Search results for "Phylogenetics"
showing 10 items of 777 documents
A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them.
2021
AbstractThe ultimate goal of gene regulation should focus on the protein level. However, as mRNA is an obligate intermediary, and because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained following different strategies. By studying omics datasets for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CES) for functionally-related genes in the yeastSaccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the distantly related yeastSchizosaccharomyces pombeand cultur…
Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions
2016
AbstractGenome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalizatio…
Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria.
2019
International audience; Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic ]; alternatively, they have been linked to the complex Ambulacraria (echinoderms and hemichordates) in a clade called the Xenambulacraria , suggesting their simplicity evolved by reduction from a complex ancestor. The difficulty resolving this problem implies the phylogenetic signal supporting the correct solution is weak and affected by inadequate modeling, creating a misleading non-phylogenetic signal. …
Genomic characterization of Algerian Guelmoise cattle and their genetic relationship with other North African populations inferred from SNP genotypin…
2018
International audience; Understanding between and within-breeds genetic variability is essential in the choice of conservation management decisions for threatened populations. In this study we assessed the genetic diversity of the Algerian Guelmoise cattle (GUE) by analyzing data on 24 GUE individuals genotyped for the Illumina BovineSNP50 BeadChipv2. We also provided a detailed description of the population structure of GUE using comparisons with 23 worldwide cattle populations, selected as being representative of African, South European and indicine populations, in addition to four North African populations. We show that GUE is an admixed population which has strong genetic similarity to …
Bacterial community diversity harboured by interacting species
2016
International audience; All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the…
Temporal frames of 45S rDNA site-number variation in diploid plant lineages: lessons from the rock rose genus Cistus (Cistaceae)
2016
The perception that the turnover of 45S rDNA site number in plants is highly dynamic pervades the literature on rDNA evolution. However, most reported evidences come from the study of polyploid systems and from crop species subjected to intense agronomic selection. In sharp contrast with polyploids, the evolutionary patterns of rDNA loci number in predominantly diploid lineages have received less attention. Most studies on rDNA loci changes lack explicit temporal frames, and hence their dynamics could not be assessed. Here, we assess the temporal patterns of rDNA site evolution in Cistus, an entirely diploid lineage. We assessed the number and chromosomal position of 45S rDNA loci in Cistus…
Acute and Repeated Treatment with 5-PAHSA or 9-PAHSA Isomers Does Not Improve Glucose Control in Mice
2018
Summary Fatty acid esters of hydroxylated fatty acids (FAHFAs) were discovered as a novel class of endogenous mammalian lipids whose profound effects on metabolism have been shown. In the current study, in vitro and in vivo the metabolic effects of two of these FAHFAs, namely palmitic acid-5- (or -9) -hydroxy-stearic acid (5- or 9-PAHSA, respectively) were profiled. In DIO mice fed with differentially composed low- or high-fat diets, acute and subchronic treatment with 5-PAHSA and 9-PAHSA alone, or in combination, did not significantly improve the deranged metabolic status. Neither racemic 5- or 9-PAHSA, nor the enantiomers were able to: (1) increase basal or insulin-stimulated glucose upta…
Carbonic anhydrase and metazoan biocalcification: a focus on molluscs.
2015
Carbonic anhydrase is a super-family of metallo-enzymes (containing α, β, γ, ζ and δ-CA families) that catalyse the reversible hydration of carbon dioxide. Among their numerous functions, CAs - in particular that of the α-CA family - are known to play a key role in biocalcification processes, i.e., the ability to deposit calcium carbonate crystallites in a controlled manner to form exoskeletons. In the gastropod mollusc Haliotistuberculata – the European abalone – we identified two CA transcripts, htCA1 and htCA2, in the mantle, the calcifying organ responsible for shell formation from an extracellular organic matrix and a mixture of inorganic ions. Because these two transcripts are specifi…
How Hosts Taxonomy, Trophy, and Endosymbionts Shape Microbiome Diversity in Beetles.
2019
Bacterial communities play a crucial role in the biology, ecology, and evolution of multicellular organisms. In this research, the microbiome of 24 selected beetle species representing five families (Carabidae, Staphylinidae, Curculionidae, Chrysomelidae, Scarabaeidae) and three trophic guilds (carnivorous, herbivorous, detrivorous) was examined using 16S rDNA sequencing on the Illumina platform. The aim of the study was to compare diversity within and among species on various levels of organization, including evaluation of the impact of endosymbiotic bacteria. Collected data showed that beetles possess various bacterial communities and that microbiota of individuals of particular species h…
Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses
2017
The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp. TR9 and T. jamesii in long-distance populations. To date, studies involving phycobiont diversity within entire thalli are based on Sanger sequencing, but this method see…