2014), and Colchicaceae (Chacón et al. The development of new molecular and bioinformatic techniques has facilitated the inference of ancient WGDs. A list of the genetically placed scaffolds and their locations is presented in File S5 (http://datadryad.org/resource/doi:10.5061/dryad.635ds). To compute the expected number of changes along each branch, as well as the ancestral haploid chromosome numbers at internal nodes, the best-fitted model for both data sets was rerun using 5,000 simulations. ex = 4, x = 9, x = 23 (reviewed by Sancho and Freire (2009), chapter15. Saffron has long been the world's most costly spice by weight. In these situations, the age estimate more consistent with previous estimations was selected. endstream endobj startxref Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2014: Colchicaceae; Pellicer et al. Chromosome Number of the Most Recent Common Ancestor of the Asteraceae Family and of the Main Tribes, under the Best Model of Chromosome Evolution for Each Coding Scheme (Polymorphic and Single Data) and Considering Both Methods of chromEvol for Inferring Ancestral States (Bayesian Phylogenetic Inference, Bayes). 2010) and to estimate the ancestral chromosome numbers at the internal nodes of the tree (Glick and Mayrose 2014). dx = 9 seems to be available for all or nearly all the base numbers listed. 2014: Araceae). 2008, 2016) to be shared with Calyceraceae (the sister family of Asteraceae) was not observed in our case. The branch lengths were scaled according with the software author’s instructions. The frequency of each chromosome number was calculated considering all the species within a genus. 2009; Fawcett and Van de Peer 2010; Vanneste et al. (2009), chapter 36. oVallès et al. A detailed analysis of the results obtained for each tribe reveals that in 71.74% of the cases the use of polymorphic data resulted in higher posterior probabilities than single data in 27.27% of the tribes with a PP higher than 0.90. Overall, our results are in agreement with previous hypotheses of ancestral chromosome numbers for the Asteraceae and for many of its tribes (table 3); i.e., n = 9 (under Bayesian inference) is the most probable ancestral haploid chromosome number (Solbrig 1977; Cronquist 1981; Bremer 1994; Semple and Watanabe 2009; Bala and Gupta 2013). been reported in a number of plant species [2â 7], but reports on cytomictic variations in safflower is meager due to pure staining ability, problem of chromosome stickiness and … q2Watanabe et al. Section Pachysedum, Chromosome numbers in the tribes Anthemideae and Inuleae (Asteraceae), The evolutionary significance of ancient genome duplications, Tangled up in two : a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution, Chromosome numbers and karyotypes in Asteraceae, Phylocom: software for the analysis of phylogenetic community structure and trait evolution, The frequency of polyploid speciation in vascular plants. The linear rate parameters (i.e., linear chromosome loss, δ1, and linear chromosome gain, λ1, rates) and the base chromosome number rate for transitions (ν) always presented very low values (table 2). This result supports the conclusion that genome duplications (including whole- and demiduplications), and dysploidy (including both ascending and descending) were very important events in the evolution of Asteraceae. Based on the best-fitted model, we found a significant number (n = 22, or 28.95% of the total) of polyploidy events with an expectation ≥ 0.95 (fig. 2007); x = 17–19 (Smith 1975) and x = 8 (Stuessy 1977) cited in Robinson (1981). 2009; Wood et al. 2003; Bowers et al. In all cases, the observed differences were very small (table 2). Safflower / kusume BN:- Carthamus tinctorius Family:- Compositae Origin:- Mediterranean and Persian gulf Chromosome no:- 2n=24 Cultivated spp. More than two hundred chromosome duplications (including demiduplications) were inferred by the best model (table 2). 1 and Supplementary Data, Supplementary Data online). All models were fitted twice considering either single or polymorphic data, and the null hypothesis (no polyploidy) was tested using an AIC test. 1 Names, taxonomy and centres of diversity9 1.1 Names 9 1.2 Species 9 1.3 Cultivated safflower and its relatives 9 1.4 Centres of similarity of C. tinctorius11 1.5 Other Carthamusspecies with 12 pairs of chromosomes 11 1.6Carthamusspecies with 10 pairs of chromosomes 12 1.7Carthamusspecies with 11, 22 and 32 pairs of chromosomes 12 1.8 Alloploids of cultivated safflower with species of different … Fenugreek (Trigonella foenum-graecum L.) is an annual forage legume and a traditional spice and aromatic crop that has been grown for centuries across the Indian subcontinent. All the cultivars showed 2n=2x=24 chromosome number having meta and sub-meta centric chromosomes ranging in size from 1.55 to 4.63 µm. 2014). Alternative methods such as comparative genetic mapping, analysis of specific gene families, identification of duplicated genes in expressed sequence tag (EST) collections, and fingerprinting techniques (e.g., AFLP) have also been used (Ainouche et al. Each species was counted only one time, for each chromosome number. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. 2007; Jiao et al. 2014). For full access to this pdf, sign in to an existing account, or purchase an annual subscription. 2014: Melanthiaceae; Sousa et al. Both sets have a null model (Mc0 and Ml0) that assumes no polyploidization events. In addition, the Mc0 model that considers no polyploidization events on the evolution of haploid chromosome number was always the model with the worst score (table 1); this result further supports the importance of genome duplications in the evolution of Asteraceae. Syst. In contrast, dysploidy has been thought to arise accidentally, and no adaptive reason has been found that could explain its predominant occurrence in particular clades (Chacón et al. In addition, those lineages that have experienced WGDs before their diversification, such as Hyalideae, Wunderlichieae, Oldenburgieae, or Tarchonantheae, are much less species rich than other lineages where WGDs were not observed, such as in Senecioneae, Astereae, Anthemideae, and Cichorieae. We performed low-coverage, whole-genome shotgun sequencing on 96 F6 recombinant inbred lines (RILs) of a cross between safflower ( Carthamus tinctorius L.) and its wild progenitor ( C. palaestinus Eig). This sunflower species is also used as wild bird food, as livestock forage (as a meal or a silage plant), in some industrial applications, and as an ornamental in domestic gardens. = Arctotidinae subtribe; Gort. Overall, our approach did not infer any paleoploidization events near the base of the family, nor any paleoploidization shared with the sister family, Calyceraceae. This model inferred that the most probable ancestral chromosome number of Asteraceae is n = 9. The software offers 10 models based on different combinations of nine parameters: chromosome loss rate (δ) that considers that the number of chromosomes might decrease by one, with rate δ; chromosome gain rate (λ) that assumes that the number of chromosomes might increase by one, with rate λ; chromosome duplication rate (ρ) that considers that the number of chromosomes might … 2012: Araceae; Ocampo and Columbus 2012: Portulaca, Portulaceae; Cristiano et al. In these studies, no particular bias toward any of the chromosomal events that the model considers was observed. Note.—The maximum likelihood (ML) and AIC value of the best model in each case is also given. The number of chromosomes of the genera and species that belong to Asteraceae and of the outgroup families Calyceraceae and Goodeniaceae were collected from the Index to Chromosome numbers in Asteraceae (http://www.lib.kobe-u.ac.jp/infolib/meta_pub/G0000003asteraceae_e; last assessed 17 July 2014) and from the Chromosome Counts Database (CCDB; http://ccdb.tau.ac.il/; last assessed 22 February 2016; Rice et al. Bot 12:781–802. %%EOF 2010). Only the polymorphic coding scheme was used as it includes all chromosome numbers, being the most complete data set under analysis and the one with the highest amount of genetic variation observed at this level. The absence of polyploidization events at the base of the tree is in agreement with the maintenance of the ancestral chromosome number of n = 9 inferred for the main tribes (fig. This is in accordance with the chromosome number transition observed between the ancestor (n = 9) and the common ancestor of these tribes (n = 27 and n = 18, respectively) (fig. Note.—The base numbers already reported in the literature for Asteraceae and its main tribes are also given. 2002; Barker et al. 2010) has been applied to the study of chromosome number evolution in about a dozen cases, either using simulated or empirical data sets (Mayrose et al. Note.—For the root fixed analyses, the ancestral number given by ML method and the two best ancestral numbers as inferred by the Bayesian analyses were considered. As chromEvol only enables identification of those branches in which a polyploidization event occurred, but not the exact period of time along the branch, polyploidization events were simply depicted in the middle of the respective branches. 1960) or also x = 18 (Watanabe et al. 2009). Karyotypic changes through dysploidy persist longer over evolutionary time than polyploid changes, Angiosperm polyploids and their road to evolutionary success, Everywhere but Antarctica : using a supertree to understand the diversity and distribution of the Compositae, ChromEvol: assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny, Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size, Genomic clues to the evolutionary success of polyploid plants, Molecular phylogeny of Eupatorieae (Asteraceae) estimated from cpDNA RFLP and its implication for the polyploid origin hypothesis of the tribe, The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Ancestral polyploidy in seed plants and angiosperms, A genome triplication associated with early diversification of the core eudicots, Rapid chromosome evolution in recently formed polyploids in, Plant Genome Diversity: Physical Structure, Behaviour and Evolution of Plant Genomes, Fast diploidization in close mesopolyploid relatives of, Probabilistic models of chromosome number evolution and the inference of polyploidy, Recently formed polyploid plants diversify at lower rates, Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis, Diversification and reticulation in the circumboreal fern genus, Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses, Reconciling Gene and Genome Duplication Events: Using Multiple Nuclear Gene Families to Infer the Phylogeny of the Aquatic Plant Family Pontederiaceae, Molecular phylogenetics, historical biogeography, and chromosome number evolution of. When more than one chromosome number had the same frequency, the smallest chromosome number was selected. 2011), a considerable phylogenetic distance from the origin of Asteraceae. Barker et al. (2008) may have occurred somewhere after the divergence of Asteraceae and Solanaceae, namely in the split between Campanulids and Lamiids (Soltis et al. Mandáková TJoly SKrzywinski MMummenhoff KLysak MA. One WGD was placed near the origin of the family just prior to the rapid radiation of its tribes, whereas the other two were located near the base of the tribes Mutisieae and Heliantheae (Barker et al. 2010), chromosome numbers vary from n = 2 in six angiosperm species (Vanzela et al. �G 2013: Thalictrum, Ranunculaceae; Chacón et al. The best-fitted evolutionary model (Mc2 model) showed that dysploidy and polyploidy were very frequent events (table 1). (2016) using a new algorithm, MAPS, evidenced the occurrence of a shared paleotetraploidization event at the base of Calyceraceae, and that most Asteraceae (except Barnadesia) are descendants of a paleohexaploid. We believe that the use of chromEvol gives valuable estimates of chromosomal evolution, providing exciting hypotheses that can be examined in the future. May have originated from two related spp. Variability in the number, size, and location of the two repeated sequences provided identification of most of the chromosomes in the otherwise not too distinctive homologues within the complement. Therefore, it is now possible to evaluate the importance of genomic events, such as WGDs, dysploidy, and demipolyploidy, in the evolution of a group. Systematics, Evolution, and Biogeography of Compositae, The evolution of Colchicaceae, with a focus on chromosome numbers, Cytogenetic and molecular analyses reveal a divergence between, An integrated system of classification of flowering plants, A global perspective on Campanulaceae: biogeographic, genomic, and floral evolution, Maximum likelihood inference implies a high, not a low, ancestral haploid chromosome number in Araceae, with a critique of the bias introduced by "x". Safflower / kusume BN:- Carthamus tinctorius Family:- Compositae Origin:- Mediterranean and Persian gulf Chromosome no:- 2n=24 Cultivated spp. For most of the main lineages of Asteraceae, the estimated ancestral haploid numbers were mainly n = 9 and n = 10 with some exceptions, ranging from n = 7 to n = 27 (table 3, fig. Chromosome cytology and evolution in Eupatorieae (Asteraceae). 2009). The largest eukaryotic genome of them all ? The software offers 10 models based on different combinations of nine parameters: chromosome loss rate (δ) that considers that the number of chromosomes might decrease by one, with rate δ; chromosome gain rate (λ) that assumes that the number of chromosomes might increase by one, with rate λ; chromosome duplication rate (ρ) that considers that the number of chromosomes might double, with rate ρ; chromosome demiduplication rate (μ) that assumes the union of reduced and unreduced gametes leading to, for example, triplication events, with rate μ; linear chromosome loss rate (δ1) that considers that the chromosome loss rate depends on the current number of chromosomes; linear chromosome gain rate (λ1) that considers that the chromosome gain rate depends on the current number of chromosomes; base chromosome number (β) that is the monoploid chromosome number; base chromosome number rate for transitions (ν); and the possibility to define whether the base-number is optimized by the program or not. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In each coding scheme, the rates of chromosome loss (δ), gain (λ), and duplication (ρ) were equal when the best model or all models were averaged (using the weighting procedure). 2012; Glick and Mayrose 2014), to describe the evolution of chromosome numbers in a given lineage, working under a robust probabilistic inference framework that considers both dysploidy and polyploidy. It was observed that the base chromosome number in all the studied populations was X = 12 and the somatic number 2n = 2X = 24. Ultrametric trees or phylograms for ancestral state reconstruction: does it matter? 2013: Atta and Acromyrmex, leafcutter ants of tribe Attini; Harpke et al. In our study, which includes 11 species/genera of the tribe, three WGD events were observed: two events along the evolution of Brachyclados and Chaptalia and another before the diversification of Adenocaulon, together with two demiduplication events along the evolution of Trichocline and Leibnitzia. The duplication and demiduplication events inferred in the best-fitted model were mapped onto the phylogenetic tree. A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae, Chromosome numbers in Compositae. 2011; Jiao et al. The chromosome number in the five accessions is 2n=22 (x=11). is considered a very complex group that still lacks full resolution of its phylogenetic relationships (Funk et al. Therefore, all these results should be considered with caution and deserve further detailed analyses once the present limitations are overcome. 2008) observed at the origin of Asteraceae might be due to the use of different approaches. This paper deals mainly with the stages of somatic cycle of Safflower chromosomes with special reference to the chromosome number and the prophasic and anaphasic structure in relation to the chromomeric hypo-thesis of chromosome structure. In our case, the use of different chromosome number coding schemes affected the number of events that occurred along the branches of the tree, but did not affect the selection of the best model of chromosome evolution. 2008, 2016) were not observed in our study (fig. The chromosome number of the progenitor is, probably, = 10, and the two telocentric chromosomes of C. divaricatus (n = 11) are believed to be derived from the large metacentric chromosome of = 10 species (probably C. dentatus). 2014; Tank et al. 1 and Supplementary Data, Supplementary Data online), as suggested by Barker et al. (2005), Watanabe (2009) cited in Watanabe et al. 2005). Cytogenetic studies concerning karyotype and meiotic analyses were performed in thirty-seven cultivars of C. tinctorius grown in Iran. aSolbrig (1977), Cronquist (1981), Bremer (1994), and Bala and Gupta (2013). 1; for further and more precise information on all the ancestral numbers inferred, see Supplementary Data Figure S1). vRobinson (1981) and Baldwin et al. May have originated from two related spp. Prepared by, HASANALI NADAF Jr M.Sc (GPB) safflower 2. Mondragón-Palomino MHiese LHärter AKoch MATheiβen G. Pellicer JKelly LJLeitch IJZomlefer WBFay MF. Safflower belongs to a Genomic DNA of two safflower accessions (PI: 560172 and 560175) was used as template for standardization of PCR conditions. bIn brackets, the numbers indicate the descending order of the best model. 2009). The number of chromosome duplications was higher than the number of chromosome demiduplications independently of the coding scheme (table 2). If you are not fond of the flavor of saffron but want your dish to have a bright yellow color, safflower may be ideal for you. In some cases, the age clade data were not consistent among sources. 2008, 2016) are highlighted as red and orange branches, respectively. You can use saffron in place of safflower in dishes where its strong flavor will not be a problem. 2011: Pontederiaceae; Cusimano et al. Nutritional parameters of vegetable safflower… The obtained results and potential causes of these discrepancies are discussed. This result, as well as the lack of congruence with the results of Barker et al. (2007), and Ward et al. 1 ), mainly grown in dry hot climates as an oil seed, birdseed or for its flowers, used as dyes and for medicinal purposes. 2005; Baldwin 2009; Kilian et al. Most of the age estimates were selected based on molecular dating through fossil calibration although other dating methods were also considered in particular cases (e.g., geological dating; see Supplementary Data, Supplementary Data online). This approach allowed us to incorporate a very high number of taxa (588 taxa), in an attempt to improve precision in the detection and localization of chromosomal change events in the evolution of Asteraceae. The present study also revealed the occurrence of several WGDs along the evolution of several lineages of Asteraceae. A chromosome number of 2n= 24 was observed in five Indian forms of safflower, and 12 bivalents were also observed at meiosis. The discrepancy between our study and previous work (Barker et al. Chromosome Number of Different Crop Material Agronomy Horticulture Plant Pathology Entemology Plant Breeding Genetics Current Affairs The safflower seed also used to produce oil. 2009) was first translated into a Newick tree file format. Data deposition: The chromosomal data was deposited under figshare (polymorphic data: https://figshare.com/s/9f61f12e0f33a8e7f78d, DOI: 10.6084/m9.figshare.4083264; single data: https://figshare.com/s/7b8b50a16d56d43fec66, DOI: 10.6084/m9.figshare.4083267; supertree: https://figshare.com/s/96f46a607a7cdaced33c, DOI: 10.6084/m9.figshare.4082370). The duplication event reported by Barker et al.