31 research outputs found
Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones:Sequencing haploid honey bee drones
International audienceHoney bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environment and mate naturally with queens from the local subspecies. The resulting admixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to subspecies, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP-chip or by low-pass sequencing, or (iii) selecting SNPs compatible with the requirements of genotyping chips
Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones
Honey bee subspecies originate from specific geographical areas in Africa, Europe
and the Middle East, and beekeepers interested in specific phenotypes have imported
genetic material to regions outside of the bees' original range for use either in pure
lines or controlled crosses. Moreover, imported drones are present in the environment
and mate naturally with queens from the local subspecies. The resulting admixture
complicates population genetics analyses, and population stratification can
be a major problem for association studies. To better understand Western European
honey bee populations, we produced a whole genome sequence and single nucleotide
polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate
its utility for the identification of nine genetic backgrounds and various degrees of
admixture in a subset of 629 samples. Five backgrounds identified correspond to subspecies,
two to isolated populations on islands and two to managed populations. We
also highlight several large haplotype blocks, some of which coincide with the position
of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds
identified. This large naturally phased data set is available as a single vcf file that can
now serve as a reference for subsequent populations genomics studies in the honey
bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds
as references, (ii) imputing genotypes from a lower-density
data set generated by an
SNP-chip
or by low-pass
sequencing, or (iii) selecting SNPs compatible with the requirements
of genotyping chips.This work was performed in collaboration with the GeT platform,
Toulouse (France), a partner of the National Infrastructure France
GĂ©nomique, thanks to support by the Commissariat aux Grands
Invetissements (ANR-10-INBS-0009).
Bioinformatics analyses were
performed on the GenoToul Bioinfo computer cluster. This work
was funded by a grant from the INRA Département de Génétique
Animale (INRA Animal Genetics division) and by the SeqApiPop programme,
funded by the FranceAgriMer grant 14-21-AT.
We thank John Kefuss for helpful discussions. We thank Andrew Abrahams
for providing honey bee samples from Colonsay (Scotland), the
Association Conservatoire de l'Abeille Noire Bretonne (ACANB) for
samples from Ouessant (France), CETA de Savoie for sample from
Savoie, ADAPI for samples from Porquerolles and all beekeepers and
bee breeders who kindly participated in this study by providing samples
from their colonies.info:eu-repo/semantics/publishedVersio
Transformations agricoles et agroalimentaires
Ă lâheure des robots et du numĂ©rique, la terre (habitat, agriculture, paysage, planĂšte) et la nourriture (du corps et de lâĂąme) sont parmi les prĂ©occupations majeures dans les espaces mĂ©diatiques et politiques. Le pĂ©trole et lâabondance qui lâa accompagnĂ© nous avaient fait oublier quâelles sont au fondement des sociĂ©tĂ©s humaines. La « crise alimentaire » de 2008, qui a secouĂ© plusieurs continents, a rappelĂ© aux gouvernements lâenjeu de la sĂ©curitĂ© alimentaire. AprĂšs des dĂ©cennies dâexcĂ©dents, de baisse du prix des produits agricoles de base, la question de la valeur de la terre et de lâagriculture est de retour. La question de la santĂ© et celle des droits humains prennent une place Ă©largie tant dans les politiques publiques et dans la production de normes alimentaires. Des mouvements sociaux transnationaux sâemparent de la question de lâavenir de lâagriculture et de lâalimentation, et de celle de la « bonne vie ». Pour contribuer Ă cette rĂ©flexion sur lâavenir de la terre et de la nourriture, cet ouvrage Ă©tudie la socialisation de lâagriculture, câest-Ă -dire sa prise en charge tant par les politiques agricoles (essentiellement nationales) que par lâorganisation des marchĂ©s dans un cadre national et international. Il le fait en prenant un large recul et mobilise trois temporalitĂ©s. La premiĂšre est celle de la planĂšte. La seconde, celle des rĂ©gimes mĂ©taboliques, façons dont lâhumanitĂ© Ă diffĂ©rents stades de dĂ©veloppement, mobilise matĂ©riaux et Ă©nergie. La troisiĂšme est celle du capitalisme, avec la succession de systĂšmes hĂ©gĂ©moniques (ce qui nâexclue pas de multiples polaritĂ©s). Cet ouvrage rĂ©unit des recherches rĂ©centes dâĂ©conomistes, de sociologues, dâhistoriens et dâagronomes, de diffĂ©rents pays, recherches qui ont en commun de concerner la place de lâagriculture dans lâĂ©volution des capitalismes
Autosomal and mitochondrial adaptation following admixture: a case study on the honeybees of Reunion Island.
The honeybee population of the tropical Reunion Island is a genetic admixture of the Apis mellifera unicolor subspecies, originally described in Madagascar, and of European subspecies, mainly A.m. carnica and A. m. ligustica, regularly imported to the island since the late 19th century. We took advantage of this population to study genetic admixing of the tropical-adapted indigenous and temperate-adapted European genetic backgrounds. Whole genome sequencing of 30 workers and 6 males from Reunion, compared to samples from Europe, Madagascar, Mauritius, Rodrigues and the Seychelles, revealed the Reunion honeybee population to be composed on average of 53.2 ± 5.9% A. m. unicolor nuclear genomic background, the rest being mainly composed of A. m. carnica and to a lesser extent A. m. ligustica. In striking contrast to this, only one out of the 36 honeybees from Reunion had a mitochondrial genome of European origin, suggesting selection has favoured the A. m. unicolor mitotype, which is possibly better adapted to the island's bioclimate. Local ancestry was determined along the chromosomes for all Reunion samples, and a test for preferential selection for the A. m. unicolor or European background revealed 15 regions significantly associated with the A. m. unicolor lineage and 9 regions with the European lineage. Our results provide insights into the long-term consequences of introducing exotic specimen on the nuclear and mitochondrial genomes of locally-adapted populations. (Résumé d'auteur
DĂ©tection des abeilles sauvages et domestiques par ADN environnemental
International audienc
Four functional profiles for fibre and mucin metabolism in the human gut microbiome
International audienceBackground With the emergence of metagenomic data, multiple links between the gut microbiome and the host health have been shown. Deciphering these complex interactions require evolved analysis methods focusing on the microbial ecosystem functions. Despite the fact that host or diet-derived fibres are the most abundant nutrients available in the gut, the presence of distinct functional traits regarding fibre and mucin hydrolysis, fermentation and hydrogenotrophic processes has never been investigated. Results After manually selecting 91 KEGG orthologies and 33 glycoside hydrolases further aggregated in 101 functional descriptors representative of fibre and mucin degradation pathways in the gut microbiome, we used non-negative matrix factorization to mine metagenomic datasets. Four distinct metabolic profiles were further identified on a training set of 1153 samples and thoroughly validated on a large database of 2571 unseen samples from 5 external metagenomic cohorts. Profiles 1 and 2 are the main contributors to the fibre-degradation-related metagenome: they present contrasted involvement in fibre degradation and sugar metabolism and are differentially linked to dysbiosis, metabolic disease and inflammation. Profile 1 takes over Profile 2 inhealthy samples, and unbalance of these profiles characterize dysbiotic samples. Furthermore, high fibre diet favours a healthy balance between Profiles 1 and Profile 2. Profile 3 takes over Profile 2 during Crohnâs disease, inducing functional reorientations towards unusual metabolism such as fucose and H2S degradation or propionate, acetone and butanediol production. Profile 4 gathers under-represented functions, like methanogenesis. Two taxonomic makes up of the profiles were investigated, using either the covariation of 203 prevalent genomes or metagenomic species, both providing consistent results in line with their functional characteristics. This taxonomic characterization showed that Profiles 1 and 2 were respectively mainly composed of bacteria from the phyla Bacteroidetes and Firmicutes while Profile 3 is representative of Proteobacteria and Profile 4 of methanogens.Conclusions Integrating anaerobic microbiology knowledge with statistical learning can narrow down the metagenomic analysis to investigate functional profiles. Applying this approach to fibre degradation in the gut ended with 4 distinct functional profiles that can be easily monitored as markers of diet, dysbiosis, inflammation and disease
Exploring the Bacterial Impact on Cholesterol Cycle: A Numerical Study
International audienceHigh blood cholesterol levels are often associated with cardiovascular diseases. Therapeutic strategies, targeting different functions involved in cholesterol transport or synthesis, were developed to control cholesterolemia in human. However, the gut microbiota is also involved in cholesterol regulation by direct biotransformation of luminal cholesterol or conversion of bile salts, opening the way to the design of new strategies to manage cholesterol level. In this report, we developed for the first time a whole-body human model of cholesterol metabolism including the gut microbiota in order to investigate the relative impact of host and microbial pathways. We first used an animal model to investigate the ingested cholesterol distribution in vivo. Then, using in vitro bacterial growth experiments and metabolite measurements, we modeled the population dynamics of bacterial strains in the presence of cholesterol or bile salts, together with their bioconversion function. Next, after correct rescaling to mimic the activity of a complex microbiota, we developed a whole body model of cholesterol metabolism integrating host and microbiota mechanisms. This global model was validated with the animal experiments. Finally, the model was numerically explored to give a further insight into the different flux involved in cholesterol turnover. According to this model, bacterial pathways appear as an important driver of cholesterol regulation, reinforcing the need for development of novel 'bacteria-based' strategies for cholesterol management