Anisotropic flow in event-by-event ideal hydrodynamic simulations of sqrt(s_{NN})=200 GeV Au+Au collisions

We calculate flow observables with the NeXSPheRIO ideal hydrodynamic model and make the first comparison to the complete set of mid-rapidity flow measurements made by the PHENIX collaboration in top energy Au+Au collisions. A simultaneous calculation of v_2, v_3, v_4, and the first event-by-event calculation of quadrangular flow defined with respect to the v_2 event plane (v_4{Psi_2}) gives good agreement with measured values, including the dependence on both transverse momentum and centrality. This provides confirmation that the collision system is indeed well described as a quark-gluon plasma with an extremely small viscosity, and that correlations are dominantly generated from collective effects. In addition we present a prediction for v_5.Comment: 5 pages, 2 figures. Revised version. Corrections in eq.(7) and Fig.

Directed flow at mid-rapidity in event-by-event hydrodynamics

Fluctuations in the initial geometry of a nucleus-nucleus collision have been recently shown to result in a new type of directed flow (v_1) that, unlike the usual directed flow, is also present at midrapidity. We compute this new v_1 versus transverse momentum and centrality for Au-Au collisions at RHIC using the hydrodynamic code NeXSPheRIO. We find that the event plane of v_1 is correlated with the angle of the initial dipole of the distribution, as predicted, though with a large dispersion. It is uncorrelated with the reaction plane. Our results are in excellent agreement with results inferred from STAR correlation data.Comment: 7 pages, 6 figures; Figure data files included with source; Version accepted for publication (minor changes

Mapping the hydrodynamic response to the initial geometry in heavy-ion collisions

We investigate how the initial geometry of a heavy-ion collision is transformed into final flow observables by solving event-by-event ideal hydrodynamics with realistic fluctuating initial conditions. We study quantitatively to what extent anisotropic flow (nu(n)) is determined by the initial eccentricity epsilon(n) for a set of realistic simulations, and we discuss which definition of epsilon(n) gives the best estimator of nu(n). We find that the common practice of using an r(2) weight in the definition of epsilon(n) in general results in a poorer predictor of nu(n) than when using r(n) weight, for n > 2. We similarly study the importance of additional properties of the initial state. For example, we show that in order to correctly predict nu(4) and nu(5) for noncentral collisions, one must take into account nonlinear terms proportional to epsilon(2)(2) and epsilon(2)epsilon(3), respectively. We find that it makes no difference whether one calculates the eccentricities over a range of rapidity or in a single slice at z = 0, nor is it important whether one uses an energy or entropy density weight. This knowledge will be important for making a more direct link between experimental observables and hydrodynamic initial conditions, the latter being poorly constrained at present.Agence Nationale de la RechercheAgence Nationale de la Recherche [ANR-08-BLAN-0093-01]Cofecub [Uc Ph 113/08Cofecub [Uc Ph 113/082007.1.875.43.9]2007.1.875.43.9]FAPESP [09/50180-0, 09/16860-3]FAPESPCNPqCNPq [301141/2010-0]European Research CouncilEuropean Research Council [ERC-AD-267258

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

Background: Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin x sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results: Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions: A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents

Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers.

Background and Aims The origin of limes and lemons has been a source of conflicting taxonomic opinions. Biochemical studies, numerical taxonomy and recent molecular studies suggested that cultivated Citrus species result from interspecific hybridization between four basic taxa (C. reticulata, C. maxima, C. medica and C. micrantha). However, the origin of most lemons and limes remains controversial or unknown. The aim of this study was to perform extended analyses of the diversity, genetic structure and origin of limes and lemons. Methods The study was based on 133 Citrus accessions. It combined maternal phylogeny studies based on mitochondrial and chloroplastic markers, and nuclear structure analysis based on the evaluation of ploidy level and the use of 123 markers, including 73 basic taxa diagnostic single nucleotide polymorphism (SNP) and indel markers. Key Results The lime and lemon horticultural group appears to be highly polymorphic, with diploid, triploid and tetraploid varieties, and to result from many independent reticulation events which defined the sub-groups. Maternal phylogeny involves four cytoplasmic types out of the six encountered in the Citrus genus. All lime and lemon accessions were highly heterozygous, with interspecific admixture of two, three and even the four ancestral taxa genomes. Molecular polymorphism between varieties of the same sub-group was very low. ConclusionsCitrus medica contributed to all limes and lemons and was the direct male parent for the main sub-groups in combination with C. micrantha or close papeda species (for C. aurata, C. excelsa, C. macrophylla and C. aurantifolia – ‘Mexican’ lime types of Tanaka’s taxa), C. reticulata (for C. limonia, C. karna and C. jambhiri varieties of Tanaka’s taxa, including popular citrus rootstocks such as ‘Rangpur’ lime, ‘Volkamer’ and ‘Rough’ lemons), C. aurantium (for C. limetta and C. limon – yellow lemon types – varieties of Tanaka’s taxa) or the C. maxima × C. reticulata hybrid (for C. limettioides – ‘Palestine sweet’ lime types – and C. meyeri). Among triploid limes, C. latifolia accessions (‘Tahiti’ and ‘Persian’ lime types) result from the fertilization of a haploid ovule of C. limon by a diploid gamete of C. aurantifolia, while C. aurantifolia triploid accessions (‘Tanepao’ lime types and ‘Madagascar’ lemon) probably result from an interspecific backcross (a diploid ovule of C. aurantifolia fertilized by C. medica). As limes and lemons were vegetatively propagated (apomixis, horticultural practices) the intra-sub-group phenotypic diversity results from asexual variations

COMPARATIVE VALUES OF SSRS, SNPS AND INDELS FOR CITRUS GENETIC DIVERSITY ANALYSIS

SSRs have been considered as almost ideal markers for genetic diversity analysis. With the increasing availability of sequencing data, SNPs and InDels become major classes of codominant markers with genome wide coverage. We have analyzed the respective values of SSRs, InDels, and SNPs for intra and interspecific Citrus genetic diversity analysis. Moreover, we have compared the diversity structure revealed by markers mined in a single heterozygous genotype (clementine) and markers mined from a large interspecific survey. A random set of markers was selected for each marker class to genotype 48 citrus accessions. SSRs were the most polymorphic markers at the intraspecific level allowing complete varietal differentiation within basic taxa (C. reticulata, C. maxima, C. medica). However, SSRs gave the lowest values for interspecific differentiation, followed by SNPs and InDels, that in average displayed low intraspecific variability but high interspecific differentiation. A clear effect of the discovery panel was observed for SNPs and InDels. The ascertainment biases associated with the clementine heterozygosity mining resulted mainly in an over estimation of within C. reticulata diversity and an underestimation of the interspecific differentiation. In conclusion pluri-allelic SSRs are very useful for intraspecific structure analysis but have limitations for interspecific and phylogenetic studies. SNPs and InDels mined in large discovery panels appear to allow efficient selection of more specialized markers with high potential for phylogenetic diagnosis and to decipher the interspecific mosaic structure of secondary cultivated species or to analyze intraspecific diversity. Several SNP genotyping methods are available for different analysis scales, from high throughput genotyping to small set of data production. With the ongoing resequencing projects, SNPs markers will soon be the most important class of markers for citrus genetics

Acta Horticulturae

SSRs have been considered as almost ideal markers for genetic diversity analysis. With the increasing availability of sequencing data, SNPs and InDels become major classes of codominant markers with genome wide coverage. We have analyzed the respective values of SSRs, InDels, and SNPs for intra and interspecific Citrus genetic diversity analysis. Moreover, we have compared the diversity structure revealed by markers mined in a single heterozygous genotype (clementine) and markers mined from a large interspecific survey. A random set of markers was selected for each marker class to genotype 48 citrus accessions. SSRs were the most polymorphic markers at the intraspecific level allowing complete varietal differentiation within basic taxa (C. reticulata, C. maxima, C. medica). However, SSRs gave the lowest values for interspecific differentiation, followed by SNPs and InDels, that in average displayed low intraspecific variability but high interspecific differentiation. A clear effect of the discovery panel was observed for SNPs and InDels. The ascertainment biases associated with the clementine heterozygosity mining resulted mainly in an over estimation of within C. reticulata diversity and an underestimation of the interspecific differentiation. In conclusion pluri-allelic SSRs are very useful for intraspecific structure analysis but have limitations for interspecific and phylogenetic studies. SNPs and InDels mined in large discovery panels appear to allow efficient selection of more specialized markers with high potential for phylogenetic diagnosis and to decipher the interspecific mosaic structure of secondary cultivated species or to analyze intraspecific diversity. Several SNP genotyping methods are available for different analysis scales, from high throughput genotyping to small set of data production. With the ongoing resequencing projects, SNPs markers will soon be the most important class of markers for citrus genetics

Cumulants of conserved charges in hydrodynamic simulations

We introduce a fast and simple method of computing cumulants of net-proton or net-charge fluctuations in event-by-event hydrodynamic simulations of heavy-ion collisions. One evaluates the mean numbers of particles in every hydrodynamic event. Cumulants are then expressed as a function of these mean numbers. We implement the corrections due to global conservation laws. The method is tested using ideal hydrodynamic simulations of Au+Au collisions at $\sqrt{s_{NN}}=200$ AGeV with the NeXSPheRIO code. Results are in good agreement with experimental data on net-proton and net-charge fluctuations by the STAR collaboration