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Article: Whole genome sequencing of

Chhettri, Saroja / Sevigny, Joseph / Pesce, Céline / Sarkar, Indrani / Thomas, W Kelley / Nouioui, Imen / Sen, Gargi / Tisa, Louis S / Sen, Arnab

Journal of genomics

2024 Volume 12, Page(s) 6–13

Abstract: ... ...

Abstract	Streptomyces
Language	English
Publishing date	2024-01-01
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2692697-0
ISSN	1839-9940
ISSN	1839-9940
DOI	10.7150/jgen.87156
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Article ; Online: Nematode mitochondrial metagenomics: A new tool for biodiversity analysis

Gendron, Eli M. / Sevigny, Joseph L. / Byiringiro, Innocent / Thomas, W. Kelley / Powers, Thomas O. / Porazinska, Dorota L.

Molecular Ecology Resources. 2023 July, v. 23, no. 5 p.975-989

2023

Abstract: DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable ... ...

Abstract	DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito‐metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.
Keywords	DNA ; DNA barcoding ; Rhabditida ; biodiversity ; databases ; metagenomics ; mitochondria ; mitochondrial genome ; mitochondrial proteins ; phylogeny
Language	English
Dates of publication	2023-07
Size	p. 975-989.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13761
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Article ; Online: RepeatFS: a file system providing reproducibility through provenance and automation.

Westbrook, Anthony / Varki, Elizabeth / Thomas, W Kelley

Bioinformatics (Oxford, England)

2020 Volume 37, Issue 9, Page(s) 1292–1296

Abstract: Motivation: Reproducibility is of central importance to the scientific process. The difficulty of consistently replicating and verifying experimental results is magnified in the era of big data, in which bioinformatics analysis often involves complex ... ...

Abstract	Motivation: Reproducibility is of central importance to the scientific process. The difficulty of consistently replicating and verifying experimental results is magnified in the era of big data, in which bioinformatics analysis often involves complex multi-application pipelines operating on terabytes of data. These processes result in thousands of possible permutations of data preparation steps, software versions and command-line arguments. Existing reproducibility frameworks are cumbersome and involve redesigning computational methods. To address these issues, we developed RepeatFS, a file system that records, replicates and verifies informatics workflows with no alteration to the original methods. RepeatFS also provides several other features to help promote analytical transparency and reproducibility, including provenance visualization and task automation. Results: We used RepeatFS to successfully visualize and replicate a variety of bioinformatics tasks consisting of over a million operations with no alteration to the original methods. RepeatFS correctly identified all software inconsistencies that resulted in replication differences. Availabilityand implementation: RepeatFS is implemented in Python 3. Its source code and documentation are available at https://github.com/ToniWestbrook/repeatfs. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Automation ; Computational Biology ; Reproducibility of Results ; Software ; Workflow
Language	English
Publishing date	2020-11-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btaa950
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Article ; Online: Draft Genome Sequences for Bacteria Associated with Root Nodules of Alnus incana in New England.

Mercurio, Kelsey / Sevigny, Joseph / Pesce, Céline / Thomas, W Kelley / Tisa, Louis S

Microbiology resource announcements

2022 Volume 11, Issue 12, Page(s) e0091422

Abstract: Nine bacterial strains isolated from the root nodules of Alnus incana were sequenced to determine their potential roles in plant health. The selected bacterial isolates belonged to the ... ...

Abstract	Nine bacterial strains isolated from the root nodules of Alnus incana were sequenced to determine their potential roles in plant health. The selected bacterial isolates belonged to the genera
Language	English
Publishing date	2022-11-07
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/mra.00914-22
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Article ; Online: Nematode mitochondrial metagenomics: A new tool for biodiversity analysis.

Gendron, Eli M / Sevigny, Joseph L / Byiringiro, Innocent / Thomas, W Kelley / Powers, Thomas O / Porazinska, Dorota L

Molecular ecology resources

2023 Volume 23, Issue 5, Page(s) 975–989

Abstract	DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.
MeSH term(s)	Animals ; Phylogeny ; Metagenomics ; Nematoda/genetics ; Biodiversity ; DNA ; DNA Barcoding, Taxonomic ; Genome, Mitochondrial/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-02-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13761
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Article ; Online: Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery.

Benham, Phred M / Cicero, Carla / Escalona, Merly / Beraut, Eric / Fairbairn, Colin / Marimuthu, Mohan P A / Nguyen, Oanh / Sahasrabudhe, Ruta / King, Benjamin L / Thomas, W Kelley / Kovach, Adrienne I / Nachman, Michael W / Bowie, Rauri C K

Genome biology and evolution

2024 Volume 16, Issue 4

Abstract: Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased ... ...

Abstract	Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.
MeSH term(s)	Animals ; DNA Transposable Elements/genetics ; Sparrows/genetics ; Sequence Analysis, DNA
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evae067
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Article: Target enrichment of metazoan mitochondrial DNA with hybridization capture probes

Sevigny, Joseph / Leasi, Francesca / Simpson, Stephen / Di Domenico, Maikon / Jörger, Katharina M / Norenburg, Jon L / Thomas, W. Kelley

Ecological indicators. 2021 Feb., v. 121

2021

Abstract: High-throughput DNA sequencing studies allow rapid and widescale investigations into complex assemblages of organisms that would otherwise remain infeasible. Recently scientists have begun to apply metagenomic sequencing (sequencing of the complete pool ... ...

Abstract	High-throughput DNA sequencing studies allow rapid and widescale investigations into complex assemblages of organisms that would otherwise remain infeasible. Recently scientists have begun to apply metagenomic sequencing (sequencing of the complete pool of DNA from a sample) to investigate microscopic animal communities. Mitochondrial genomes are an important locus for such studies; however, current databases of complete mitochondrial genomes remain incomplete, and many important meiofaunal clades are underrepresented or missing entirely. This underrepresentation is likely due to the low amount of input DNA acquired from meiofaunal individuals, the impossibility of pooling animals because of high levels of cryptic speciation, and the paucity of researchers collecting and studying these animals. Here we help to alleviate the first two barriers by developing a method of enriching animal mtDNA from next-generation sequencing libraries by using hybridization capture probes. These hybrid-capture probes were designed based on the complete collection of mitochondrial genomes available from GenBank and are suitable for enrichment of diverse animal lineages. We demonstrate the protocol on forty-seven meiofaunal specimens spanning four different phyla. Overall, we observed an average of ~450× fold enrichment over standard NGS sequencing library preparation. In addition, we were able to enrich the mtDNA from taxa distantly related to those in the database, indicating that even animals that were not directly targeted by the probe design can be enriched with this method.
Keywords	Animalia ; animals ; cryptic speciation ; databases ; hybridization ; loci ; metagenomics ; mitochondrial DNA ; mitochondrial genome
Language	English
Dates of publication	2021-02
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2036774-0
ISSN	1872-7034 ; 1470-160X
ISSN (online)	1872-7034
ISSN	1470-160X
DOI	10.1016/j.ecolind.2020.106973
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Article ; Online: FlowClus: efficiently filtering and denoising pyrosequenced amplicons.

Gaspar, John M / Thomas, W Kelley

BMC bioinformatics

2015 Volume 16, Page(s) 105

Abstract: Background: Reducing the effects of sequencing errors and PCR artifacts has emerged as an essential component in amplicon-based metagenomic studies. Denoising algorithms have been designed that can reduce error rates in mock community data, but they ... ...

Abstract	Background: Reducing the effects of sequencing errors and PCR artifacts has emerged as an essential component in amplicon-based metagenomic studies. Denoising algorithms have been designed that can reduce error rates in mock community data, but they change the sequence data in a manner that can be inconsistent with the process of removing errors in studies of real communities. In addition, they are limited by the size of the dataset and the sequencing technology used. Results: FlowClus uses a systematic approach to filter and denoise reads efficiently. When denoising real datasets, FlowClus provides feedback about the process that can be used as the basis to adjust the parameters of the algorithm to suit the particular dataset. When used to analyze a mock community dataset, FlowClus produced a lower error rate compared to other denoising algorithms, while retaining significantly more sequence information. Among its other attributes, FlowClus can analyze longer reads being generated from all stages of 454 sequencing technology, as well as from Ion Torrent. It has processed a large dataset of 2.2 million GS-FLX Titanium reads in twelve hours; using its more efficient (but less precise) trie analysis option, this time was further reduced, to seven minutes. Conclusions: Many of the amplicon-based metagenomics datasets generated over the last several years have been processed through a denoising pipeline that likely caused deleterious effects on the raw data. By using FlowClus, one can avoid such negative outcomes while maintaining control over the filtering and denoising processes. Because of its efficiency, FlowClus can be used to re-analyze multiple large datasets together, thereby leading to more standardized conclusions. FlowClus is freely available on GitHub (jsh58/FlowClus); it is written in C and supported on Linux.
MeSH term(s)	Algorithms ; Metagenomics ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2015-03-27
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-015-0532-1
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Article: Draft Genomes Sequences of 11

Ennis, Nathaniel J / Dharumadurai, Dhanasekaran / Sevigny, Joseph L / Wilmot, Ryan / Alnaimat, Sulaiman M / Bryce, Julia G / Thomas, W Kelley / Tisa, Louis S

Journal of genomics

2022 Volume 10, Page(s) 69–77

Abstract: Metagenomic analysis of stone microbiome from samples collected in New England, USA and Tamil Nadu, India identified numerous Actinobacteria ... ...

Abstract	Metagenomic analysis of stone microbiome from samples collected in New England, USA and Tamil Nadu, India identified numerous Actinobacteria including
Language	English
Publishing date	2022-09-21
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2692697-0
ISSN	1839-9940
ISSN	1839-9940
DOI	10.7150/jgen.76121
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Article: Evidence for a genetic basis in functional trait tradeoffs with microbial growth rate but not growth yield

Morrison, Eric W. / Whitney, Shana A. / Geyer, Kevin M. / Sevigny, Joseph L. / Grandy, A. Stuart / Thomas, W. Kelley / DeAngelis, Kristen M. / Frey, Serita D.

Soil biology & biochemistry. 2022 Sept., v. 172

2022

Abstract: Tradeoffs in microbial functional traits have been a focus of recently described ecological frameworks and of mathematical models of microbial community functioning. Tradeoffs in key traits such as growth rate, growth yield, resource acquisition, and ... ...

Abstract	Tradeoffs in microbial functional traits have been a focus of recently described ecological frameworks and of mathematical models of microbial community functioning. Tradeoffs in key traits such as growth rate, growth yield, resource acquisition, and stress tolerance may have either a genetic basis or a physiological basis, and the type of tradeoff can inform how traits are modeled and measured. Here we provide evidence that growth rate/decomposition and growth rate/stress tolerance tradeoffs have a primarily genetic basis in a phylogenetically diverse suite of ten leaf litter-inhabiting fungi. In contrast, growth yield tradeoffs with functional traits are more likely to have a physiological basis. Consideration of the type of tradeoff, genetic or physiological, should help to inform efforts to model microbial contributions to ecosystem processes, especially when considering different scales. Consideration of physiological tradeoffs may be important for understanding short-term variability (e.g., pulse events) and fine spatial scales, whereas genetic tradeoffs are likely to be useful for understanding regional- to continental-scale and medium- to long-term contributions of microbes to ecosystem processes.
Keywords	biochemistry ; ecosystems ; leaves ; microbial communities ; microbial growth ; phylogeny ; soil biology ; stress tolerance
Language	English
Dates of publication	2022-09
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	280810-9
ISSN	0038-0717
ISSN	0038-0717
DOI	10.1016/j.soilbio.2022.108765
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