Search results for "Orthology"
showing 5 items of 5 documents
The Search for Common Origin: Homology Revisited
2018
Understanding the evolution of biodiversity on Earth is a central aim in biology. Currently, various disciplines of science contribute to unravel evolution at all levels of life, from individual organisms to species and higher ranks, using different approaches and specific terminologies. The search for common origin, traditionally called homology, is a connecting paradigm of all studies related to evolution. However, it is not always sufficiently taken into account that defining homology depends on the hierarchical level studied (organism, population, and species), which can cause confusion. Therefore, we propose a framework to define homologies making use of existing terms, which refer to …
Evidence of gene orthology and trans-species polymorphism, but not of parallel evolution, despite high levels of concerted evolution in the major his…
2016
17 pages; International audience; The major histocompatibility complex (MHC) is a cornerstone in the study of adaptive genetic diversity. Intriguingly, highly polymorphic MHC sequences are often not more similar within species than between closely related species. Divergent selection of gene duplicates, balancing selection maintaining trans-species polymorphism (TSP) that predate speciation and parallel evolution of species sharing similar selection pressures can all lead to higher sequence similarity between species. In contrast, high rates of concerted evolution increase sequence similarity of duplicated loci within species. Assessing these evolutionary models remains difficult as related…
Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants.
2006
The internal transcribed spacers (ITS) of the nuclear ribosomal 18S–5.8S–26S cistron continue to be the most popular non-plastid region for species-level phylogenetic studies of plant groups despite the early warnings about their potential Xaws, which may ultimately result in incorrect assumptions of orthology. It has been gradually realized that the alternative target regions in the nuclear genome (lowcopy nuclear genes, LCNG) are burdened with similar problems. The consequence is that, to date, developing useful LCNG for nonmodel organisms requires an investment in time and eVort that hinders its use as a real practical alternative for many labs. It is here argued that ITS sequences, desp…
The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein
2021
Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence in eukaryotes. Studying their conservation could help provide hypotheses about their function. To obtain the appropriate evolutionary focus for this rapidly evolving feature, here we study the conservation of LCRs in bacterial strains and compare their high variability to the closeness of the strains. For this, we selected 20 taxonomically diverse bacterial species and obtained the completely sequenced proteomes of t…
Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
2023
Legumes, and especially pulses, are an important source of protein for food and feed, and are appreciated for their positive impact on the “one health”. However, their unstable yields and their susceptibility to biotic and abiotic stresses highlight the need for varietal improvement in order to increase the cultivated areas and productivity. With the advent of sequencing technologies, a large pool of genetic and -omics resources, heterogeneous at the inter- and intra-species scale, is emerging. Thus, it is important to capitalize on these scattered heterogeneous data to develop translational research to boost breeding projects and crop diversification. To meet this need, we undertook the de…