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Codon optimization underpins generalist parasitism in fungi
No full textThe range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitis
Rapid spread of the tomato leafminer, Tuta absoluta (Lepidoptera: Gelechiidae), an invasive pest in Sub-Saharan Africa
No full textThe invasive tomato leafminer, Tuta absoluta (Meyrick) (Lepidoptera, Gelechiidae) has become a real threat for the continued production of tomatoes across Sub-Saharan Africa since its first detection in Senegal. However, little is known of its geographical expansion, seasonal population dynamics, and damage to crops. A trapping network was deployed in 2014 and 2015 in Senegal to monitor the dynamics of T. absoluta populations at a regional and nationwide scale. A field network was also implemented in the most infested area to get information on the pest incidence during the 2013-2014 cropping season. In 2014, pheromone traps did not detect the presence of T absoluta moths in remote areas of Eastern Senegal. In 2015, moths were detected in all the fifteen monitored areas deployed throughout the country. Abundance of trapped moths was greatest in 'Mayes', the main tomato-producing area. Unexpectedly, T absoluta moths were trapped in some areas with few or no tomato crops, including off-season in the 'Vallee du fleuve', hot drylands ('Matam' and 'Kidira') and urban environments ('Dakar'). This suggests high mobility of moth populations and capacity to survive in harsh environments and to persist on alternative host plants. Field monitoring in the main tomato-producing area showed a very low incidence of T absoluta over the early dry season (0-2% mined leaves), followed by severe outbreaks during the late dry season (up to 60% mined leaves). Results on the invasive pest occurrence will be helpful to decision-makers with a view to develop alternative strategies such as biological control by indigenous natural enemies or collective management strategies based on the temporal or spatial exclusion of host crops
Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria
No full textRNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor. Two PPR proteins, dually targeted to mitochondria and chloroplasts, were identified as potential partners of CLB19. These two proteins, a P-type PPR and a member of a small PPR-DYW subfamily, were shown to interact in yeast. Insertional mutations resulted in embryo lethality that could be rescued by embryo-specific complementation. A transcriptome analysis of these complemented plants showed major editing defects in both organelles with a very high PPR type specificity, indicating that the two proteins are core members of E+-type PPR editosomes
Non-intentional impacts of the bioinsecticide Bacillus thuringiensis on non-target insect species
No full textEnvironmental and health issues resulting from the intensive use of broad-spectrum chemical insecticides, have favored the spread of biological insecticides in the last decades. The most common, Bacillus thuringiensis (Bt), is a spore-forming bacterium which produces a varied range of insecticidal toxins. However, the field accumulation of spores and toxins of Bt kurstaki (Btk), the Bt subspecies most commonly used against lepidopteran pests, potentially increases the risk for non-target biodiversity. Using mainly the Lepidoptera-targeting Bt subspecies kurstaki (Btk) and the well-studied laboratory models Drosophila spp. as non-target insects, we tested the potential non-intentional effects of the ingestion of commercial Btk formulations on traits related to the fly development and the adult fitness. We observed a delayed and reduced emergence of Drosophila melanogaster flies at doses above 107 CFU/g of food (close to the doses used for fields treatments), regardless of the fly strain, the commercial formulation, and the rearing medium. Mortality affected mainly the early larval stage while all the larvae died before pupation at the highest dose (109 CFU/g). We analyzed the respective roles of the formulation components (spores, toxins, additives…), and found that the developmental and lethal effects may result from a synergy between Btk spores and toxins. Developmental and lethal impacts were also observed for other Drosophila species, with variation in the LD50 and in the effect amplitude. Our work suggests that the environmental accumulation of Bt may have possible non-intentional effects on non-target Drosophila species and the associated species communities
Molecular diversity of sunflower populations maintained as genetic resources is affected by multiplication processes and breeding for major traits.
No full textThe molecular diversity in a set of 114 cultivated sunflower populations was studied by single-nucleotide polymorphism genotyping. These populations were chosen as representative of the 400 entries in the INRA collection received or developed between 1962 and 2011 and made up of land races, open-pollinated varieties, and breeding pools. Mean allele number varied from 1.07 to 1.90. Intra population variability was slightly reduced according to the number of multiplications since entry but some entries were probably largely homozygous when received. A principal component analysis was used to study inter-population variability. The first 3 axes accounted for 17% of total intra-population variability. The first axis was significantly correlated with seed oil content, more closely than just the distinction between oil and confectionary types. The second axis was related to the presence or absence of restorer genes and the third axis to flowering date and possibly to adaptation to different climates. Our results provide argument shighlighting the effect of the maintenance process on the within population genetic variability as well as on the impact of breeding for major agronomic traits on the between population variability of the collection. Propositions are made to improve sunflower population maintenance procedures to keep maximum genetic variability for future breeding
Characterisation of a Meloidogyne species complex parasitising rice in southern Brazil
No full textRoot-knot nematodes (RKN) are important plant pathogens affecting rice in South-East Asia and southern Brazil in irrigated rice fields. In order to investigate the specific diversity of RKN associated with irrigated rice in southern Brazil, Meloidogyne spp. from Rio Grande do Sul (RS) and Santa Catarina (SC) States were characterised biochemically by esterase (Est) and malate dehydrogenase (Mdh) phenotypes. Fifty-six Meloidogyne spp. populations were detected in 48% of rice samples, and a total of fiveesterase phenotypes were identified, four of which presented as drawn-out bands in different positions. In RS State, M. graminicola (Est VS1), Meloidogyne sp. 2 (Est R2) and Meloidogyne sp. 3 (Est R3) were identified, which corresponded to ca 80, 40 and 10% of samples, respectively. In SC State, M. graminicola, M. javanica (Est J3), Meloidogyne sp. 1 (Est R1), Meloidogyne sp. 2 and Meloidogyne sp.3 accounted for ca 93.75, 12.50, 62.50, 12.25 and 6.25% of samples, respectively. The esterase phenotypes R1, R2 and R3 are new, never having been detected on rice before. Meloidogyne javanica showed a N1 Mdh phenotype (Rm: 1.0), while four other populations exhibited a N1a (Rm: 1.4) phenotype. All populations were tested with two SCAR markers specific to M. graminicola, which confirmed that, but no specificity was obtained with both markers in relation to the atypical populations analysed. Sequencing and phylogenetic analyses of internal transcribed spacer-rRNA (ITS) were performed to infer the phylogenetic relationship of these atypical Meloidogyne spp. populations. Meloidogyne sp. 1 grouped with the mitotic parthenogenetic species, while the two others (Meloidogyne sp. 2 and sp. 3) clustered with M. graminicola and other meiotic parthenogenetic species. Taken together, these data highlight the unprecedented specific diversity of RKN associated with irrigated rice in southern Brazil. Further morphological and phylogenetic studies involvingthese atypical isolates will be carried out to identify this complex of species
A new paramutation-like example at the Delta gene of Drosophila
No full textThe hereditary transmission of a phenotype independent from DNA sequence implies epigenetic effects. Paramutation is a heritable epigenetic phenomenon observed in plants and animals. To investigate paramutation in Drosophila, we used the P{ry+t7.2 = PZ}Dl05151 P-element insertion in the Drosophila melanogaster genome that causes a dominant visible phenotype: the presence of characteristic extra-veins in the fly wings. This extra-vein phenotype presents variable expressivity and incomplete penetrance. The insert is a PZ element located 680 bp upstream from the ATG of the Delta (Dl) gene, encoding the Notch ligand involved in wing vein development, and acts as a null allele. In the G2 offspring from a cross between the heterozygous transgenic stock and wild-type flies, we observed the transmission of the extra-vein phenotype to wild-type flies without the transgene, independently of gender and across many generations. This is a “paramutation-like” example in the fly: the heritable transmission of a phenotypic change not linked to a classical genetic mutation. A “paramutagenic” allele in heterozygotes transmits the phenotype of the heterozygotes to the wild-type allele (“paramutant”) in a stable manner through generations. Distinct from paramutation events so far described in Drosophila, here we deal with a dominant effect on a single gene involving variable hereditary signals
Eggplant Resistance to the Ralstonia solanacearum Species Complex Involves Both Broad-Spectrum and Strain-Specific Quantitative Trait Loci
No full textBacterial wilt (BW) is a major disease of solanaceous crops caused by the Ralstonia solanacearum species complex (RSSC). Strains are grouped into five phylotypes (I, IIA, IIB, III, and IV). Varietal resistance is the most sustainable strategy for managing BW. Nevertheless, breeding to improve cultivar resistance has been limited by the pathogen's extensive genetic diversity. Identifying the genetic bases of specific and non-specific resistance is a prerequisite to breed improvement. A major gene (ERs1) was previously mapped in eggplant (Solanum melongena L.) using an intraspecific population of recombinant inbred lines derived from the cross of susceptible MM738 (S) x resistant AG91-25 (R). ERs1 was originally found to control three strains from phylotype I, while being totally ineffective against a virulent strain from the same phylotype. We tested this population against four additional RSSC strains, representing phylotypes I, IIA, IIB, and III in order to clarify the action spectrum of ERs1. We recorded wilting symptoms and bacterial stem colonization under controlled artificial inoculation. We constructed a high-density genetic map of the population using single nucleotide polymorphisms (SNPs) developed from genotyping-by-sequencing and added 168 molecular markers [amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and sequence-related amplified polymorphisms (SRAPs)] developed previously. The new linkage map based on a total of 1,035 markers was anchored on eggplant, tomato, and potato genomes. Quantitative trait locus (QTL) mapping for resistance against a total of eight RSSC strains resulted in the detection of one major phylotype-specific QTL and two broad-spectrum QTLs. The major QTL, which specifically controls three phylotype I strains, was located at the bottom of chromosome 9 and corresponded to the previously identified major gene ERs1. Five candidate R-genes were underlying this QTL, with different alleles between the parents. The two other QTLs detected on chromosomes 2 and 5 were found to be associated with partial resistance to strains of phylotypes I, IIA, III and strains of phylotypes IIA and III, respectively. Markers closely linked to these three QTLs will be crucial for breeding eggplant with broad-spectrum resistance to BW. Furthermore, our study provides an important contribution to the molecular characterization of ERs1, which was initially considered to be a major resistance gene
Low Complexity Beam Selection for Sparse Massive MIMO Systems
No full textInternational audienceIn this work, we propose a beam selection scheme that exploits the geometric sparsity of the multi-user (MU) massive multiple input and multiple output (MIMO) channel, using its beamspace representation. Assuming knowledge of the beamspace channel, the beamspace precoder consists in selecting and weighting the beams steered to the users, in order to maximize the signal-to-interference-and-noise ratio (SINR) at the user equipment (UE). Low complexity solutions are proposed through three simple heuristics. In a first step, the heuristics use the maximal ratio transmission (MRT) principle to determine the beam gains. In a second step, the beams are selected to enhance the SINRs. For all heuristics, we solve this problem in two steps i) selection of beams ii) power allocation. We show that using MRT as base, adding and/or removing some beams improve the system performance. Simulation results show that, compared to the linear MRT precoder, the proposed heuristics can improve the performance under a scenario with channel sparsity