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Article ; Online: DrosOMA: the

Thiébaut, Antonin / Altenhoff, Adrian M / Campli, Giulia / Glover, Natasha / Dessimoz, Christophe / Waterhouse, Robert M

F1000Research

2024 Volume 12, Page(s) 936

Abstract: Background: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, ... ...

Abstract	Background: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Methods: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. Results: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. Conclusions: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.
MeSH term(s)	Animals ; Drosophila/genetics ; Comparative Genomic Hybridization ; Databases, Factual ; Evolution, Molecular ; Genomics
Language	English
Publishing date	2024-01-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2699932-8
ISSN	2046-1402 ; 2046-1402
ISSN (online)	2046-1402
ISSN	2046-1402
DOI	10.12688/f1000research.135250.2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Quality assessment of gene repertoire annotations with OMArk.

Nevers, Yannis / Warwick Vesztrocy, Alex / Rossier, Victor / Train, Clément-Marie / Altenhoff, Adrian / Dessimoz, Christophe / Glover, Natasha M

Nature biotechnology

2024

Abstract: In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, ...

Abstract	In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-024-02147-w
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Article ; Online: OMAMO: orthology-based alternative model organism selection.

Nicheperovich, Alina / Altenhoff, Adrian M / Dessimoz, Christophe / Majidian, Sina

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 10, Page(s) 2965–2966

Abstract: Summary: The conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology. However, the use of traditional model systems such as mice, rats and zebrafish is ... ...

Abstract	Summary: The conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology. However, the use of traditional model systems such as mice, rats and zebrafish is costly, time-consuming and increasingly raises ethical concerns, which highlights the need to search for less complex model organisms. Existing tools only focus on the few well-studied model systems, most of which are complex animals. To address these issues, we have developed Orthologous Matrix and Alternative Model Organism (OMAMO), a software and a web service that provides the user with the best non-complex organism for research into a biological process of interest based on orthologous relationships between human and the species. The outputs provided by OMAMO were supported by a systematic literature review. Availability and implementation: https://omabrowser.org/omamo/, https://github.com/DessimozLab/omamo. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Animals ; Mice ; Rats ; Software ; Zebrafish/genetics
Language	English
Publishing date	2022-03-18
Publishing country	England
Document type	Journal Article ; Systematic Review ; 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/btac163
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Article: Assigning confidence scores to homoeologs using fuzzy logic.

Glover, Natasha M / Altenhoff, Adrian / Dessimoz, Christophe

PeerJ

2019 Volume 6, Page(s) e6231

Abstract: In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton ( ...

Abstract	In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (
Language	English
Publishing date	2019-01-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.6231
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Article ; Online: Inferring Orthology and Paralogy.

Altenhoff, Adrian M / Glover, Natasha M / Dessimoz, Christophe

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1910, Page(s) 149–175

Abstract: The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide ... ...

Abstract	The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.
MeSH term(s)	Algorithms ; Animals ; Computational Biology/methods ; Evolution, Molecular ; Genome ; Genomics/methods ; Humans ; Multigene Family ; Phylogeny
Language	English
Publishing date	2019-07-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9074-0_5
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Article ; Online: How to build phylogenetic species trees with OMA [version 2; peer review

Yannis Nevers / David Dylus / Natasha M. Glover / Antoine Gürtler / Christophe Dessimoz / Adrian M. Altenhoff

F1000Research, Vol

2 approved]

2022 Volume 9

Abstract: Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This ... ...

Abstract	Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and error prone if done ad hoc. This tutorial provides protocols to make use of OMA Orthologous Groups, a set of genes all orthologous to each other, to infer a phylogenetic species tree. It is designed to be user-friendly and computationally inexpensive, by providing two options: (1) Using only precomputed groups with species available on the OMA Browser, or (2) Computing orthologs using OMA Standalone for additional species, with the option of using precomputed orthology relations for those present in OMA. A protocol for downstream analyses is provided as well, including creating a supermatrix, tree inference, and visualization. All protocols use publicly available software, and we provide scripts and code snippets to facilitate data handling. The protocols are accompanied with practical examples.
Keywords	phylogenetics ; phylogenomics ; species tree ; OMA ; Orthologous Matrix ; eng ; Medicine ; R ; Science ; Q
Subject code	590 ; 580
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: How to build phylogenetic species trees with OMA.

Dylus, David / Nevers, Yannis / Altenhoff, Adrian M / Gürtler, Antoine / Dessimoz, Christophe / Glover, Natasha M

F1000Research

2020 Volume 9, Page(s) 511

Abstract	Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and error prone if done
Language	English
Publishing date	2020-06-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2699932-8
ISSN	2046-1402 ; 2046-1402
ISSN (online)	2046-1402
ISSN	2046-1402
DOI	10.12688/f1000research.23790.2
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Article ; Online: OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.

Altenhoff, Adrian M / Warwick Vesztrocy, Alex / Bernard, Charles / Train, Clement-Marie / Nicheperovich, Alina / Prieto Baños, Silvia / Julca, Irene / Moi, David / Nevers, Yannis / Majidian, Sina / Dessimoz, Christophe / Glover, Natasha M

Nucleic acids research

2023 Volume 52, Issue D1, Page(s) D513–D521

Abstract: In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of ... ...

Abstract	In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
MeSH term(s)	Ecosystem ; Genome/genetics ; Phylogeny ; Proteome ; Synteny ; Internet ; Databases, Genetic ; Gene Order/genetics
Chemical Substances	Proteome
Language	English
Publishing date	2023-10-11
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1020
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Article ; Online: Assigning confidence scores to homoeologs using fuzzy logic

Natasha M. Glover / Adrian Altenhoff / Christophe Dessimoz

PeerJ, Vol 6, p e

2019 Volume 6231

Abstract	In polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
Keywords	Homoeology ; Fuzzy logic ; Polyploidy ; Confidence scores ; Comparative genomics ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Read2Tree: scalable and accurate phylogenetic trees from raw reads

Dylus, David / Altenhoff, Adrian M / Majidian, Sina / Sedlazeck, Fritz J / Dessimoz, Christophe

bioRxiv

Abstract: The inference of phylogenetic trees from raw sequencing reads is foundational to biology. However, state of the art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing ...

Abstract	The inference of phylogenetic trees from raw sequencing reads is foundational to biology. However, state of the art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly free approach was 10 to 100x faster than conventional approaches, and in most cases more accurate the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolution. Applied to Coronaviridae samples, Read2Tree accurately classified highly diverse animal samples and near-identical SARSCoV2 sequences on a single tree - thereby exhibiting remarkable breadth and depth. The speed, accuracy, and versatility of Read2Tree enables comparative genomics at scale.
Keywords	covid19
Language	English
Publishing date	2022-04-19
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.04.18.488678
Database	COVID19

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