Future-Proofing Your  Microbiology Resource Announcements  Genome Assembly for Reproducibility and Clarity

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Abstract

Descriptions of resources, like the genome assemblies reported in Microbiology Resource Announcements, are often frozen at their time of publication, yet they will need to be interpreted in the midst of continually evolving technologies. It is therefore important to ensure that researchers accessing published resources have access to all of the information required to repeat, interpret, and extend these original analyses.

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Most cited references 5

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The minimum information about a genome sequence (MIGS) specification.

Dawn Field, George Garrity, Tanya Gray … (2008)

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

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Measuring the reproducibility and quality of Hi-C data

Galip Gürkan Yardımcı, Hakan Ozadam, Michael Sauria … (2019)

Background Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study. Results Using real and simulated data, we profile the performance of several recently proposed methods for assessing reproducibility of population Hi-C data, including HiCRep, GenomeDISCO, HiC-Spector, and QuASAR-Rep. By explicitly controlling noise and sparsity through simulations, we demonstrate the deficiencies of performing simple correlation analysis on pairs of matrices, and we show that methods developed specifically for Hi-C data produce better measures of reproducibility. We also show how to use established measures, such as the ratio of intra- to interchromosomal interactions, and novel ones, such as QuASAR-QC, to identify low-quality experiments. Conclusions In this work, we assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices. Through this extensive validation and benchmarking of Hi-C data, we describe best practices for reproducibility and quality assessment of Hi-C experiments. We make all software publicly available at http://github.com/kundajelab/3DChromatin_ReplicateQC to facilitate adoption in the community. Electronic supplementary material The online version of this article (10.1186/s13059-019-1658-7) contains supplementary material, which is available to authorized users.

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The genome-sequenced variant of Campylobacter jejuni NCTC 11168 and the original clonal clinical isolate differ markedly in colonization, gene expression, and virulence-associated phenotypes.

Peter D. Newell, Shaun A. Cawthraw, Stanley Falkow … (2003)

The genome sequence of the enteric bacterial pathogen Campylobacter jejuni NCTC 11168 (11168-GS) was published in 2000, providing a valuable resource for the identification of C. jejuni-specific colonization and virulence factors. Surprisingly, the 11168-GS clone was subsequently found to colonize 1-day-old chicks following oral challenge very poorly compared to other strains. In contrast, we have found that the original clinical isolate from which 11168-GS was derived, 11168-O, is an excellent colonizer of chicks. Other marked phenotypic differences were also identified: 11168-O invaded and translocated through tissue culture cells far more efficiently and rapidly than 11168-GS, was significantly more motile, and displayed a different morphology. Serotyping, multiple high-resolution molecular genotyping procedures, and subtractive hybridization did not yield observable genetic differences between the variants, suggesting that they are clonal. However, microarray transcriptional profiling of these strains under microaerobic and severely oxygen-limited conditions revealed dramatic expression differences for several gene families. Many of the differences were in respiration and metabolism genes and operons, suggesting that adaptation to different oxygen tensions may influence colonization potential. This correlates biologically with our observation that anaerobically priming 11168-GS or aerobically passaging 11168-O caused an increase or decrease, respectively, in colonization compared to the parent strain. Expression differences were also observed for several flagellar genes and other less well-characterized genes that may participate in motility. Targeted sequencing of the sigma factors revealed specific DNA differences undetected by the other genomic methods [corrected].

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Author and article information

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (hwp): ga

Journal ID (pmc): mra

Journal ID (publisher-id): MRA

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic): 5 September 2019

Publication date Collection: September 2019

Volume: 8

Issue: 36

Electronic Location Identifier: e00954-19

Affiliations

[a ]School of Plant Sciences, University of Arizona, Tucson, Arizona, USA

[b ]Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

[c ]Queens College of The City University of New York, Queens, New York, USA

[d ]The Graduate Center of The City University of New York, New York, New York, USA

[e ]Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, Maryland, USA

[f ]Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, USA

[g ]Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore, Baltimore, Maryland, USA

[h ]Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA

[i ]Department of Biology, Indiana University, Bloomington, Indiana, USA

[j ]Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA

[k ]Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA

[l ]Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA

[m ]DOE Joint Genome Institute, Walnut Creek, California, USA

[n ]Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California—Riverside, Riverside, California, USA

Author notes

Address correspondence to David A. Baltrus, baltrus@ 123456email.arizona.edu .

Citation Baltrus DA, Cuomo CA, Dennehy JJ, Dunning Hotopp JC, Maresca JA, Newton ILG, Rasko DA, Rokas A, Roux S, Stajich JE. 2019. Future-proofing your Microbiology Resource Announcements genome assembly for reproducibility and clarity. Microbiol Resour Announc 8:e00954-19. https://doi.org/10.1128/MRA.00954-19.

Author information

David A. Baltrus https://orcid.org/0000-0002-5166-9551

Christina A. Cuomo https://orcid.org/0000-0002-5778-960X

Julia A. Maresca https://orcid.org/0000-0002-3955-1585

David A. Rasko https://orcid.org/0000-0002-7337-7154

Antonis Rokas https://orcid.org/0000-0002-7248-6551

Simon Roux https://orcid.org/0000-0002-5831-5895

Jason E. Stajich https://orcid.org/0000-0002-7591-0020

Article

Publisher ID: MRA00954-19

DOI: 10.1128/MRA.00954-19

PMC ID: 6728651

PubMed ID: 31488541

SO-VID: e4e0d36b-fe8c-4a0a-b39c-2230cb0471fb

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This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity

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Most cited references 5

The minimum information about a genome sequence (MIGS) specification.

Measuring the reproducibility and quality of Hi-C data

The genome-sequenced variant of Campylobacter jejuni NCTC 11168 and the original clonal clinical isolate differ markedly in colonization, gene expression, and virulence-associated phenotypes.

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