Quantitative Analysis of Target Peptides Related to Resistance Against Ascochyta Blight (Peyronellaea pinodes) in Pea.

Peyronellaea pinodes causes Ascochyta blight, one of the major diseases in pea worldwide. Cultivated pea plants have a low resistance to this disease. Although quantitative trait loci (QTLs) involved in the resistance to Ascochyta blight have been identified, the specific genes associated with these QTLs remain unknown, which makes marker-assisted selection difficult. Complex traits alter proteins and their abundance. Quantitative estimation of proteins in pea might therefore be useful in selecting potential markers for breeding. In this work, we developed a strategy using a combination of shotgun proteomics (viz., high performance liquid chromatography-mass spectrometry data-dependent acquisition) and data-independent acquisition (DIA) analysis, to identify putative protein markers associated with resistance to Ascochyta blight and explored its use for breeding selection. For this purpose, an initial list of target peptides based on proteins closely related to resistance to P. pinodes was compiled by using two genotypes with contrasting responses to the disease. Then, targeted data analysis (viz., shotgun proteomics-DIA) was used for constitutive quantification of the target peptides in a representative number of the recombinant inbred line population segregated for resistance as derived from a cross between the two genotypes. Finally, a peptide panel of potential markers for resistance to P. pinodes was built. The results thus obtained are discussed and compared with those of previous gene expression studies using the same parental pea genotypes responding to the pathogen. Also, a molecular defense mechanism against Ascochyta blight in pea is proposed. To the authors' knowledge, this is the first time a targeted proteomics approach based on data analysis has been used to identify peptides associated with resistance to this disease.

Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula.

Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.

Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome.

Because of a loss-of-function mutation in the GGTA1 gene, humans are unable to synthetize α1,3-Galactose (Gal) decorated glycans and develop high levels of circulating anti-α1,3-Galactose antibodies (anti-Gal Abs). Anti-Gal Abs have been identified as a major obstacle of organ xenotransplantation and play a role in several host-pathogen relationships including potential susceptibility to infection. Anti-Gal Abs are supposed to stem from immunization against the gut microbiota, an assumption derived from the observation that some pathogens display α1,3-Gal and that antibiotic treatment decreases the level of anti-Gal. However, there is little information to date concerning the microorganisms producing α1,3-Gal in the human gut microbiome. Here, available α1,3-Galactosyltransferase (GT) gene sequences from gut bacteria were selectively quantified for the first time in the gut microbiome shotgun sequences of 163 adult individuals from three published population-based metagenomics analyses. We showed that most of the gut microbiome of adult individuals contained a small set of bacteria bearing α1,3-GT genes. These bacteria belong mainly to the Enterobacteriaceae family, including Escherichia coli, but also to Pasteurellaceae genera, Haemophilus influenza and Lactobacillus species. α1,3-Gal antigens and α1,3-GT activity were detected in healthy stools of individuals exhibiting α1,3-GT bacterial gene sequences in their shotgun data.