Dataset Information

Improved genomic island predictions with IslandPath-DIMOB.

ABSTRACT: Motivation:Genomic islands (GIs) are clusters of genes of probable horizontal origin that play a major role in bacterial and archaeal genome evolution and microbial adaptability. They are of high medical and industrial interest, due to their enrichment in virulence factors, some antimicrobial resistance genes and adaptive metabolic pathways. The development of more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed as large-scale analyses of microbial genomes increase. Results:IslandPath-DIMOB, a leading GI prediction tool in the IslandViewer webserver, has now been significantly improved by modifying both the decision algorithm to determine sequence composition biases, and the underlying database of HMM profiles for associated mobility genes. The accuracy of IslandPath-DIMOB and other major software has been assessed using a reference GI dataset predicted by comparative genomics, plus a manually curated dataset from literature review. Compared to the previous version (v0.2.0), this IslandPath-DIMOB v1.0.0 achieves 11.7% and 5.3% increase in recall and precision, respectively. IslandPath-DIMOB has the highest Matthews correlation coefficient among individual prediction methods tested, combining one of the highest recall measures (46.9%) at high precision (87.4%). The only method with higher recall had notably lower precision (55.1%). This new IslandPath-DIMOB v1.0.0 will facilitate more accurate studies of GIs, including their key roles in microbial adaptability of medical, environmental and industrial interest. Availability and implementation:IslandPath-DIMOB v1.0.0 is freely available through the IslandViewer webserver {{http://www.pathogenomics.sfu.ca/islandviewer/}} and as standalone software {{https://github.com/brinkmanlab/islandpath/}} under the GNU-GPLv3. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Bertelli C

PROVIDER: S-EPMC6022643 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Improved genomic island predictions with IslandPath-DIMOB.

Bertelli Claire C Brinkman Fiona S L FSL

Bioinformatics (Oxford, England) 20180701 13

<h4>Motivation</h4>Genomic islands (GIs) are clusters of genes of probable horizontal origin that play a major role in bacterial and archaeal genome evolution and microbial adaptability. They are of high medical and industrial interest, due to their enrichment in virulence factors, some antimicrobial resistance genes and adaptive metabolic pathways. The development of more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed a ...[more]

PMID: 29905770

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Project description:Most of the genomic studies in plants and animals have used additive models for studying genetic parameters and prediction accuracies. In this study, we used genomic models with additive and nonadditive effects to analyze the genetic architecture of growth and wood traits in an open-pollinated (OP) population of Eucalyptus pellita We used two progeny trials consisting of 5742 trees from 244 OP families to estimate genetic parameters and to test genomic prediction accuracies of three growth traits (diameter at breast height - DBH, total height - Ht and tree volume - Vol) and kraft pulp yield (KPY). From 5742 trees, 468 trees from 28 families were genotyped with 2023 pre-selected markers from candidate genes. We used the pedigree-based additive best linear unbiased prediction (ABLUP) model and two marker-based models (single-step genomic BLUP - ssGBLUP and genomic BLUP - GBLUP) to estimate the genetic parameters and compare the prediction accuracies. Analyses with the two genomic models revealed large dominant effects influencing the growth traits but not KPY. Theoretical breeding value accuracies were higher with the dominance effect in ssGBLUP model for the three growth traits. Accuracies of cross-validation with random folding in the genotyped trees have ranged from 0.60 to 0.82 in different models. Accuracies of ABLUP were lower than the genomic models. Accuracies ranging from 0.50 to 0.76 were observed for within family cross-validation predictions with low relationships between training and validation populations indicating part of the functional variation is captured by the markers through short-range linkage disequilibrium (LD). Within-family phenotype predictive abilities and prediction accuracies of genetic values with dominance effects are higher than the additive models for growth traits indicating the importance of dominance effects in predicting phenotypes and genetic values. This study demonstrates the importance of genomic approaches in OP families to study nonadditive effects. To capture the LD between markers and the quantitative trait loci (QTL) it may be important to use informative markers from candidate genes.

Project description:BackgroundMathematical models are needed for the design of breeding programs using genomic prediction. While deterministic models for selection on pedigree-based estimates of breeding values (PEBV) are available, these have not been fully developed for genomic selection, with a key missing component being the accuracy of genomic EBV (GEBV) of selection candidates. Here, a deterministic method was developed to predict this accuracy within a closed breeding population based on the accuracy of GEBV and PEBV in the reference population and the distance of selection candidates from their closest ancestors in the reference population.MethodsThe accuracy of GEBV was modeled as a combination of the accuracy of PEBV and of EBV based on genomic relationships deviated from pedigree (DEBV). Loss of the accuracy of DEBV from the reference to the target population was modeled based on the effective number of independent chromosome segments in the reference population (Me). Measures of Me derived from the inverse of the variance of relationships and from the accuracies of GEBV and PEBV in the reference population, derived using either a Fisher information or a selection index approach, were compared by simulation.ResultsUsing simulation, both the Fisher and the selection index approach correctly predicted accuracy in the target population over time, both with and without selection. The index approach, however, resulted in estimates of Me that were less affected by heritability, reference size, and selection, and which are, therefore, more appropriate as a population parameter. The variance of relationships underpredicted Me and was greatly affected by selection. A leave-one-out cross-validation approach was proposed to estimate required accuracies of EBV in the reference population. Aspects of the methods were validated using real data.ConclusionsA deterministic method was developed to predict the accuracy of GEBV in selection candidates in a closed breeding population. The population parameter Me that is required for these predictions can be derived from an available reference data set, and applied to other reference data sets and traits for that population. This method can be used to evaluate the benefit of genomic prediction and to optimize genomic selection breeding programs.

Dataset Information

Improved genomic island predictions with IslandPath-DIMOB.

Publications

Improved genomic island predictions with IslandPath-DIMOB.

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