Assessing the performance of single-copy genes for recovering robust phylogenies

Phylogenies involving nonmodel species are based on a few genes, mostly chosen following historical or practical criteria. Because gene trees are sometimes incongruent with species trees, the resulting phylogenies may not accurately reflect the evolutionary relationships among species. The increase in availability of genome sequences now provides large numbers of genes that could be used for building phylogenies. However, for practical reasons only a few genes can be sequenced for a wide range of species. Here we asked whether we can identify a few genes, among the single-copy genes common to most fungal genomes, that are sufficient for recovering accurate and well-supported phylogenies. Fungi represent a model group for phylogenomics because many complete fungal genomes are available. An automated procedure was developed to extract single-copy orthologous genes from complete fungal genomes using a Markov Clustering Algorithm (Tribe-MCL). Using 21 complete, publicly available fungal genomes with reliable protein predictions, 246 single-copy orthologous gene clusters were identified. We inferred the maximum likelihood trees using the individual orthologous sequences and constructed a reference tree from concatenated protein alignments. The topologies of the individual gene trees were compared to that of the reference tree using three different methods. The performance of individual genes in recovering the reference tree was highly variable. Gene size and the number of variable sites were highly correlated and significantly affected the performance of the genes, but the average substitution rate did not. Two genes recovered exactly the same topology as the reference tree, and when concatenated provided high bootstrap values. The genes typically used for fungal phylogenies did not perform well, which suggests that current fungal phylogenies based on these genes may not accurately reflect the evolutionary relationships among species. Analyses on subsets of species showed that the phylogenetic performance did not seem to depend strongly on the sample. We expect that the best-performing genes identified here will be very useful for phylogenetic studies of fungi, at least at a large taxonomic scale. Furthermore, we compare the method developed here for finding genes for building robust phylogenies with previous ones and we advocate that our method could be applied to other groups of organisms when more complete genomes are available.

Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens

Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely related pathogens specialized on different hosts. For this goal, we sequenced c. 17,000-32,000 ESTs from each of four Microbotryum species, which are fungal pathogens responsible for anther smut disease on host plants in the Caryophyllaceae. Forty-two of the 372 predicted orthologous genes showed significant signal of positive selection, which represents a good number of candidate genes for further investigation. Sequencing 16 of these genes in 9 additional Microbotryum species confirmed that they have indeed been rapidly evolving in the pathogen species specialized on different hosts. The genes showing significant signals of positive selection were putatively involved in nutrient uptake from the host, secondary metabolite synthesis and secretion, respiration under stressful conditions and stress response, hyphal growth and differentiation, and regulation of expression by other genes. Many of these genes had transmembrane domains and may therefore also be involved in pathogen recognition by the host. Our approach thus revealed fruitful and should be feasible for many non-model organisms for which candidate genes for diversifying selection are needed.

Translation conditional models for protein coding sequences

A coding sequence is defined as a DNA sequence coding the primary structure of a protein (a polypeptide). Such a sequence must satisfy a specific constraint, which consists in coding a functional protein. As the genetic code is degenerated, there exists, for a given polypeptide, a set of synonymous sequences which would code the same polypeptide. Translation conditional models are being defined on such sets. The aim of this paper is to give a common formalism. Besides the codon bias model, a few other conditional models will be defined. Statistical estimators and comparison methods will be briefly presented. These models can be used for gene classification, or to find out, in a real sequence, remarkable features. An example will be presented on Escherichia coli genes.

Estimation and test for linkage between markers: a comparison of lod score and χ (2) test in a linkage study of maritime pine (Pinus pinaster Ait.)

The first step in the construction of a linkage map involves the estimation and test for linkage between all possible pairs of markers. The lod score method is used in many linkage studies for the latter purpose. In contrast with classical statistical tests, this method does not rely on the choice of a first-type error level. We thus provide a comparison between the lod score and a χ (2) test on linkage data from a gymnosperm, the maritime pine. The lod score appears to be a very conservative test with the usual thresholds. Its severity depends on the type of data used.

An estimation of the genome length of maritime pine (Pinus pinaster Ait.)

The genome length, in units of Morgans or centimorgans, is a fundamental feature of a species. It can be calculated from a complete linkage map. However, the genome size can be estimated with partial linkage data. Using linkage data obtained by the analysis of a two-dimensional electrophoresis of the proteins contained in an haploid organ, the megagametophyte, we suggest an estimation and a confidence interval of the genome length of a gymnosperm, the maritime pine (Pinus pinaster Ait.). The results indicate an important gap between the physical and the genetic maps.

A multi-marker model for detecting chromosomal segments displaying QTL activity

A statistical method is presented for detecting quantitative trait loci (QTLs), based on the linear model. Unlike methods able to detect a few well separated QTLs and to estimate their effects and positions, this method considers the genome as a whole and enables the detection of chromosomal segments involved in the differences between two homozygous lines, and their backcross, doubled haploid, or F2 progenies, for a quantitative trait. Genetic markers must be codominant, but missing markers are accepted, provided they are missing independently from the experiment. Asymptotic properties, which are of practical use, are developed. This method does not rely on strong genetic hypotheses, and thus does not permit any precise genetic analysis of the trait under study, but it does assess which regions of the genome are involved, whatever the complexity of the genetic determinism (number, effects and interactions among QTLs). Simultaneous use of several methods, including this one, should lead to better efficiency in QTL detection.

Seed-protein variation in maritime pine (Pinus pinaster Ait.) revealed by two-dimensional electrophoresis: genetic determinism and construction of a linkage map

Proteins from haploid megagametophytes from 18 trees were studied by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). A total of 222 seeds, an average of 12 per tree, were analysed individually. 150 protein spots appeared to segregate on the polyacrylamide gels in at least tree. Genetic interpretations were made to define the number of loci responsible for the presence versus absence, staining differences or position variation of the segregating spots. The complete covariation observed between some spots could be the result of either the separation of a single gene product into two or more constituents, very close linkage, or the action of a pleiotropic gene. Human genetics techniques were used to map the 84 putative loci detected. Sixty-five loci were organised in 17 linkage groups, whereas 19 remained unlinked.

Genetic neighbourhood structure in a population of Picea abies L

Natural populations are currently the basic material for studying forest tree breeding, but little is known on the genotypic spatial structures in these stands. The use of gene markers, such as isozymes, leads to the determination of part of the allelic constitution of individuals. A method is presented here to estimate the degree of genetic relationship between any pair of genotypes. A French Picea abies population is analyzed by these means and a slight but significant correlation between estimated genetic relationship and topographic distance is found.

Biochemical and genetic properties of oligomeric structures: a general approach

The oligomers constituted by association of different subunits can exist under multiple forms. In the case of the genetically variable proteins, such a multiplicity leads to numerous questions (i) on the enumerations: what is the number of active forms when a given subunit can make the oligomer inactive, or when the subunits are encoded by s alleles; (ii) on the subunit effects on biochemical properties: how to estimate these effects, are they equal, are there interactions between subunits, etc. Theoretical methods for the study of such oligomeric structures are developed, which mainly rely on linear model techniques. Peculiar properties examined are Vmax and Km, but also the quantities of the various oligomers, which depend on their association law. This approach is extended to the oligomers composed of different sets of subunits, as are for example some enzymes. These aspects are discussed from numerous bibliographic examples, with special reference to molecular interactions (protein complementation or molecular heterosis). Otherwise the genetic application of this theoretical approach is presented: it is possible to consider a genotype as an oligomer of alleles, and thus to study their effects and their interactions, in the one-locus case as well as in the several-loci case. The relevance of this generalization is discussed in connection with two other concepts, the "sequence space" used in molecular evolution and the regression of the genotypic values on the number of alleles used in quantitative genetics.