An exploration of linkage fine-mapping on sequences from case-control studies

Linkage analysis maps genetic loci for a heritable trait by identifying genomic regions with excess relatedness among individuals with similar trait values. Analysis may be conducted on related individuals from families, or on samples of unrelated individuals from a population. For allelically heterogeneous traits, population-based linkage analysis can be more powerful than genotypic-association analysis. Here, we focus on linkage analysis in a population sample, but use sequences rather than individuals as our unit of observation. Earlier investigations of sequence-based linkage mapping relied on known sequence relatedness, whereas we infer relatedness from the sequence data. We propose two ways to associate similarity in relatedness of sequences with similarity in their trait values and compare the resulting linkage methods to two genotypic- association methods. We also introduce a procedure to label case sequences as potential carriers or non-carriers of causal variants after an association has been found. This post-hoc labeling of case sequences is based on inferred relatedness to other case sequences. Our simulation results indicate that methods based on sequence-relatedness improve localization and perform as well as genotypic-association methods for detecting rare causal variants. Sequence-based linkage analysis therefore has potential to fine-map allelically heterogeneous disease traits.

Acuticoccus mangrovi sp. nov., with an antibacterial property, isolated from mangrove sediment

A Gram-stain-negative, aerobic, milky white bacterium, designated B2012T, was isolated from mangrove sediment collected at Beibu Gulf, South China Sea. Antimicrobial activity assay revealed that the isolate possesses the capability of producing antibacterial compounds. Strain B2012T shared the highest 16S rRNA gene sequence relatedness (96.9–95.5 %) with members of the genus Acuticoccus . The isolate and all known Acuticoccus species contain Q-10 as the main respiratory quinone and have the same polar lipid components (phosphatidylcholine, unidentified glycolipid, unidentified lipid, unidentified amino lipid and phosphatidylglycerol). However, genomic relatedness referred by values of average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity and the percentage of conserved proteins between strain B2012T and other type strains of the genus Acuticoccus were below the proposed thresholds for species discrimination. The genome of strain B2012T was assembled into 65 scaffolds with an N50 size of 244239 bp, resulting in a 5.5 Mb genome size. Eight secondary metabolite biosynthetic gene clusters were detected in this genome, including three non-ribosomal peptide biosynthetic loci encoding yet unknown natural products. Strain B2012T displayed moderately halophilic and alkaliphilic properties, growing optimally at 2–3 % (w/v) NaCl concentration and at pH 8–9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0, C16 : 0 dimethyl aldehyde (DMA) and C16 : 0. Combined data from phenotypic, genotypic and chemotaxonomic analyses suggested that strain B2012T represents a novel species of the genus Acuticoccus , for which the name Acuticoccus mangrovi sp. nov. is proposed. The type strain of the type species is B2012T (=MCCC 1K04418T=KCTC 72962T).

History of safe exposure and bioinformatic assessment of phosphomannose-isomerase (PMI) for allergenic risk

Newly expressed proteins in genetically engineered crops are evaluated for potential cross reactivity to known allergens as part of their safety assessment. This assessment uses a weight-of-evidence approach. Two key components of this allergenicity assessment include any history of safe human exposure to the protein and/or the source organism from which it was originally derived, and bioinformatic analysis identifying amino acid sequence relatedness to known allergens. Phosphomannose-isomerase (PMI) has been expressed in commercialized genetically engineered (GE) crops as a selectable marker since 2010 with no known reports of allergy, which supports a history of safe exposure, and GE events expressing the PMI protein have been approved globally based on expert safety analysis. Bioinformatic analyses identified an eight-amino-acid contiguous match between PMI and a frog parvalbumin allergen (CAC83047.1). While short amino acid matches have been shown to be a poor predictor of allergen cross reactivity, most regulatory bodies require such matches be assessed in support of the allergenicity risk assessment. Here, this match is shown to be of negligible risk of conferring cross reactivity with known allergens.

A rapid and simple method for assessing and representing genome sequence relatedness

Coherent genomic groups are frequently used as a proxy for bacterial species delineation through computation of overall genome relatedness indices (OGRI). Average nucleotide identity (ANI) is a widely employed method for estimating relatedness between genomic sequences. However, pairwise comparisons of genome sequences based on ANI is relatively computationally intensive and therefore precludes analyses of large datasets composed of thousands of genome sequences.In this work we proposed a workflow to compute and visualize relationships between genomic sequences. A dataset containing more than 3,500 Pseudomonas genome sequences was successfully classified with an alternative OGRI based on k-mer counts in few hours with the same precision as ANI. A new visualization method based on zoomable circle packing was employed for assessing relationships among the 350 groups generated. Amendment of databases with these Pseudomonas groups greatly improved the classification of metagenomic read sets with k-mer-based classifier.The developed workflow was integrated in the user-friendly KI-S tool that is available at the following address:https://iris.angers.inra.fr/galaxypub-cfbp.

Genome Mining of Non-Conventional Yeasts: Search and Analysis of MAL Clusters and Proteins

Genomic clustering of functionally related genes is rare in yeasts and other eukaryotes with only few examples available. Here, we summarize our data on a nontelomeric MAL cluster of a non-conventional methylotrophic yeast Ogataea (Hansenula) polymorpha containing genes for α-glucosidase MAL1, α-glucoside permease MAL2 and two hypothetical transcriptional activators. Using genome mining, we detected MAL clusters of varied number, position and composition in many other maltose-assimilating non-conventional yeasts from different phylogenetic groups. The highest number of MAL clusters was detected in Lipomyces starkeyi while no MAL clusters were found in Schizosaccharomyces pombe and Blastobotrys adeninivorans. Phylograms of α-glucosidases and α-glucoside transporters of yeasts agreed with phylogenesis of the respective yeast species. Substrate specificity of unstudied α-glucosidases was predicted from protein sequence analysis. Specific activities of Scheffersomycesstipitis α-glucosidases MAL7, MAL8, and MAL9 heterologously expressed in Escherichia coli confirmed the correctness of the prediction—these proteins were verified promiscuous maltase-isomaltases. α-Glucosidases of earlier diverged yeasts L. starkeyi, B. adeninivorans and S. pombe showed sequence relatedness with α-glucosidases of filamentous fungi and bacilli.

Characterization of potential drug targeting folate transporter proteins from Eukaryotic Pathogens

Background: Medically important pathogens are responsible for the death of millions every year. For many of these pathogens, there are limited options for therapy and resistance to commonly used drugs is fast emerging. The availability of genome sequences of many eukaryotic microbes is providing critical biological information for understanding parasite biology and identifying new drug and vaccine targets. Methods: We developed automated search strategies in the Eukaryotic Pathogen Database Resources (EuPathDB) to construct a protein list and retrieve protein sequences of folate transporters encoded in the genomes of 200 eukaryotic microbes. The folate transporters were categorized according to features including mitochondrial localization, number of transmembrane helix, and protein sequence relatedness. Results: We identified 234 folate transporter proteins associated with 63 eukaryotic microbes including 48 protozoa, 13 fungi the others being algae and bacteria. Phylogenetic analysis placed 219 proteins into a major clade and 15 proteins into a minor clade. All the folate transporter sequences from the malaria parasite, Plasmodium, belonged to the major clade. The identified folate transporters include folate-binding protein YgfZ, folate/pteridine transporter, folate/biopterin transporter, reduced folate carrier family protein and folate/methotrexate transporter FT1. About 60% of the identified proteins are reported for the first time. Phylogeny computation shows the similarity of the proteins identified. Conclusion: These findings offer new possibilities for potential drug development targeting folate-salvage proteins in eukaryotic pathogens.

Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus

ABSTRACTWe present the complete genome sequences of four members of a novel group of phages infectingStreptococcus thermophilus, designated here as the 987 group. Members of this phage group appear to have resulted from genetic exchange events, as evidenced by their “hybrid” genomic architecture, exhibiting DNA sequence relatedness to the morphogenesis modules of certain P335 groupLactococcus lactisphages and to the replication modules ofS. thermophilusphages. All four identified members of the 987 phage group were shown to elicit adsorption affinity to both their cognateS. thermophilushosts and a particularL. lactisstarter strain. The receptor binding protein of one of these phages (as a representative of this novel group) was defined using an adsorption inhibition assay. The emergence of a novel phage group infectingS. thermophilushighlights the continuous need for phage monitoring and development of new phage control measures.IMPORTANCEPhage predation ofS. thermophilusis an important issue for the dairy industry, where viral contamination can lead to fermentation inefficiency or complete fermentation failure. Genome information and phage-host interaction studies ofS. thermophilusphages, particularly those emerging in the marketplace, are an important part of limiting the detrimental impact of these viruses in the dairy environment.