Variation of DNA amount in 47 populations of the subtribe Artemisiinae and related taxa (Asteraceae, Anthemideae): karyological, ecological, and systematic implications

Cytogenetic diversity of the diploid Korean wild Chrysanthemum (Asteraceae) inferred from genome size variations and chromosomal distributions of 5 S and 18 S rDNAs

BACKGROUND

The genus Chrysanthemum (Asteraceae) consists of a series of polyploids, ranging from diploid (2x) to decaploid (10x), with a basic chromosome number of x = 9. They vary widely within and among species owing to natural hybridization and polyploidization in natural habitats, and this has made recognizing the taxonomic boundaries among them difficult. Karyotype analysis has been played a powerful methodology to investigate the cytogenetic difference of the plant species but it was not applicable to define the species boundary and discuss their relationship of the Korean Chrysanthemum because of unstable karyotypes within the species. In this study, 28 natural diploid populations of the Korean Chrysanthemum, which were identified based on their morphological characteristics, were collected from their natural habitats to understand their cytogenetic relationships at the diploid level. We measured the genome size and compared the karyotype and distribution pattern of two ribosomal DNAs (rDNAs) using FISH (fluorescence in situ hybridization).

RESULTS

The results confirmed that C. zawadskii populations had smaller 1 C values than C. boreale and C. indicum did even for infraspecific variations. FISH analysis showed that 5 S and 18 S rDNA genes were present in one and two pairs (cytotype I) in the diploid populations of C. zawadskii regardless of the differences observed in individual karyotypes. In contrast, one pair of 5 S rDNA genes was commonly observed on different chromosomes in C. boreale, C. indicum, and their intermediate-type populations. In the case of the 18 S rDNA genes, two major types with three or four pairs on the short arms were observed (cytotypes II and IV), and an additional signal was detected in a few individuals (cytotype III). In total, five cytotypes were identified in the diploid Korean Chrysanthemum, including cytotype V, which was observed in only one individual of C. indicum with colocalized 5 S and 18 S rDNA signals on chromosome 4.

CONCLUSIONS

Consequently, we concluded that C. zawadskii with white ray flowers was cytogenetically distinguished from C. boreale and C. indicum, whereas there were no distinctive features between C. boreale and C. indicum with yellow ray flowers.

Relationship Between Genetic and Phenotypic Variations in Natural Populations of Perennial and Biennial Sagebrush

Plant responses to environmental heterogeneity depend on life-history traits, which could relate to phenotypical and genetic characteristics. To elucidate this relationship, we examined the variation in population genetics and functional traits of short- and long-lived Artemisia species that are co-occurring in the steppes of Mongolia. Mongolian steppes represent stressful and water-limited habitats, demanding phenotypic modifications in the short term and/or genetic adaptation in the long term. However, detailed knowledge is missing about both plant phenotypic and genetic differentiation, and their interrelationships in temperate grasslands. Here, we investigated 21 populations of the widely distributed subshrub Artemisia frigida and the herbaceous biennial Artemisia scoparia. Genetic variation was assessed with newly developed simple sequence repeats (SSRs) markers. Functional trait data were collected from each individual, and data on environmental variables was collected for each population. We detected significantly higher genetic diversity in the biennial species (H E = 0.86) compared with the perennial (H E = 0.79). For both species, the largest share of genetic variation was partitioned within populations (96%). Population genetic structure in the biennial A. scoparia was weak, while the perennial A. frigida showed some spatial genetic structure, which was impacted by geographical factors, soil nutrients, and precipitation amount. Morphology-related functional traits (i.e., plant height) were predominantly associated with environmental variables rather than with genetic variation, whereas physiology-related trait (i.e., specific leaf area [SLA]) was partly genetically determined.

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.

Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution

Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex morphological information and variation in ploidy level and nuclear DNA content have presented challenges for evolution studies of this genus. Consequently, taxonomic inconsistencies within the genus persist, hindering the utilization of such large plant resources. Researchers have utilized satellite DNAs to aid in chromosome identification, species classification, and evolutionary studies due to their significant sequence and copy number variation between species and close relatives. In the present study, the RepeatExplorer2 pipeline was utilized to identify 10 satellite DNAs from three species (Artemisia annua, Artemisia vulgaris, Artemisia viridisquama), and fluorescence in situ hybridization confirmed their distribution on chromosomes in 24 species, including 19 Artemisia species with 5 outgroup species from Ajania and Chrysanthemum. Signals of satellite DNAs exhibited substantial differences between species. We obtained one genus-specific satellite from the sequences. Additionally, molecular cytogenetic maps were constructed for Artemisia vulgaris, Artemisia leucophylla, and Artemisia viridisquama. One species (Artemisia verbenacea) showed a FISH distribution pattern suggestive of an allotriploid origin. Heteromorphic FISH signals between homologous chromosomes in Artemisia plants were observed at a high level. Additionally, the relative relationships between species were discussed by comparing ideograms. The results of the present study provide new insights into the accurate identification and taxonomy of the Artemisia genus using molecular cytological methods.

Traditional uses, Phytochemistry, Pharmacology, and Toxicology of the Genus Artemisia L. (Asteraceae): A High-value Medicinal Plant

Biologically active secondary metabolites, essential oils, and volatile compounds derived from medicinal and aromatic plants play a crucial role in promoting human health. Within the large family Asteraceae, the genus Artemisia consists of approximately 500 species. Artemisia species have a rich history in traditional medicine worldwide, offering remedies for a wide range of ailments, such as malaria, jaundice, toothache, gastrointestinal problems, wounds, inflammatory diseases, diarrhoea, menstrual pains, skin disorders, headache, and intestinal parasites. The therapeutic potential of Artemisia species is derived from a multitude of phytoconstituents, including terpenoids, phenols, flavonoids, coumarins, sesquiterpene lactones, lignans, and alkaloids that serve as active pharmaceutical ingredients (API). The remarkable antimalarial, antimicrobial, anthelmintic, antidiabetic, anti-inflammatory, anticancer, antispasmodic, antioxidative and insecticidal properties possessed by the species are attributed to these APIs. Interestingly, several commercially utilized pharmaceutical drugs, including arglabin, artemisinin, artemether, artesunate, santonin, and tarralin have also been derived from different Artemisia species. However, despite the vast medicinal potential, only a limited number of Artemisia species have been exploited commercially. Further, the available literature on traditional and pharmacological uses of Artemisia lacks comprehensive reviews. Therefore, there is an urgent need to bridge the existing knowledge gaps and provide a scientific foundation for future Artemisia research endeavours. It is in this context, the present review aims to provide a comprehensive account of the traditional uses, phytochemistry, documented biological properties and toxicity of all the species of Artemisia and offers useful insights for practitioners and researchers into underutilized species and their potential applications. This review aims to stimulate further exploration, experimentation and collaboration to fully realize the therapeutic potential of Artemisia in augmenting human health and well-being.

Intraspecific variation in genome size in Artemisia argyi determined using flow cytometry and a genome survey

Different collections and accessions of Artemisia argyi (Chinese mugwort) harbour considerable diversity in morphology and bioactive compounds, but no mechanisms have been reported that explain these variations. We studied genome size in A. argyi accessions from different regions of China by flow cytometry. Genome size was significantly distinct among origins of these 42 Chinese mugwort accessions, ranging from 8.428 to 11.717 pg. There were no significant intraspecific differences among the 42 accessions from the five regions of China. The clustering analysis showed that these 42 A. argyi accessions could be divided into three groups, which had no significant relationship with geographical location. In a genome survey, the total genome size of A. argyi (A15) was estimated to be 7.852 Gb (or 8.029 pg) by K-mer analysis. This indicated that the results from the two independent methods are consistent, and that the genome survey can be used as an adjunct to flow cytometry to compensate for its deficiencies. In addition, genome survey can provide the information about heterozygosity, repeat sequences, GC content and ploidy of A. argyi genome. The nuclear DNA contents determined here provide a new reference for intraspecific variation in genome size in A. argyi, and may also be a potential resource for the study of genetic diversity and for breeding new cultivar.

Genetic and chemical markers for authentication of three Artemisia species: A. capillaris, A. gmelinii, and A. fukudo

The genus Artemisia is an important source of medicines in both traditional and modern pharmaceutics, particularly in East Asia. Despite the great benefits of herbal medicine, quality assessment methods for these medicinal herbs are lacking. The young leaves from Artemisia species are generally used, and most of the species have similar morphology, which often leads to adulteration and misuse. This study assembled five complete chloroplast genomes of three Artemisia species, two accessions of A. gmelinii and A. capillaris, and one A. fukudo. Through comparative analysis, we revealed genomic variations and phylogenetic relationships between these species and developed seven InDel-based barcode markers which discriminated the tested species from each other. Additionally, we analyzed specialized metabolites from the species using LC-MS and suggested chemical markers for the identification and authentication of these herbs. We expect that this integrated and complementary authentication method would aid in reducing the misuse of Artemisia species.

Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia

Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping-by-sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 - trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment.

The karyotype, genome survey, and assembly of Mud artemisia (Artemisia selengensis)

BACKGROUND

Artemisia selengensis is traditional Chinese medicine and phytochemical analysis indicated that A. selengensis contains essential oils, fatty acids and phenolic acids. The lack of reference genomic information may lead to tardiness in molecular biology research of A. selengensis.

METHOD AND RESULTS

Karyotype analysis, genome survey, and genome assembly was employed to acquire information on the genome structure of A. selengensis. The chromosome number is 2n = 2x = 36, karyotype formula is 28 m + 8Sm, karyotype asymmetry coefficient is 58.8%, and karyotypes were symmetric to Stebbins' type 2A. Besides, the flow cytometry findings reported that the mean peak value of fluorescent intensity is 1,170,677, 2C DNA content is 12 pg and the genome size was estimated to be approximately 5.87 Gb. Furthermore, the genome survey generates 341,478,078 clean reads, unfortunately, after K-mer analysis, no significant peak can be observed, the heterozygosity, repetitive rate and genome size was unable to estimated. It is speculated that this phenomenon might be due to the complexity of genome structure. 37,266 contigs are preliminary assembled with Oxford Nanopore Technology (ONT) sequencing, totaling 804 Mb and GC content was 34.08%. The total length is 804,475,881 bp, N50 is 29,624 bp, and the largest contig length is 239,792 bp.

CONCLUSION

This study reveals the preliminary information of genome size of A. selengensis. These findings may provide supportive information for sequencing and assembly of whole-genome sequencing and encourage the progress of functional gene discovery, genetic improvement, evolutionary study, and structural studies of A. selengensis.

Contrasting effects of local environment and grazing pressure on the genetic diversity and structure of Artemisia frigida

Drylands count among the most globally extensive biomes, and while many desert and dry rangeland ecosystems are under threat, genetic structures of dryland species are still rarely studied. Artemisia frigida is one of the most widely distributed plant species in the temperate rangelands of Eurasia and North America, and it also dominates in many habitats of Mongolia due to its tolerance to low temperatures, drought and disturbance. Local environmental conditions and grazing pressure can influence species performance and affect spatial patterns of genetic diversity in contrasting ways, and our study set out to evaluate such effects on the genetic diversity and structure of A. frigida. We first developed new species-specific Simple Sequence Repeats (SSRs) markers using whole genome sequencing. We then analysed 11 populations of A. frigida that had been sampled along a large climatic gradient in Mongolia, which were sub-structured according to three levels of grazing intensity. Estimates of genetic diversity at the population level were high (HO = 0.56, HE = 0.73) and tended to increase with higher precipitation and soil nutrient availability. Grazing had no effect on genetic diversity, however, a high number of grazing-specific indicator alleles was found at grazed sites. Genetic differentiation among populations was extremely low (global GST = 0.034). Analysis of Molecular Variance revealed 5% variance between populations along the climatic gradient, with 3% of the variance being partitioned among different grazing intensity levels. We found no relationship between geographic and genetic distances, and thus no isolation by distance in this widely distributed species. The relatively low genetic structuring suggests that considerable gene flow exists among A. frigida populations across the rangelands of Mongolia, in spite of the pervasive grazing in the region.

The Application of Flow Cytometry for Estimating Genome Size, Ploidy Level Endopolyploidy, and Reproductive Modes in Plants

Over the years, the amount of DNA in a nucleus (genome size) has been estimated using a variety of methods, but increasingly, flow cytometry (FCM) has become the method of choice. The popularity of this technique lies in the ease of sample preparation and in the large number of particles (i.e., nuclei) that can be analyzed in a very short period of time. This chapter presents a step-by-step guide to estimating the nuclear DNA content of plant nuclei using FCM. Attempting to serve as a tool for daily laboratory practice, we list, in detail, the equipment required, specific reagents and buffers needed, as well as the most frequently used protocols to carry out nuclei isolation. In addition, solutions to the most common problems that users may encounter when working with plant material and troubleshooting advice are provided. Finally, information about the correct terminology to use and the importance of obtaining chromosome counts to avoid cytological misinterpretations of the FCM data are discussed.

Assessing Diversity in the Camelina Genus Provides Insights into the Genome Structure of Camelina sativa

Camelina sativa (L.) Crantz an oilseed crop of the Brassicaceae family is gaining attention due to its potential as a source of high value oil for food, feed or fuel. The hexaploid domesticated C. sativa has limited genetic diversity, encouraging the exploration of related species for novel allelic variation for traits of interest. The current study utilized genotyping by sequencing to characterize 193 Camelina accessions belonging to seven different species collected primarily from the Ukrainian-Russian region and Eastern Europe. Population analyses among Camelina accessions with a 2n = 40 karyotype identified three subpopulations, two composed of domesticated C. sativa and one of C. microcarpa species. Winter type Camelina lines were identified as admixtures of C. sativa and C. microcarpa. Eighteen genotypes of related C. microcarpa unexpectedly shared only two subgenomes with C. sativa, suggesting a novel or cryptic sub-species of C. microcarpa with 19 haploid chromosomes. One C. microcarpa accession (2n = 26) was found to comprise the first two subgenomes of C. sativa suggesting a tetraploid structure. The defined chromosome series among C. microcarpa germplasm, including the newly designated C. neglecta diploid née C. microcarpa, suggested an evolutionary trajectory for the formation of the C. sativa hexaploid genome and re-defined the underlying subgenome structure of the reference genome.

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.

Assessment of Iranian endemic Artemisia khorassanica: karyological, genome size, and gene expressions involved in artemisinin production

The species of Artemisia, one of the largest genera of the family Asteraceae, are frequently utilized for the treatment of diseases such as malaria, hepatitis, cancer, inflammation, and infections by fungi, bacteria, and viruses. Karyological studies were performed on 18 Artemisia khorassanica populations: eleven were diploid (2n = 18) and seven were tetraploid (2n = 36). The mean chromosome lengths were 3.61 and 3.84 µm for diploids and tetraploids, respectively. Two chromosome types ("m", "sm") formed karyotype formulas "18m" for diploids and "36m" and "34m + 2sm" for tetraploids. The mean 2C DNA contents were 5.91 and 11.53 pg in diploids and tetraploids, respectively. The transcription levels of key genes involved in artemisinin production were compared in diploid (B, D, H) and tetraploid (O, P, R) A. khorassanica relative to A. annua as a standard species. No artemisinin content was detected in diploid and tetraploid A. khorassanica populations. No significant diefrences were detected between diploids and tetraploids in terms of DXR , HMGR, FDS, and ADS gene expression. This implies that most of the genomic amplification likely occurs in the amount of repetitive DNA and not in unique sequences. The DBR2 gene was expressed in the diploid A. khorassanica in a low amount but silenced in the autotetraploid A. khorassanica.

Genome Size Diversity in Lilium (Liliaceae) Is Correlated with Karyotype and Environmental Traits

Genome size (GS) diversity is of fundamental biological importance. The occurrence of giant genomes in angiosperms is restricted to just a few lineages in the analyzed genome size of plant species so far. It is still an open question whether GS diversity is shaped by neutral or natural selection. The genus Lilium, with giant genomes, is phylogenetically and horticulturally important and is distributed throughout the northern hemisphere. GS diversity in Lilium and the underlying evolutionary mechanisms are poorly understood. We performed a comprehensive study involving phylogenetically independent analysis on 71 species to explore the diversity and evolution of GS and its correlation with karyological and environmental traits within Lilium (including Nomocharis). The strong phylogenetic signal detected for GS in the genus provides evidence consistent with that the repetitive DNA may be the primary contributors to the GS diversity, while the significant positive relationships detected between GS and the haploid chromosome length (HCL) provide insights into patterns of genome evolution. The relationships between GS and karyotypes indicate that ancestral karyotypes of Lilium are likely to have exhibited small genomes, low diversity in centromeric index (CVCI) values and relatively high relative variation in chromosome length (CVCL) values. Significant relationships identified between GS and annual temperature and between GS and annual precipitation suggest that adaptation to habitat strongly influences GS diversity. We conclude that GS in Lilium is shaped by both neutral (genetic drift) and adaptive evolution. These findings will have important consequences for understanding the evolution of giant plant genomes, and exploring the role of repetitive DNA fraction and chromosome changes in a plant group with large genomes and conservation of chromosome number.

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 application of flow cytometry for estimating genome size and ploidy level in plants

Over the years, the amount of DNA in a nucleus (genome size) has been estimated using a variety of methods, but increasingly, flow cytometry (FCM) has become the method of choice. The popularity of this technique lies in the ease of sample preparation and in the large number of particles (i.e., nuclei) that can be analyzed in a very short period of time. This chapter presents a step-by-step guide to estimating the nuclear DNA content of plant nuclei using FCM. Attempting to serve as a tool for daily laboratory practice, we list, in detail, the equipment required, specific reagents, and buffers needed, as well as the most frequently used protocols to carry out nuclei isolation. In addition, solutions to the most common problems that users may encounter when working with plant material and troubleshooting advice are provided. Finally, information about the correct terminology to use and the importance of obtaining chromosome counts to avoid cytological misinterpretations of the FCM data are discussed.

Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants

Background

Artemisia frigida Willd. is an important Mongolian traditional medicinal plant with pharmacological functions of stanch and detumescence. However, there is little sequence and genomic information available for Artemisia frigida, which makes phylogenetic identification, evolutionary studies, and genetic improvement of its value very difficult. We report the complete chloroplast genome sequence of Artemisia frigida based on 454 pyrosequencing.

Methodology/Principal Findings

The complete chloroplast genome of Artemisia frigida is 151,076 bp including a large single copy (LSC) region of 82,740 bp, a small single copy (SSC) region of 18,394 bp and a pair of inverted repeats (IRs) of 24,971 bp. The genome contains 114 unique genes and 18 duplicated genes. The chloroplast genome of Artemisia frigida contains a small 3.4 kb inversion within a large 23 kb inversion in the LSC region, a unique feature in Asteraceae. The gene order in the SSC region of Artemisia frigida is inverted compared with the other 6 Asteraceae species with the chloroplast genomes sequenced. This inversion is likely caused by an intramolecular recombination event only occurred in Artemisia frigida. The existence of rich SSR loci in the Artemisia frigida chloroplast genome provides a rare opportunity to study population genetics of this Mongolian medicinal plant. Phylogenetic analysis demonstrates a sister relationship between Artemisia frigida and four other species in Asteraceae, including Ageratina adenophora, Helianthus annuus, Guizotia abyssinica and Lactuca sativa, based on 61 protein-coding sequences. Furthermore, Artemisia frigida was placed in the tribe Anthemideae in the subfamily Asteroideae (Asteraceae) based on ndhF and trnL-F sequence comparisons.

Conclusion

The chloroplast genome sequence of Artemisia frigida was assembled and analyzed in this study, representing the first plastid genome sequenced in the Anthemideae tribe. This complete chloroplast genome sequence will be useful for molecular ecology and molecular phylogeny studies within Artemisia species and also within the Asteraceae family.

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.

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.

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.

Genome size in Hieracium subgenus Hieracium (Asteraceae) is strongly correlated with major phylogenetic groups

BACKGROUND AND AIMS

Hieracium subgenus Hieracium is one of the taxonomically most intricate groups of vascular plants, due to polyploidy and a diversity of breeeding systems (sexuality vs. apomixis). The aim of the present study was to analyse nuclear genome size in a phylogenetic framework and to assess relationships between genome size and ploidy, breeding system and selected ecogeographic features.

METHODS

Holoploid and monoploid genome sizes (C- and Cx-values) of 215 cultivated plants from 89 field populations of 42 so-called 'basic' Hieracium species were determined using propidium iodide flow cytometry. Chromosome counts were available for all analysed plants, and all plants were tested experimentally for their mode of reproduction (sexuality vs. apomixis). For constructing molecular phylogenetic trees, the external transcribed spacer region of nuclear ribosomal DNA was used.

KEY RESULTS

The mean 2C values differed up to 2.37-fold among different species (from 7.03 pg in diploid to 16.67 in tetraploid accessions). The 1Cx values varied 1.22-fold (between 3.51 and 4.34 pg). Variation in 1Cx values between conspecific (species in a broad sense) accessions ranged from 0.24% to 7.2%. Little variation (not exceeding the approximate measurement inaccurracy threshold of 3.5%) was found in 33 species, whereas variation higher than 3.5% was detected in seven species. Most of the latter may have a polytopic origin. Mean 1Cx values of the three cytotypes (2n, 3n and 4n) differed significantly (average of 3.93 pg in diploids, 3.82 pg in triploids and 3.78 pg in tetraploids) indicating downsizing of genomes in polyploids. The pattern of genome size variation correlated well with two major phylogenetic clades which were composed of species with western or eastern European origin. The monoploid genome size in the 'western' species was significantly lower than in the 'eastern' ones. Correlation of genome size with latitude, altitude and selected ecological characters (light and temperature) was not significant. A longitudinal component was only apparent for the whole data set, but absent within the major lineages.

CONCLUSIONS

Phylogeny was the most important factor explaining the pattern of genome size variation in Hieracium sensu stricto, species of western European origin having significantly lower genome size in comparison with those of eastern European origin. Any correlation with ecogeographic variables, including longitude, was outweighed by the divergence of the genus into two major phylogenetic lineages.

Linkage of 35S and 5S rRNA genes in Artemisia (family Asteraceae): first evidence from angiosperms

Typically in plants, the 5S and 35S ribosomal DNA (rDNA) encoding two major ribosomal RNA species occur at separate loci. However, in some algae, bryophytes and ferns, they are at the same locus (linked arranged). Southern blot hybridisation, polymerase chain reactions (PCR), fluorescent in situ hybridisation, cloning and sequencing were used to reveal 5S and 35S rDNA genomic organisation in Artemisia. We observed thousands of rDNA units at two-three loci containing 5S rDNA in an inverted orientation within the inter-genic spacer (IGS) of 35S rDNA. The sequenced clones of 26-18S IGS from Artemisia absinthium appeared to contain a conserved 5S gene insertion proximal to the 26S gene terminus (5S rDNA-1) and a second less conserved 5S insertion (5S rDNA-2) further downstream. Whilst the 5S rDNA-1 showed all the structural features of a functional gene, the 5S-rDNA-2 had a deletion in the internal promoter and probably represents a pseudogene. The linked arrangement probably evolved before the divergence of Artemisia from the rest of Asteraceae (>10 Myrs). This arrangement may have involved retrotransposons and once formed spread via mechanisms of concerted evolution. Heterogeneity in unit structure may reflect ongoing homogenisation of variant unit types without fixation for any particular variant.

Genome size variation in the Artemisia arborescens complex (Asteraceae, Anthemideae) and its cultivars

Different wild Mediterranean populations of Artemisia arborescens from diverse locations representing its geographical distribution, as well as some of its well-known cultivars and some specimens cultivated as ornamentals in gardens, streets, roads and nurseries, were analysed for genome size. Other closely related species endemic to Macaronesia, Artemisia canariensis, Artemisia argentea, and Artemisia gorgonum, were also analysed, and their nuclear DNA amount has been related to the biogeography of this group of species. Additionally, 5 populations of the closely related Artemisia absinthium were analysed to establish comparisons. Measurements acquired by flow cytometry ranged from 8.29 to 11.61 pg for 2C values. Statistically significant differences of 2C nuclear DNA amounts with respect to factors such as insularity or domestication have been detected. However, quite a low intraspecific genome size variation has been found in these species. Furthermore, the study also addressed the possible hybrid origins and possible misidentifications of some of the supposed cultivars of A. arborescens.