Dataset Information

Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

ABSTRACT: The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models. Neptune uses parallel computing to efficiently identify and extract these loci from draft genome assemblies without requiring multiple sequence alignments or other computationally expensive comparative sequence analyses. Tests on simulated and real datasets showed that Neptune rapidly identifies regions that are both sensitive and specific. We demonstrate that this system can identify trait-specific loci from different bacterial lineages. Neptune is broadly applicable for comparative bacterial analyses, yet will particularly benefit pathogenomic applications, owing to efficient and sensitive discovery of differentially abundant genomic loci. The software is available for download at: http://github.com/phac-nml/neptune.

SUBMITTER: Marinier E

PROVIDER: S-EPMC5737611 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

Marinier Eric E Zaheer Rahat R Berry Chrystal C Weedmark Kelly A KA Domaratzki Michael M Mabon Philip P Knox Natalie C NC Reimer Aleisha R AR Graham Morag R MR Chui Linda L Patterson-Fortin Laura L Zhang Jian J Pagotto Franco F Farber Jeff J Mahony Jim J Seyer Karine K Bekal Sadjia S Tremblay Cécile C Isaac-Renton Judy J Prystajecky Natalie N Chen Jessica J Slade Peter P Van Domselaar Gary G

Nucleic acids research 20171001 18

The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-t ...[more]

PMID: 29048594

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Project description:BACKGROUND:Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species' ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic. RESULTS:Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county. CONCLUSIONS:Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.

Dataset Information

Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

Publications

Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

Similar Datasets

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