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hdmax2, an R package to perform high dimension mediation analysis

High-dimensional mediation analysis: Unraveling pathways linking external exposures to health outcomes

Recommended by based on reviews by Pierre Neuvial and Gaspard Kerner

Pittion et al. (2025) introduce an R package called hdmax2, which implements an enhanced version of the “High-Dimensional Mediation Analysis using the Max-Squared” (HDMAX2) method originally proposed by Jumentier et al. (2023) for high-dimensional mediation analysis. The goal of mediation analysis is to quantify the indirect effect of a variable M in the causal relationship between exposure X and outcome Y. The fundamental concept behind HDMAX2 methods is to use a latent factor mixed model to estimate the effects of unobserved confounders and a max-squared test to identify significant mediators. The HDMAX2 method represents a significant advancement in the case of high-dimensional mediation, such as DNA methylation or gene expression analysis, where the number of mediators often far exceeds the sample size.

The main contributions of this article are the implementation of the HDMAX2 method as an R package, and an extension of the original method to binary outcomes and to binary, categorical, and multivariate exposures, as opposed to only continuous variables. The package includes visualization tools, helper functions for mediator selection, and options for handling multivariate exposures. A key strength of the package lies in its versatility. The new package, hdmax2, accommodates a variety of data types. This flexibility makes it a valuable tool for researchers analyzing high-throughput molecular data. Finally to illustrate this flexibility, the authors present two case studies that were not described in the Jumentier et al. (2023) analysis. In the first case study, the authors employed mediation analysis to assess the potential causal role of DNA methylation in the pathway linking the HER2 status of breast cancer (a marker for an aggressive breast cancer subtype) to a survival risk score, which was derived from a six-gene expression signature and is inversely correlated with patient survival. In the second case study, the authors conducted mediation analysis to explore the role of gene expression in the pathway linking patient gender to the occurrence of multiple sclerosis specific subtypes: clinically isolated syndrome and relapsing-remitting multiple sclerosis. These illustrate the relevance of hdmax2 to study the transcriptome and the methylome.

In conclusion, the hdmax2 R package will be invaluable for handling high-dimensional molecular data in the study of the intricate pathways through which exposures influence health outcomes.

                           

References

Jumentier B, Barrot C-C, Estavoyer M, Tost J, Heude B, François O, Lepeule J (2023) High-dimensional mediation analysis: A new method applied to maternal smoking, placental DNA methylation, and birth outcomes. Environmental Health Perspectives, 131, 047011. https://doi.org/10.1289/EHP11559

Pittion F, Jumentier B, Nakamura A, Lepeule J, Francois O, Richard M (2025) hdmax2, an R package to perform high dimension mediation analysis. HAL, ver. 4 peer-reviewed and recommended by PCI Genomics. https://hal.science/hal-04658960 

hdmax2, an R package to perform high dimension mediation analysisFlorence Pittion, Basile Jumentier, Aurélie Nakamura, Johanna Lepeule, Olivier François, Magali Richard<p>Mediation analysis plays a crucial role in epidemiology, unraveling the intricate pathways through which exposures exert influence on health outcomes. Recent advances in high-throughput sequencing techniques have generated growing interest in a...BioinformaticsGuillaume Laval2024-09-10 11:49:02 View
26 Feb 2025
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Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae family

Onagre, monster, invasion and genetics

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

The first time I heard of ”onagres” in French was when I was a teenager, through the books of Pierre Bordage as fantastic monsters, or through historical games as Roman siege weapons (onagers). At this time, I was far from imagining that “onagre” also refers to a very large flowering plant family, as it is the French term for evening primroses.

In this family, the genus Ludwigia comprises species that are invasive (resembling in that way the ancient armies using onagers to invade cities) in aquatic environments, degrading ecosystems already fragilized by human activities. To counteract this phenomenon, it is of high importance to understand their propagation of these species. However, the knowledge about their genetics and diversity is very scarce, and thus tracking their dispersal using genetic information is complicated, and in fact almost impossible.

Barloy-Hubler et al. (2024) proposed in the present manuscript a new set of chloroplastic genomes from two of these species, Ludwigia grandiflora subsp. hexapetala and Ludwigia peploides subsp. montevidensis, and compared them to the published chloroplastic genome of Ludwigia octovalis. They explored the possibility of assembling these genomes relying solely on short reads and showed that long reads were necessary to obtain an almost complete assembly for these plastid genomes. In addition, through this approach, they detected two haplotypes in Ludwigia grandiflora subsp. hexapetala as compared to one in a short-read assembly. This highlights the need for long reads data to assess the structure and diversity of chloroplastic genomes. The authors were also able to clarify the phylogeny of the genus Ludwigia. Finally, they identified multiple potential single nucleotide polymorphisms and simple sequence repeats for future evaluation of diversity and dispersal of those invasive species.

This analysis, while appearing more technical than biological at first glance, is in fact of high importance for the understanding of ecology and preservation of fragile ecosystems, such as the European watersheds. Indeed, new scientific results and insights are generally linked to a reevaluation of previously analyzed data or samples through new technologies, and this paper is a quite clever example of that matter.

                                

References

Barloy-Hubler F, Gac A-LL, Boury C, Guichoux E, Barloy D (2024) Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae family. bioRxiv, ver. 5 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2023.10.20.563230

Bordage, P (1993) Les Guerriers du Silence, L'Atalante, ISBN 9782905158697

 

Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae familyF Barloy-Hubler, A-L Le Gac, C Boury, E Guichoux, D Barloy<p>The Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera. This family includes the genus <em>Ludwigia </em>L., which is comprised of 82 species. In this study, we focused on the two aquatic...Bioinformatics, PlantsFrancois Sabot2023-12-12 18:05:20 View
22 Jan 2025
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Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite

Genomic and transcriptomic insights into the genetic basis of anthelmintic resistance in a cyathostomin parasitic nematode

Recommended by based on reviews by 2 anonymous reviewers

Parasitic worms infect billions of animals worldwide. While parasitism is now considered a context-dependent relation along a symbiosis continuum, most of these parasitic worms, also known as helminths, can cause diseases that have a significant impact (Hopkins et al. 2017; Selzer, Epe 2021). When considering livestock animals, these impacts have a high economic cost, and therefore, prophylactic drugs are widely used (Selzer and Epe 2021). Consequently, drug resistance has become increasingly common across all parasites and concerns about drug effects on non-target organisms have been raised (de Souza and Guimarães 2022). This is why understanding the relationship between parasitic worms and their animal hosts and the diseases they cause at the genetic and molecular level is high on the agenda of parasitologists (Doyle 2022). The development of genomics resources plays a pivotal role in this agenda and is at the origin of Sallé and colleagues' article (2025).

The most common intestinal parasites in equids are helminths of the cyathostomin nematode complex. These are the primary parasitic cause of death in young horses and also exhibit a reduced sensitivity to anthelmintic drugs. Therefore, Sallé and colleagues embarked on the arduous journey to build a reference annotated genome of the Cylicocylus nassatus nematode. They used cutting-edge molecular genetics methods to amplify and sequence the genome of a single individual and obtained chromosomal-level contiguity using Hi-C technology for six chromosomes and an assembly of 514.7 Mbp. Remarkably, transposable elements occupy more than half of the C. nassatus genome and may have led to an increase in genome size in this nematode. In parallel, the authors built a gene catalogue using transcriptomic data, reaching a BUSCO gene completion score of 94.1% with 22,718 protein-coding genes. They quantified allele frequencies based on the resequencing of nine populations, including an ancient Egyptian worm from the 19th century, indicating a recent loss of genetic diversity in European cyathostomin even if geographical sampling  was limited. They also analysed transcriptomic differences between sexes and found differences linked with drug treatment. While there may be confounding effects due to global differences between sex that could explain this finding, these results will likely fuel future transcriptomic analyses investigating the response to antiparasitic drugs.

The Cylicocylus nassatus genome assembly obtained will be invaluable for studying nematode genome evolution and analysing the genetic and molecular basis of drug resistance in these parasites. 

             

References

Doyle SR (2022) Improving helminth genome resources in the post-genomic era. Trends in Parasitology, 38, 831–840. https://doi.org/10.1016/j.pt.2022.06.002

Hopkins SR, Wojdak JM, Belden LK (2017) Defensive symbionts mediate host–parasite interactions at multiple scales. Trends in Parasitology, 33, 53–64. https://doi.org/10.1016/j.pt.2016.10.003

Sallé G, Courtot É, Cabau C, Parrinello H, Serreau D, Reigner F, Gesbert A, Jacquinot L, Lenhof O, Aimé A, Picandet V, Kuzmina T, Holovachov O, Bellaw J, Nielsen MK, Samson-Himmelstjerna G von, Valière S, Gislard M, Lluch J, Kuchly C, Klopp C (2024) Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite. bioRxiv, ver. 2 peer-reviewed and recommended by PCI Genomics https://doi.org/10.1101/2023.07.19.549683

Selzer PM, Epe C (2021) Antiparasitics in animal health: quo vadis? Trends in Parasitology, 37, 77–89. https://doi.org/10.1016/j.pt.2020.09.004

de Souza RB, Guimarães JR (2022) Effects of avermectins on the environment based on its toxicity to plants and soil invertebrates–a review. Water, Air, and Soil Pollution, 233, 259. https://doi.org/10.1007/s11270-022-05744-0

 

Spatio-temporal diversity and genetic architecture of pyrantel resistance in *Cylicocyclus nassatus*, the most abundant horse parasiteGuillaume Sallé, Élise Courtot, Cédric Cabau, Hugues Parrinello, Delphine Serreau, Fabrice Reigner, Amandine Gesbert, Lauriane Jacquinot, Océane Lenhof, Annabelle Aimé, Valérie Picandet, Tetiana Kuzmina, Oleksandr Holovachov, Jennifer Bellaw, Mart...<p>Cyathostomins are a complex of 50 intestinal parasite species infecting horses and wild equids. The massive administration of modern anthelmintic drugs has increased their relative abundance in horse helminth communities and selected drug-resis...Terrestrial invertebratesNicolas Pollet Jane Hodgkinson, Anonymous2023-07-27 20:45:09 View
14 Jan 2025
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Chromosome-level reference genome assembly for the mountain hare (Lepus timidus)

The genomic foundations of adaptation: evaluating the mountain hare

Recommended by ORCID_LOGO based on reviews by Theodore Squires and 1 anonymous reviewer

Fekete et al. (2024) generated a chromosome-level reference genome assembly for the mountain hare (Lepus timidus). This represents a significant advancement in genomic research for non-model organisms, achieving high quality through advanced sequencing and curation techniques. This achievement serves as a foundational blueprint for future efforts in other species, particularly those with ecological or evolutionary importance. The assembly has high continuity and completeness, with an N50 scaffold length of 125.8 Mb and a contig N50 of 4.9 Mb, meeting the Earth BioGenome Project's stringent criteria for reference-grade genomes (Mc Cartney et al., 2024). The combination of PacBio HiFi sequencing and Hi-C scaffolding techniques enabled robust assembly and chromosomal scaffolding of all 23 autosomes and the X and Y sex chromosomes. Additionally, manual curation enhanced the assembly quality, accurately representing genomic sequences. Although the genome provides valuable structural insights, the limited functional annotations highlight a need for further investigation into the genetic underpinnings of the ecological and adaptive traits of the mountain hare.

The ecological and evolutionary implications of resolving this genome are considerable, particularly given the mountain hare’s adaptations to cold, snowy environments and its role in boreal ecosystems. The assembly facilitates the study of adaptations, such as camouflage and snowshoe-like feet, which are critical for survival in its rapidly changing habitat. Comparative genomic analyses reveal the evolutionary relationship between Lepus timidus and closely related species, such as the brown hare (L. europaeus) and Irish hare (L. t. hibernicus), providing insights into gene flow, hybridization, and speciation. These findings have practical implications for conservation genetics, particularly for subspecies threatened by habitat loss and climate change. However, the study does not identify specific adaptive loci or functional variants, limiting its immediate applicability to understanding the molecular basis of traits crucial for survival in extreme environments. Expanding the functional annotation of this genome would significantly enhance its utility in conservation and ecological genomics. Moreover, the high repetitive element content (42.35%) underscores the need for detailed annotation to facilitate downstream studies. These issues suggest that additional refinement and validation are warranted. Despite these limitations, the assembly is invaluable for studying genetic adaptations, hybridization, and hare conservation. Future research should focus on functional annotation, population-level comparisons, and targeted studies of ecological traits to fully realize the potential of this high-quality reference genome.

             

References

Fekete Z, Absolon DE, Michell C, Wood JMD, Goffart S, Pohjoismäki JLO (2024) Chromosome-level reference genome assembly for the mountain hare (Lepus timidus). bioRxiv, ver. 2 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2024.06.10.598177

Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitão HG, Diedericks G, Kirangwa J, Morselli M, Salces-Ortiz J, Escudero N, Iannucci A, Natali C, Svardal H, Fernández R, De Pooter T, Joris G, Strazisar M, Wood JMD, Herron KE, …, Mazzoni CJ (2024) The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj Biodiversity, 3, 28. https://doi.org/10.1038/s44185-024-00054-6

 

Chromosome-level reference genome assembly for the mountain hare (*Lepus timidus*)Zsofia Fekete, Dominic E. Absolon, Craig Michell, Jonathan M. D. Wood, Steffi Goffart, Jaakko L. O. Pohjoismaki<p>&nbsp;We present here a high-quality genome assembly of a male mountain hare (<em>Lepus timidus</em> Linnaeus), from Ilomantsi, Eastern Finland, utilizing an isolated fibroblast cell line as the source for high quality DNA and RNA. Following th...Bioinformatics, ERGA Pilot, Evolutionary genomics, VertebratesJitendra Narayan2024-06-11 08:52:32 View
28 Nov 2024
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Factors influencing the accuracy and precision in dating single gene trees

Dating single gene trees in the age of phylogenomics

Recommended by based on reviews by Sishuo Wang, David Duchêne and 1 anonymous reviewer

Dating evolutionary trees is a critical task that allows us to connect biological history to ecological and geological events, helping us explore connections between environmental change and genetic innovations. The central idea behind these techniques is to link changes at the sequence level to divergence times, under the general assumption that substitutions accumulate steadily over time. So, sequences that diverged earlier are expected to be more different than sequences that diverged more recently. For a number of biological and statistical reasons, the relationship between sequence divergence and time is not linear, so it is not always the case that more divergent sequences have accumulated more substitutions than less divergent ones. In the case of organismal-level divergences, a natural approach to mitigate these challenges is to incorporate as many genes as possible into the analyses. However, this route is not available when we are focusing our interest on a single gene or a gene family. Thus, exploring how different features of single gene trees impact the accuracy and precision of divergence time estimates is of interest. In this study, Louvel and Roest Crollius (2024), select a well-studied group of mammals, primates, extract single copy genes from their genomes, and explore how different factors such as alignment size, evolutionary rate variation and discordance between the gene and species trees impact divergence time estimates. 

There are many strengths of this study. The central ones are the number of factors considered and the transparent discussion of the limitations. In this regard, the study is an elegant combination of empirical and simulated data. Some of the results match intuitive expectations. For example, the authors find that longer alignments are more informative than shorter ones, that differences in evolutionary rate among branches lead to loss in precision, and that slow-evolving genes perform worse. Intriguingly, they also find differences in performance among genes with different ontologies. The empirical data used in this study is limited to a single group, and generally considers genes that have apparently remained as single copies. Accordingly, the conclusions that can be drawn are somewhat limited, calling for future studies building on and expanding the concepts of the study by Louvel and colleagues. For example, including genes that have been lost or duplicated would be of interest because changes in gene complement are a prevalent source of variation at the genome level in mammals in general (Demuth et al. 2006), and particularly in primates (Hahn et al. 2007).

                        

References

Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW (2006) The evolution of mammalian gene families. PLoS One, e85. https://doi.org/10.1371/journal.pone.0000085

Hahn MW, Demuth JP, Han SG (2007) Accelerated rate of gene gain and loss in primates. Genetics, 177,1941-1949. https://doi.org/10.1534/genetics.107.080077

Louvel, G and Roest Crollius, H (2024) Factors influencing the accuracy and precision in dating single gene trees. bioRxiv, ver. 6 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2020.08.24.264671

 

Factors influencing the accuracy and precision in dating single gene treesGuillaume Louvel and Hugues Roest Crollius<p>Molecular dating is the inference of divergence time from genetic sequences. Knowing the time of appearance of a taxon sets the evolutionary context by connecting it with past ecosystems and species. Knowing the divergence times of gene lineage...Bioinformatics, Evolutionary genomics, VertebratesFederico Hoffmann2023-08-15 12:06:09 View
13 Nov 2024
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Re-annotation of SARS-CoV-2 proteins using an HHpred-based approach opens new opportunities for a better understanding of this virus

Leveraging HHpred with rigorous validation for improved detection of host-virus homologies

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

The assessment by Brézellec (2024) of the quality of HHpred-based SARS-CoV-2 protein annotations against the traditional Pfam annotations is highly justified and valuable. HHpred’s ability to detect remote homologies offers an expanded view of viral protein similarities, potentially uncovering subtle functional mimicries that Pfam may miss due to its sensitivity limitations when dealing with divergent sequences. However, the accuracy and specificity of HHpred results can be compromised by false positives, especially when dealing with complex viral proteins that feature transmembrane or low-complexity regions prone to spurious matches.

To address this, the author made a thoughtful decision to implement a multi-step validation protocol. This approach included establishing progressively lower probability thresholds to capture weaker but biologically plausible hits, and organizing hits into “families” of similarly located alignments to validate the robustness of matches. They also cross-verified results by running SARS-CoV-2 protein queries against non-human proteomes (plants, fruit flies, bacteria, and archaea), allowing them to discern between biologically meaningful matches and potentially random alignments. By adding manual verification with InterPro domain annotations, the authors took additional steps to ensure that identified similarities were not only statistically significant but also biologically relevant.

This rigorous validation strategy adds a layer of reliability to HHpred results, demonstrating an effective maximization of sensitivity while maintaining specificity. This approach yielded biologically intriguing and previously undocumented similarities, such as between the Spike-prominin and ORF3a-GPCR, underscoring the quality and depth of the annotation process. These findings highlight a pathway for further experimental validation and illustrate the potential of HHpred to contribute high-quality insights when applied with careful quality control measures.

In summary, the decision to adopt HHpred (Gabler et al. 2020) and enhance its outputs with a robust quality validation process not only improved the depth of SARS-CoV-2 protein annotations but also established a high standard for future viral annotation projects, striking an effective balance between discovery potential and annotation quality​. The authors have conducted a study that is methodologically rigorous, well-detailed, and highly pertinent to the field. This work stands as a significant contribution to the scientific community, providing resources and insights that are likely to guide future research in this area. 

              
References

Brézellec, P (2024) Re-annotation of SARS-CoV-2 proteins using an HHpred-based approach opens new opportunities for a better understanding of this virus. bioRxiv, ver. 3 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2023.06.06.543855

Gabler F, Nam S-Z, Till S, Mirdita M, Steinegger M, Söding J, Lupas AN, Alva V (2020) Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. Current Protocols in Bioinformatics, 72, e108. https://doi.org/10.1002/cpbi.108

 

Re-annotation of SARS-CoV-2 proteins using an HHpred-based approach opens new opportunities for a better understanding of this virusPierre Brézellec<p>Since the publication of the genome of SARS-CoV-2 – the causative agent of COVID-19 – in January 2020, many bioinformatic tools have been applied to annotate its proteins. Although efficient methods have been used, such as the identification of...Bioinformatics, Evolutionary genomics, Viruses and transposable elementsJitendra Narayan2023-06-08 10:17:04 View
23 Oct 2024
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mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms

One tool to metabarcode them all

Recommended by based on reviews by Ali Hakimzadeh and Sourakhata Tirera

One way to identify all organisms at their various life stages is by their genetic signature. DNA-based taxonomy, gene tagging and barcoding are different shortcuts used to name such strategies (Lamb et al. 2019; Tautz et al. 2003). Reading and analyzing nucleic acid sequences to perform genetic inventories is now faster than ever, and the latest nucleic acid sequencing technologies reveal an impressive taxonomic, genetic, and functional diversity hidden in all ecosystems (Lamb et al. 2019; Sunagawa et al. 2015). This knowledge should enable us to evaluate biodiversity across its scales, from genetic to species to ecosystem and is sometimes referred to with the neologism of ecogenomics (Dicke et al. 2004).

The metabarcoding approach is a key workhorse of ecogenomics. At the core of metabarcoding strategies lies the sequencing of amplicons obtained from so-called multi-template PCR, a formidable and potent experiment with the potential to unravel hidden biosphere components from different samples obtained from organisms or the environment (Kalle et al. 2014; Rodríguez-Ezpeleta et al. 2021). Next to this core approach, and equally important, lies the bioinformatic analysis to convert the raw sequencing data into amplicon sequence variants or operational taxonomic units and interpretable abundance tables.

Methodologically, the analysis of sequences obtained from metabarcoding projects is replete with devilish details. This is why different pipelines and tools have been developed, starting with mothur (Schloss et al. 2009) and QIIME 2 (Bolyen et al. 2019), but including more user friendly tools such as FROGS (Escudié et al. 2018). Yet, across all available tools, scientists must choose the optimal algorithms and parameter values to filter raw reads, trim primers, identify chimeras and cluster reads into operational taxonomic units. In addition, the number of genetic markers used to characterize a sample using metabarcoding has increased as  sequencing methods are now less costly and more efficient. In such cases, results and interpretations may become limited or confounded. This is where the novel tools proposed by Barnabé and colleagues (2024), mbctools, will benefit researchers in this field.

The authors provide a detailed description with a walk-through of the mbctools pipeline to analyse raw reads obtained in a metabarcoding project. The mbctools pipeline can be installed under different computing environments, requires only VSEARCH and a few Python dependencies, and is easy to use with a menu-driven interface. Users need to prepare their data following simple rules, providing single or paired-end reads, primer and target database sequences. An interesting feature of mbctools output is the possibility of integration with the metaXplor visualization tool developed by the authors (Sempéré et al. 2021). As it stands, mbctools should be used for short-read sequences. The taxonomy assignment module has the advantage to enable parameters exploration in an easy way, but it may be oversimplistic for specific taxa.

The lightweight aspect of mbctools and its overall simplicity are appealing. These features will make it a useful pipeline for training workshops and to help disseminate the use of metabarcoding. It also holds the potential for further improvement, by the developers or by others. In the end, mbctools will support study reproducibility by enabling a streamlined analysis of raw reads, and like many useful tools, only time will tell whether it is widely adopted.

         
References

Barnabé C, Sempéré G, Manzanilla V, Millan JM, Amblard-Rambert A, Waleckx E (2024) mbctools: A user-friendly metabarcoding and cross-platform pipeline for analyzing multiple amplicon sequencing data across a large diversity of organisms. bioRxiv, ver. 2 peer-reviewed and recommended by PCI Genomics https://doi.org/10.1101/2024.02.08.579441

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, et al. (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857. https://doi.org/10.1038/s41587-019-0209-9

Dicke M, van Loon JJA, de Jong PW (2004) Ecogenomics benefits community ecology. Science, 305, 618–619. https://doi.org/10.1126/science.1101788

Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pascal G (2018) FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics, 34, 1287-1294. https://doi.org/10.1093/bioinformatics/btx791

Kalle E, Kubista M, Rensing C (2014) Multi-template polymerase chain reaction. Biomolecular Detection and Quantification, 2, 11–29. https://doi.org/10.1016/j.bdq.2014.11.002

Lamb CT, Ford AT, Proctor MF, Royle JA, Mowat G, Boutin S (2019) Genetic tagging in the Anthropocene: scaling ecology from alleles to ecosystems. Ecological Applications, 29, e01876. https://doi.org/10.1002/eap.1876

Rodríguez-Ezpeleta N, Zinger L, Kinziger A, Bik HM, Bonin A, Coissac E, Emerson BC, Lopes CM, Pelletier TA, Taberlet P, Narum S (2021) Biodiversity monitoring using environmental DNA. Molecular Ecology Resources, 21, 1405–1409. https://doi.org/10.1111/1755-0998.13399

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75, 7537-41. https://doi.org/10.1128/AEM.01541-09

Sempéré G, Pétel A, Abbé M, Lefeuvre P, Roumagnac P, Mahé F, Baurens G, Filloux D 2021 metaXplor: an interactive viral and microbial metagenomic data manager. Gigascience, 10, https://doi.org/10.1093/gigascience/giab001

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d’Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P (2015) Structure and function of the global ocean microbiome. Science, 348, 1261359. https://doi.org/10.1126/science.1261359

Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2003) A plea for DNA taxonomy. Trends in Ecology & Evolution, 18, 70–74. https://doi.org/10.1016/S0169-5347(02)00041-1

 

mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of OrganismsChristian Barnabé, Guilhem Sempéré, Vincent Manzanilla, Joel Moo Millan, Antoine Amblard-Rambert, Etienne Waleckx<p>We developed a python package called mbctools, designed to offer a cross-platform tool for processing amplicon data from various organisms in the context of metabarcoding studies. It can handle the most common tasks in metabarcoding pipelines s...Bioinformatics, MetagenomicsNicolas Pollet2024-02-27 11:22:41 View
22 Oct 2024
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Chromosome level genome reference of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invading the River Rhine

New chromosome-scale genome assembly for the Dwarf Goby, a River Rhine invader

Recommended by ORCID_LOGO based on reviews by Tereza Manousaki, Ruiqi Li and 1 anonymous reviewer

Since the opening of the Rhine-Main-Danube-Channel, four goby species are known to have invaded the River Rhine. Of these, the most recent and numerous is the Caucasian Dwarf Goby, which has been found in the Rhine since 2019. This study presents a new high-quality genome for this species (Knipowitschia cf. caucasica) (Schoenle et al. 2024). Currently, chromosome-scale genome assemblies represent a key first step in invasion biology, allowing the reconstruction of a species’ invasion history and monitoring its progress, as well as identifying and characterizing candidate genes that control invasiveness (McCartney et al. 2019). 

The authors sequenced the nuclear and mitochondrial genomes of this species using state-of-the art methods including long-read sequencing techniques, scaffolded based on chromatin conformation data, and annotated using both direct transcriptomic and protein homology evidence. Data analyses follow currently established pipelines for genome assembly, scaffolding, annotation, and downstream bioinformatic analyses. The quality of the final genome was thoroughly assessed and conforms to what is expected from other genomes of fishes in the family Gobiidae. This study follows other recent endeavors that generated high-quality genomes to improve our understanding of invasion biology (e.g. Shao et al. 2020 and Kitsoulis et al. 2023). These studies are successfully contributing to increasing the genomic resources for the world’s most damaging invasive species, which were not available for even a third of the top 100 invasive species just five years ago (McCarthy et al. 2019). Beyond invasion biology, the Dwarf Goby genome is also an important resource for many other applications, including evolutionary genomic analyses and phylogeography of this species and closely related ones in their native ranges.

                
References          

Kitsoulis CV, Papadogiannis V, Kristoffersen JB, Kaitetzidou E, Sterioti A, Tsigenopoulos CS, Manousaki T (2023) Near-chromosome level genome assembly of devil firefish, Pterois miles. Peer Community Journal 3:e64. https://doi.org/10.24072/pcjournal.295  

McCartney MA, Mallez S, Gohl DM (2019) Genome projects in invasion biology. Conservation Genetics 20:1201–1222. https://doi.org/10.1007/s10592-019-01224-x

Schoenle A, Guiglielmoni N, Mainz T, Greve C, Hamadou AB, Heermann L, Borcherding J, Waldvogel A-M (2024) Chromosome level genome reference of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invading the River Rhine. bioRxiv, ver. 3 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2024.04.22.590508

Shao F, Ludwig A, Mao Y, Liu N, Peng Z (2020). Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis). GigaScience 9:giaa092. https://doi.org/10.1093/gigascience/giaa092

 

Chromosome level genome reference of the Caucasian dwarf goby *Knipowitschia* cf. *caucasica*, a new alien Gobiidae invading the River RhineAlexandra Schoenle, Nadège Guiglielmoni, Tobias Mainz, Carola Greve, Alexander B. Hamadou, Lisa Heermann, Jost Borcherding, Ann-Marie Waldvogel<p>The Caucasian dwarf goby <em>Knipowitschia</em> cf. <em>caucasica</em> is a new invasive alien Gobiidae spreading in the Lower Rhine since 2019. Little is known about the invasion biology of the species and further investigations to reconstruct...ERGA, VertebratesIker Irisarri2024-04-29 17:52:25 View
19 Sep 2024
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Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds

Professionalising conservation programmes for local chicken breeds

Recommended by ORCID_LOGO based on reviews by Markus Neuditschko and Claudia Fontsere Alemany

While it is widely agreed that the conservation of local breeds is key to the maintenance of livestock biodiversity, the implementation of such programmes is often carried out by amateur breeders and may be inadequate due to a lack of knowledge and financial resources. Bortoluzzi et al. (2024) clearly demonstrate the utility of whole-genome sequencing (WGS) data for this purpose, compare two scenarios that differ in the consistency of conservation efforts, and provide valuable recommendations for conservation programmes.

Genetic diversity in livestock is generally considered to be crucial to maintaining food security and ensuring the provision of necessary nutrients to humans (Godde et al. 2021). It is also important to recognise that the preservation of local breeds is a matter of cultural identity for certain regions, and that the products of these breeds are niche products which are in high demand. Especially today, as we face extreme weather conditions, drought and other consequences of global warming, modern breeds selected to perform under constant and temperate conditions are being challenged. The possibility of tapping into the reservoir of genetic variation held by traditional, locally adapted breeds offers an important option for breeding robust livestock. The best way to characterise genetic diversity is through modern molecular methods, based on whole genome sequencing and subsequent advanced population analyses, which has been demonstrated for domesticated and wild chicken (Qanbari et al. 2019).

But are local breed conservation programmes up to the task? In their article, Bortoluzzi and colleagues show that well-designed and professionally managed conservation programmes for local chicken breeds are effective in maintaining genetic diversity. Their article is based on a comparison of two examples of conservation programmes for local chicken breeds: the Barbezieux and the Gasconne, which originated from comparably sized founder populations and for which WGS data were available in a biobank at two timepoints, 2003 and 2013, representing 10 generations. While the conservation programme for the former was continuous, that for the latter was interrupted and later started from scratch with a small number of sires and dams.

The greater loss of genomic diversity in the Gasconne than in the Barbezieux shown in this article may therefore be unsurprising, but the authors provide a range of evidence for this using their population genomics toolbox. The less well-managed breed, Gasconne, shows a lower genome-wide heterozygosity, higher lengths of runs of homozygosity, higher levels of genomic inbreeding, a smaller effective population size and a higher genetic load in terms of predicted deleterious mutations. 

The sample sizes available for population genetic analyses are typically small for local breeds, which is difficult to change as the populations are very small at any given time. It is therefore all the more important to make the most out of it, and Bortoluzzi and co-authors approach the issue from several angles that help support their claim, using WGS data and the latest genomic resources.

In addition to their analyses, the authors provide clear and valuable advice for the management of such conservation programmes. Their analysis of signatures of selection suggests that, apart from adult fertility, not much selection has been taking place. However, the authors emphasise that clear selection objectives other than maintaining the breed, such as production and product quality, can help conservation efforts by providing better guidelines for managing the programme and increasing the availability of resources for conservation programmes when the products of these local breeds become successful. 

In summary, Bortoluzzi et al. (2024) have provided a clear, well-written account of the impact of conservation programme management on the genetic diversity of local chicken breeds, using the most up-to-date genomic resources and analysis methods. As such, this article makes a significant and valuable contribution to the maintenance of genomic resources in livestock, providing approaches and lessons that will hopefully be adopted by other such initiatives.

            
References

Bortoluzzi C, Restoux G, Rouger R, Desnoues B, Petitjean F, Bosse M, Tixier-Boichard M (2024) Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds. bioRxiv, ver. 2 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2024.02.22.581528

Godde CM, Mason-D’Croz D, Mayberry DE, Thornton PK, Herrero M (2021) Impacts of climate change on the livestock food supply chain; a review of the evidence. Global Food Security 28:100488. https://doi.org/10.1016/j.gfs.2020.100488

Qanbari S, Rubin C-J, Maqbool K, Weigend S, Weigend A, Geibel J, Kerje S, Wurmser C, Peterson AT, IL Brisbin Jr., Preisinger R, Fries R, Simianer H, Andersson L (2019) Genetics of adaptation in modern chicken. PLOS Genetics, 15, e1007989. https://doi.org/10.1371/journal.pgen.1007989

Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breedsChiara Bortoluzzi, Gwendal Restoux, Romuald Rouger, Benoit Desnoues, Florence Petitjean, Mirte Bosse, Michele Tixier-Boichard<p>Livestock biodiversity is declining globally at rates unprecedented in human history. Of all avian species, chickens are among the most affected ones because many local breeds have a small effective population size that makes them more suscepti...Bioinformatics, Evolutionary genomics, Population genomics, VertebratesClaudia Kasper2024-02-26 13:01:08 View
03 Sep 2024
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A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity

Exploring evolutionary adaptations through Phoxinus phoxinus genomics

Recommended by ORCID_LOGO based on reviews by Alice Dennis and 2 anonymous reviewers

Oriowo et al. (2024) offer a thorough and meticulously conducted study that makes a substantial contribution to our understanding of the Eurasian minnow (Phoxinus phoxinus), particularly in terms of its genetic diversity, structural variations, and evolutionary adaptations. The authors have achieved an impressive feat by generating an annotated haplotype-phased, chromosome-level genome assembly (2n = 50). This was accomplished through the integration of high-fidelity long reads with chromosome conformation capture data (Hi-C), resulting in a highly complete and accurate genome assembly. The assembly is characterized by a haploid size of 940 Megabase pairs (Mbp) for haplome one and 929 Mbp for haplome two, with scaffold N50 values of 36.4 Mb and 36.6 Mb, respectively. These metrics, alongside BUSCO scores of 96.9% and 97.2%, highlight the high quality of the genome, making it a robust foundation for further genetic exploration and analyses.

The study’s findings are both novel and significant, providing deep insights into the genetic architecture of P. phoxinus. The authors report heterozygosity rate of 1.43% and a high repeat content of approximately 54%, primarily consisting of DNA transposons. These transposons play a crucial role in genome rearrangements and variations, contributing to the species' adaptability and evolution (Bourque et al. 2018). The research also identifies substantial structural variations within the genome, including insertions, deletions, inversions, and translocations (Oriowo et al. 2024). Beyond these findings, the genome annotation is exceptionally comprehensive, containing 30,980 mRNAs and 23,497 protein-coding genes. The study’s gene family evolution analysis, which compares the P. phoxinus proteome to that of ten other teleost species, reveals immune system gene families that favor histone-based disease prevention mechanisms over NLR-based immune responses. This provides new insight into the evolutionary strategies that have emerged in P. phoxinus, enabling its survival in its environment. Moreover, the demographic analysis conducted in the study reveals historical fluctuations in the effective population size of P. phoxinus, likely correlated with past climatic changes, offering insights into the species' evolutionary history.

This annotated and phased reference genome not only serves as a crucial resource for resolving taxonomic complexities within the genus Phoxinus but also highlights the importance of haplotype-phased assemblies in understanding genetic diversity, particularly in species characterized by high heterozygosity. The authors have delivered a study that is methodologically sound, richly detailed, and highly relevant to the field. The study represents a valuable and impactful contribution to the scientific community, offering resources and knowledge that will likely inform future research in the field.

              

References

Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C (2018) Ten things you should know about transposable elements. Genome Biology, 19, 199. https://doi.org/10.1186/s13059-018-1577-z

Oriowo TO, Chrysostomakis I, Martin S, Kukowka S, Brown T, Winkler S, Myers EW, Böhne A, Stange M (2024) A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity. bioRxiv, ver. 6 peer-reviewed and recommended by PCI Genomics https://doi.org/10.1101/2023.11.30.569369

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: *Phoxinus phoxinus*) provide evidence of haplotype diversityTemitope O. Oriowo, Ioannis Chrysostomakis, Sebastian Martin, Sandra Kukowka, Thomas Brown, Sylke Winkler, Eugene W. Myers, Astrid Boehne, Madlen Stange<p>In this study we present an in-depth analysis of the Eurasian minnow (<em>Phoxinus phoxinus</em>) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chrom...Evolutionary genomics, Structural genomics, VertebratesJitendra Narayan Henrik Lanz, Rui Borges, Fergal Martin, Vinod Scaria, Mihai Pop, Alice Dennis, Jin-Wu Nam, Monya Baker, Giuseppe Narzisi2023-12-04 14:49:17 View