hypotheses

The purpose of this study is to provide a new focus to contribute, from the perspective of genomic evolution, towards a better understanding of the Valerianaceae evolutionary history. Chromosome numbers were determined by Feulgen staining in 24 populations of 18 species (first count for Valerianella multidentata, 2n=2x=14–16), and DNA contents were assessed by flow cytometry in 74 populations of 35 species (first assessments in all taxa but Centranthus ruber). A molecular phylogeny based on the trnL-trnF and including 41 new sequences was established, with the first DNA sequence for Centranthus nevadensis, Valeriana rotundifolia, V. saxatilis, Valerianella multidentata, and V. turgida. This work is the first large genome size study devoted to the Valerianaceae, showing a range of DNA amounts from 2C=0.39 pg (Valerianella turgida) to 2C=8.32 pg (Valeriana officinalis). At the family level, changes in basic chromosome number and genome size coincide with or precede major shifts in the evolutionary history of the group, such as those concerning stamen number and floral symmetry.

Ribosomal DNA, heterochromatin, and correlation with genome size in diploid and polyploid North American endemic sagebrushes (Artemisia, Asteraceae)

Subgenus Tridentatae ( Artemisia , Asteraceae) can be considered a polyploid complex. Both polyploidy and hybridization have been documented in the Tridentatae. Fluorescent in situ hybridization (FISH) and fluorochrome banding were used to detect and analyze ribosomal DNA changes linked to polyploidization in this group by studying four diploid-polyploid species pairs. In addition, genome sizes and heterochromatin patterns were compared between these populations. The linked 5S and 35S rRNA genes are confirmed as characteristic for Artemisia, and a pattern at the diploid level of three rDNA loci located at telomeric positions proved to be typical. Loss of rDNA loci was observed in some polyploids, whereas others showed additivity with respect to their diploid relatives. Genome downsizing was observed in all polyploids. Banding patterns differed depending on the pair of species analysed, but some polyploid populations showed an increased number of heterochromatic bands. FISH and fluorochrome banding were useful in determining the systematic position of Artemisia bigelovii , for which a differential pattern was found as compared with the rest of the group. Additionally, FISH was used to detect the presence of the Arabidopsis-type telomere repeat for the first time in Artemisia.