Insights into the evolution, virulence and speciation of and through multiomics analyses.

Babesiosis, caused by protozoan parasites of the genus , is an emerging tick-borne disease of significance for both human and animal health. parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of new species underscores the ongoing risk of zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental changes.

GeCKO: user-friendly workflows for genotyping complex genomes using target enrichment capture. A use case on the large tetraploid durum wheat genome.

Background: Genotyping of individuals plays a pivotal role in various biological analyses, with technology choice influenced by multiple factors including genomic constraints, number of targeted loci and individuals, cost considerations, and the ease of sample preparation and data processing. Target enrichment capture of specific polymorphic regions has emerged as a flexible and cost-effective genomic reduction method for genotyping, especially adapted to the case of very large genomes. However, this approach necessitates complex bioinformatics treatment to extract genotyping data from raw reads.

Multiomics analysis reveals MO1 as a distinct species and provides insights into its evolution and virulence.

Babesiosis, caused by protozoan parasites of the genus , is an emerging tick-borne disease of significance for both human and animal health. parasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of various species underscores the ongoing risk of new zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental shifts impacting the distribution and transmission dynamics of parasites, their vectors, and reservoir hosts.

OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics.

To date, the databases built to gather information on gene orthology do not provide end-users with descriptors of the molecular evolution information and phylogenetic pattern of these orthologues. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of coding sequences in mammalian genomes. OrthoMaM version 12 includes 15,868 alignments of orthologous coding sequences (CDS) from the 190 complete mammalian genomes currently available.

Evolution of flowering time in a selfing annual plant: Roles of adaptation and genetic drift.

Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations through time. If these trait modifications correlate with the environmental changes that occurred during the time period, it suggests that the phenotypic changes could be a response to selection. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes.

A new comprehensive annotation of leucine-rich repeat-containing receptors in rice.

Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR).

EBCR: Empirical Bayes concordance ratio method to improve similarity measurement in memory-based collaborative filtering.

Recommender systems aim to provide users with a selection of items, based on predicting their preferences for items they have not yet rated, thus helping them filter out irrelevant ones from a large product catalogue. Collaborative filtering is a widely used mechanism to predict a particular user's interest in a given item, based on feedback from neighbour users with similar tastes. The way the user's neighbourhood is identified has a significant impact on prediction accuracy.

Aligning Protein-Coding Nucleotide Sequences with MACSE.

Most genomic and evolutionary comparative analyses rely on accurate multiple sequence alignments. With their underlying codon structure, protein-coding nucleotide sequences pose a specific challenge for multiple sequence alignment. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that provided the first automatic solution for aligning protein-coding gene datasets containing both functional and nonfunctional sequences (pseudogenes).

Origin and Diversity of Plant Receptor-Like Kinases.

Because of their high level of diversity and complex evolutionary histories, most studies on plant receptor-like kinase subfamilies have focused on their kinase domains. With the large amount of genome sequence data available today, particularly on basal land plants and Charophyta, more attention should be paid to primary events that shaped the diversity of the RLK gene family. We thus focus on the motifs and domains found in association with kinase domains to illustrate their origin, organization, and evolutionary dynamics.

Pervasive hybridizations in the history of wheat relatives.

Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking.

Efficient algorithms for Longest Common Subsequence of two bucket orders to speed up pairwise genetic map comparison.

Genetic maps order genetic markers along chromosomes. They are, for instance, extensively used in marker-assisted selection to accelerate breeding programs. Even for the same species, people often have to deal with several alternative maps obtained using different ordering methods or different datasets, e.

Domestication reduces alternative splicing expression variations in sorghum.

Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool).

Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations.

Gene trees and species trees can be discordant due to several processes. Standard models of reconciliations consider macro-evolutionary events at the gene level: duplications, losses and transfers of genes. However, another common source of gene tree-species tree discordance is incomplete lineage sorting (ILS), whereby gene divergences corresponding to speciations occur "out of order".

The genetic map comparator: a user-friendly application to display and compare genetic maps.

Motivation: Marker-assisted selection strongly relies on genetic maps to accelerate breeding programs. High-density maps are now available for numerous species. Dedicated tools are required to compare several high-density maps on the basis of their key characteristics, while pinpointing their differences and similarities.

Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus.

The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available.

Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment.

Background: Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming.

Genotyping by Sequencing Using Specific Allelic Capture to Build a High-Density Genetic Map of Durum Wheat.

Targeted sequence capture is a promising technology which helps reduce costs for sequencing and genotyping numerous genomic regions in large sets of individuals. Bait sequences are designed to capture specific alleles previously discovered in parents or reference populations. We studied a set of 135 RILs originating from a cross between an emmer cultivar (Dic2) and a recent durum elite cultivar (Silur).

A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality.

Background: Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach searches for a most parsimonious reconciliation between a gene tree and a (dated) species tree, considering four possible macro-evolutionary events (speciation, duplication, transfer, and loss) with specific costs. Unfortunately, many events are erroneously predicted due to errors in the input trees, inappropriate input cost values or because of the existence of several equally parsimonious scenarios.

Inferring gene duplications, transfers and losses can be done in a discrete framework.

In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family.

USI: a fast and accurate approach for conceptual document annotation.

Background: Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new entities need to be frequently annotated to enrich the corpus. However, this task is time-consuming and requires a high-level of expertise in both the domain and the related ontology.

Exploring the space of gene/species reconciliations with transfers.

Reconciliations between gene and species trees have important applications in the study of genome evolution (e.g. sequence orthology prediction or quantification of transfer events).

Impact of recurrent gene duplication on adaptation of plant genomes.

Background: Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypothesis has not been tested at the genome scale.

Results: We studied available sequenced angiosperm genomes to assess the frequency of positive selection footprints in lineage specific expanded (LSE) gene families compared to single-copy genes using a dN/dS-based test in a phylogenetic framework.