On the characterization of flowering curves using Gaussian mixture models

In this paper, we develop a statistical methodology applied to the characterization of flowering curves using Gaussian mixture models. Our study relies on a set of rosebushes flowering data, and Gaussian mixture models are mainly used to quantify the reblooming properties of each one. In this regard, we also suggest our own selection criterion to take into account the lack of symmetry of most of the flowering curves. Three classes are created on the basis of a principal component analysis conducted on a set of reblooming indicators, and a subclassification is made using a longitudinal $k$--means algorithm which also highlights the role played by the precocity of the flowering. In this way, we obtain an overview of the correlations between the features we decided to retain on each curve. In particular, results suggest the lack of correlation between reblooming and flowering precocity. The pertinent indicators obtained in this study will be a first step towards the comprehension of the environmental and genetic control of these biological processes.Comment: 28 pages, 27 figure

Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

International audienceBackground: With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus

Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots

Background: Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogenetics. Methodology/Principal Findings: Evolutionary rates of seven genes distributed along the carotenoid biosynthesis pathway

Impact de la sélection sur l'expression et la variabilité de séquence de gènes de la voie de biosynthèse des carotenoïdes chez la carotte cultivée

Document à consulter auprès du Directeur de thèse Diffusion du document : DOCUMENT EXCLU DU PRÊT - À CONSULTER CHEZ LE DIRECTEUR DE THESE Diplôme : Dr. d'UniversitéCarrot domestication and breeding have led to a diversity of cultivated carrot types exhibiting a high variability for carotenoid content in the root. Carotenoid biosynthesis genes are probably involved in carotenoid level differences, and could have been a selection target for plant breeding. The objectives of this thesis were (i) to investigate the role of transcriptional variations for carotenoid biosynthesis genes on carotenoid accumulation during root development in variously coloured carrots, and (ii) to characterise the impact of selection and demographic history, particularly genetic structure, on carotenoid biosynthesis gene sequence variability in cultivated carrots. Root transcript levels for eight carotenoid biosynthesis genes (PSY1, PSY2, PDS, ZDS1, ZDS2, LCYB1, LCYE, ZEP) were measured by quantitative RT-PCR during root development of white, yellow, orange and red cultivars. Polymorphism for partial sequences of seven carotenoid biosynthesis genes (IPI, PDS, CRTISO, LCYB1, LCYE, CHXE, ZEP) and three anonymous sequences, as well as for 17 microsatellites, were obtained for 48 individuals maximising cultivated carrot diversity. The investigated genes were expressed very early in carrot root development, and transcript levels increased, at the same rate as carotenoid accumulation. Expression patterns were not very different between colour types, which did not help to explain the differential accumulation of some carotenoids. The investigated carotenoid biosynthesis genes showed a high degree of nucleotide diversity (1 SNP in 22 bp), whereas linkage disequilibrium did not decay over a 700-1,000bp length. Sequences and microsatellites showed differentiation between Western and Eastern individuals. CRTISO, LCYE and LCYB1 genes exhibited an excess of polymorphism throughout the sample, suggesting the signature of balancing selection. PDS showed a deficit of polymorphism, suggesting directional or negative selection. LCYE and CHXE may have undergone a selective sweep during breeding for red and orange colour types, respectively. Genes acting upstream in the carotenoid biosynthesis pathway had a higher evolutionary rate than downstream genes, suggesting differential constraints. As a whole, these results show that allelic variations, more than carotenoid biosynthesis gene expression, could explain carotenoid content determinism in the carrot root. The selection signatures evidenced here will be validated by association study strategies, which need to be considered in relation to the presented results for genetic structure and linkage disequilibrium.La domestication puis la sélection de la carotte a abouti à une diversité de couleur des types variétaux cultivés associée à une grande variabilité de la teneur en caroténoïdes dans la racine. Les gènes de la voie de biosynthèse des caroténoïdes sont donc susceptibles d’être impliqués dans les différences de teneur en caroténoïdes chez la carotte et d’avoir été la cible de la sélection au cours de l’amélioration variétale. Les objectifs de cette thèse sont (i) de connaître le rôle des variations transcriptionnelles des gènes de la voie de biosynthèse des caroténoïdes dans l’accumulation de caroténoïdes au cours du développement de racines de différentes couleurs, et (ii) de déterminer l’impact de la sélection et de l’histoire démographique de l’espèce, notamment la structuration génétique, sur la variabilité de séquence des gènes de la voie de biosynthèse des caroténoïdes chez la carotte cultivée. Le niveau de transcrits racinaires de huit gènes de la voie de biosynthèse des caroténoïdes (PSY1, PSY2, PDS, ZDS1, ZDS2, LCYB1, LCYE, ZEP) a été mesuré par RT-PCR quantitative au cours du développement pour quatre cultivars à racine blanche, jaune, orange et rose. Le polymorphisme de portions de séquence de sept gènes de la voie de biosynthèse des caroténoïdes (IPI, PDS, CRTISO, LCYB1, LCYE, CHXE, ZEP) et de trois séquences anonymes ainsi que le génotype de 17 microsatellites ont été obtenus pour 48 individus maximisant la diversité de la carotte cultivée. Les gènes étudiés sont exprimés précocement au cours du développement de la racine de carotte et le niveau de transcrits s’accroît au fur et à mesure, en parallèle de l'accumulation des caroténoïdes. Les profils d’expression de ces gènes sont peu différents entre les types colorés, ne permettant pas d’expliquer l’accumulation différentielle de certains caroténoïdes. Les gènes de la voie de biosynthèse des caroténoïdes étudiés montrent une diversité nucléotidique élevée (1 SNP tous les 22 pb) mais présentent une absence de décroissance du déséquilibre de liaison sur 700-1000 pb. Le polymorphisme des gènes et des microsatellites montre une différenciation entre les individus issus de l’Occident et de l’Orient. Les gènes CRTISO, LCYE et LCYB1 présentent un excès de polymorphisme à l’échelle de l’espèce, ce qui suggère une sélection diversifiante. PDS présente un déficit de polymorphisme, ce qui suggère une sélection directionnelle ou négative. Les gènes LCYE et CHXE pourraient avoir subi un balayage sélectif lors de la sélection des types cultivés de couleur rose et orange, respectivement. Les gènes en fin de voie métabolique ont un taux d’évolution plus rapide que les gènes en début de voie, ce qui pourrait indiquer des différences de contrainte, selon la position des gènes le long de la voie. L’ensemble de ces résultats montre que les variations alléliques, davantage que l’expression des gènes de la voie de biosynthèse des caroténoïdes, permettraient d’expliquer le déterminisme de la teneur en caroténoïdes chez la carotte. Les signatures de sélection mises en évidence seront validées par des approches de génétique d’association, à raisonner en fonction des résultats présentés sur la structuration de la diversité génétique et l’étendue du déséquilibre de liaison

Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily

The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis ‘Old Blush’ genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70–80 million years ago during the Cretaceous period

Functional gene polymorphism to reveal species history: the case of the CRTISO gene in cultivated carrots.

Carrot is a vegetable cultivated worldwide for the consumption of its root. Historical data indicate that root colour has been differentially selected over time and according to geographical areas. Root pigmentation depends on the relative proportion of different carotenoids for the white, yellow, orange and red types but only internally for the purple one. The genetic control for root carotenoid content might be partially associated with carotenoid biosynthetic genes. Carotenoid isomerase (CRTISO) has emerged as a regulatory step in the carotenoid biosynthesis pathway and could be a good candidate to show how a metabolic pathway gene reflects a species genetic history.In this study, the nucleotide polymorphism and the linkage disequilibrium among the complete CRTISO sequence, and the deviation from neutral expectation were analysed by considering population subdivision revealed with 17 microsatellite markers. A sample of 39 accessions, which represented different geographical origins and root colours, was used. Cultivated carrot was divided into two genetic groups: one from Middle East and Asia (Eastern group), and another one mainly from Europe (Western group). The Western and Eastern genetic groups were suggested to be differentially affected by selection: a signature of balancing selection was detected within the first group whereas the second one showed no selection. A focus on orange-rooted carrots revealed that cultivars cultivated in Asia were mainly assigned to the Western group but showed CRTISO haplotypes common to Eastern carrots.The carotenoid pathway CRTISO gene data proved to be complementary to neutral markers in order to bring critical insight in the cultivated carrot history. We confirmed the occurrence of two migration events since domestication. Our results showed a European background in material from Japan and Central Asia. While confirming the introduction of European carrots in Japanese resources, the history of Central Asia material remains unclear

Constraint relaxation in the carotenoid biosynthesis pathway.

<p>(A) <i>ω₀</i> and (B) ratio of codons with 0<<i>ω</i>₀<1 (<i>p₀</i>) are displayed as a function of carotenoid biosynthesis pathway genes. Values shown were estimated by the M1a model calculated by CODEML <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038724#pone.0038724-Yang2" target="_blank">[65]</a>. The genes are sorted according to their pathway position.</p

Role of nonsynonymous and synonymous substitution rates in <i>d_N</i>/<i>d_S</i> ratio variation.

<p>Distribution of (A) <i>d_N</i>/<i>d_S</i> ratio , (B) nonsynonymous substitution rate <i>d_N</i> and (C) synonymous substitution rate <i>d_S</i> calculated from pairwise comparison of seven dicots are displayed as a function of carotenoid biosynthesis genes. The genes are classified according to their pathway position.</p

Selection in carotenoid biosynthesis pathway in carrot as a function of gene position.

<p>Distribution of p-values obtained according the rank of Tajima’s <i>D</i>, normalized Fay and Wu’s <i>H</i> and <i>F_ST</i> for the seven carotenoid biosynthesis genes in carrot by comparison with the expected distribution obtained by approximate Bayesian computation simulations under the divergence model. Each boxplot combines p-values obtained on pooled, geographic and color samples. The genes are sorted according to their pathway position.</p

Position of primers used for <i>CRTISO</i> amplification.

<p>Boxes and lines represent exons and introns, respectively, of the <i>CRTISO</i> sequence. Arrows indicate partial sequences amplified with primers. The hatched box above the <i>CRTISO</i> sequence corresponds to the partial sequence analysed by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070801#pone.0070801-Clotault2" target="_blank">[25]</a>.</p