Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2016, Volume and Issue: 283(1835), P. 20160569 - 20160569

Published: July 20, 2016

Complex or quantitative traits are important in medicine, agriculture and evolution, yet, until recently, few of the polymorphisms that cause variation these were known. Genome-wide association studies (GWAS), based on ability to assay thousands single nucleotide (SNPs), have revolutionized our understanding genetics complex traits. We advocate analysis GWAS data by a statistical method fits all SNP effects simultaneously, assuming drawn from prior distribution. illustrate how this can be used predict future phenotypes, map identify causal mutations, study genetic architecture The is even more than previously thought: almost every trait studied there explain variation. Methods predicting collectively known as genomic selection prediction, been widely adopted livestock crop breeding, leading increased rates improvement.

Language: Английский

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Phage-mediated horizontal gene transfer and its implications for the human gut microbiome

Gastroenterology report, Journal Year: 2022, Volume and Issue: 10

Published: Jan. 1, 2022

Horizontal gene transfer (HGT) in the microbiome has profound consequences for human health and disease. The spread of antibiotic resistance genes, virulence, pathogenicity determinants predominantly occurs by way HGT. Evidence exists extensive horizontal gut microbiome. Phage transduction is a type HGT event which bacteriophage transfers non-viral DNA from one bacterial host cell to another. abundance tailed bacteriophages suggests that could act as significant mode Here we review detail known mechanisms phage-mediated HGT, namely specialized generalized transduction, lateral gene-transfer agents, molecular piracy, well methods used detect discuss its potential implications

Language: Английский

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Natural products of pentacyclic triterpenoids: from discovery to heterologous biosynthesis

Natural Product Reports, Journal Year: 2022, Volume and Issue: 40(8), P. 1303 - 1353

Published: Dec. 1, 2022

Natural products of pentacyclic triterpenoids: from their discovery and biosynthetic pathways to heterologous biosynthesis in plant chassis microbial cell factories.

Language: Английский

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The evolutionary history of bees in time and space

Current Biology, Journal Year: 2023, Volume and Issue: 33(16), P. 3409 - 3422.e6

Published: July 27, 2023

Language: Английский

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Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species

BMC Genomics, Journal Year: 2016, Volume and Issue: 17(1)

Published: Nov. 7, 2016

Gram-positive bacteria of the Bacillales are important producers antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to wide availability whole genome sequence data and development specific mining tools, novel compounds, either ribosomally- non-ribosomally produced, various species can predicted classified. Here, we provide a classification scheme known putative in context species.We identify describe bacteriocins, synthesized peptides (NRPs), polyketides (PKs) other antimicrobials from 328 whole-genome sequenced strains 57 by using web based genome-mining prediction tools. We these update findings NRPs PKs investigate their characteristics suitability biocontrol describing per class genetic organization structure. Moreover, highlight potential several Bacillales.Our extended demonstrates rich source now readily tapped experimentally, since many new gene clusters identified.

Language: Английский

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Inconsistency of Species Tree Methods under Gene Flow

Systematic Biology, Journal Year: 2016, Volume and Issue: 65(5), P. 843 - 851

Published: May 5, 2016

Coalescent-based methods are now broadly used to infer evolutionary relationships between groups of organisms under the assumption that incomplete lineage sorting (ILS) is only source gene tree discordance. Many these known consistently estimate species when all their assumptions met. Nonetheless, little work has been done test robustness such violations assumptions. Here, we study performance two most efficient coalescent-based methods, ASTRAL and NJst, in presence flow. Gene flow violates ILS sole conflict. We find anomalous trees on three-taxon rooted four-taxon unrooted trees. These do not exist only, but appear because Our simulations show (and concatenation) may reconstruct wrong history, even from a very large number well-reconstructed In other words, can be inconsistent results underline need for like PhyloNet, account simultaneously unified framework. Although much slower, PhyloNet had better accuracy remained consistent at high levels

Language: Английский

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Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)

Published: March 14, 2017

The detection of signatures selection has the potential to elucidate identities genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant investigate levels genetic diversity a population, as represents raw material essential breeding practical implications implementation genomic selection. A total 1151 animals from nine goat populations selected different goals genotyped Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. proportion polymorphic SNPs ranged 0.902 (Nubian) 0.995 (Rangeland). overall mean HO HE was 0.374 ± 0.021 0.369 0.023, respectively. average pairwise distance (D) 0.263 (Toggenburg) 0.323 inbreeding measures FEH, FVR, FLEUT, FROH FPED 0.129, −0.012, −0.010, 0.038 0.030, Several regions located on 19 chromosomes potentially under at least one breeds. population tree constructed using all differentiated breeds based purpose, while built only most significant region showed great differentiation between LaMancha other We hypothesized that related ear morphogenesis. Furthermore, we identified reproduction traits, adult body mass, efficiency food conversion, abdominal fat deposition, conformation liver metabolism, milk fatty acids, somatic cells score, protein, thermo-tolerance In general, moderate high variability observed characterization runs homozygosity gave insights into breeds’ development history. information reported here will be useful studies goats. various genome positive smoothed FST hapFLK statistics suggested genes, which are These results can now provide foundation formulate biological hypotheses processes

Language: Английский

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damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets

Bioinformatics, Journal Year: 2015, Volume and Issue: 31(20), P. 3371 - 3373

Published: June 25, 2015

Abstract Summary: DamID is a powerful technique for identifying regions of the genome bound by DNA-binding (or DNA-associated) protein. Currently, no method exists automatically processing next-generation sequencing (DamID-seq) data, and use DamID-seq datasets with normalization based on read-counts alone can lead to high background loss signal. thus presents novel challenges in terms minimization. We describe here damidseq_pipeline, software pipeline that performs automatic reduction multiple FASTQ datasets. Availability implementation: Open-source freely available from http://owenjm.github.io/damidseq_pipeline. The damidseq_pipeline implemented Perl compatible any Unix-based operating system (e.g. Linux, Mac OSX). Contact: [email protected] Supplementary information: data are at Bioinformatics online.

Language: Английский

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An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)

Published: Jan. 18, 2017

The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances sequencing technologies have led to a multitude generated for complex genomes, although many these are fragmented nature with significant fraction bases gaps. development long-read and improved software now enable generation more contiguous assemblies. By combining data from Illumina, longer PacBio technologies, as well integrating results multiple programs, we created substantially version assembly. sequence contiguity this is increased fifty-fold proportion gap-bases has been reduced fifteen-fold. Compared other vertebrates, contains an unusual high density tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps were largely associated TRs. We show 21% TRs across assembly, 19% promoter regions 12% coding sequences heterozygous sequenced individual. inclusion reads combined use programs drastically by successfully resolving long frequency within or vicinity genes indicate considerable standing genomic variation populations, which likely evolutionary importance.

Language: Английский

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Assessment of Rumen Microbiota from a Large Dairy Cattle Cohort Reveals the Pan and Core Bacteriomes Contributing to Varied Phenotypes

Applied and Environmental Microbiology, Journal Year: 2018, Volume and Issue: 84(19)

Published: July 26, 2018

Currently, knowledge on the extent to which rumen microbiota differ in a large population of cattle fed same diet and whether such differences are associated with animal performance is limited. This study was conducted characterize cohort lactating Holstein dairy cows (

Language: Английский

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