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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
21 Aug 2024
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MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

MATEdb2 is a valuable phylogenomics resource across Metazoa

Recommended by ORCID_LOGO based on reviews by Natasha Glover and 1 anonymous reviewer

Martínez-Redondo and colleagues (2024) present MATEdb2, which provides the scientific community with Metazoa proteomes that have been predicted and annotated in a standardised way. The authors improved the taxon representation from the earlier MATEdb and their current database has a strong focus on Arthropoda, Annelida, and Mollusca. In particular, for the latter two groups not many high-quality reference genomes are available. Standardisation of the prediction and annotation process in a reproducible pipeline, as integrated in MATEdb2, is of great value, in particular to infer phylogenies as correctly as possible. Thus, I am sure that MATEdb2 will be an excellent go-to resource for phylogenomic studies, as well as for probing the biology of new, obscure species, especially marine ones.

                                    
The manuscript was evaluated by two experts in the field of orthology search and orthology databases, and computational biology. The authors diligently implemented the modifications suggested by both referees and I am gladly recommending the manuscript at this point.

                        

                
References
Martínez-Redondo GI, Vargas-Chávez C, Eleftheriadi K, Benítez-Álvarez L, Vázquez-Valls M, Fernández R (2024) MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2024.02.21.581367

MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studiesGemma I. Martínez-Redondo, Carlos Vargas-Chávez, Klara Eleftheriadi, Lisandra Benítez-Álvarez, Marçal Vázquez-Valls, Rosa Fernández<p>Recent advances in high throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, ge...Arthropods, Bioinformatics, Evolutionary genomics, Marine invertebrates, Terrestrial invertebratesPhilipp Schiffer2024-03-04 11:37:21 View
12 Aug 2024
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A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases

DefenseFinder update advances prokaryotic antiviral system research

Recommended by ORCID_LOGO based on reviews by Pierre Pontarotti , Pedro Leão and 1 anonymous reviewer

Prokaryotic antiviral systems, such as CRISPR-Cas and restriction-modification systems, provide defense against viruses through diverse mechanisms including intracellular signaling, chemical defense, and nucleotide depletion. However, bioinformatic tools and resources for identifying and cataloging these systems are still in development. The work by Tesson and colleagues (2024) presents a significant advancement in understanding the defense systems of prokaryotes. The authors have provided an update of their previously developed online service DefenseFinder, which helps to detect known antiviral systems in prokaryotes genomes (Tesson et al. 2022), plus three new databases: one serving as a wiki for defense systems, one housing experimentally determined and AlphaFold2-predicted structures, and a third one consisting of precomputed results from DefenseFinder. Users can analyze their own data through the user-friendly interface. This initiative will help promote a community-driven approach to sharing knowledge on antiphage systems, which is very useful given their complexity and diversity. The authors' commitment to maintaining an up-to-date platform and encouraging community contributions makes this resource accessible to both newcomers and experienced researchers in the rapidly growing field of defense system research. Experienced researchers will find that there are ways to contribute to the future expansion of these databases, while new users can easily access and use the platform. Overall, the updated DefenseFinder, as well as the other databases introduced in the manuscript, are well-suited  for researchers (both dry- and wet-lab ones) interested in antiphage defense. I am hopeful that the efforts by the authors will collectively create valuable online resources for researchers in this field and will foster an environment of open science and accessible bioinformatics tools.

       

References

Tesson F, Hervé A, Mordret E, Touchon M, d’Humières C, Cury J, Bernheim A (2022) Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nature Communications, 13, 2561. https://doi.org/10.1038/s41467-022-30269-9

Tesson F, Planel R, Egorov A, Georjon H, Vaysset H, Brancotte B, Néron B, Mordret E, Atkinson G, Bernheim A, Cury J (2024) A comprehensive resource for exploring antiphage defense: DefenseFinder webservice, wiki and databases. bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2024.01.25.577194

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and DatabasesF. Tesson, R. Planel, A. Egorov, H. Georjon, H. Vaysset, B. Brancotte, B. Néron, E. Mordret, A Bernheim, G. Atkinson, J. Cury<p>In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To<br>facilitate the exploration of mechanistic, ecological, and evolutionary aspects related to antiphage defense systems, we released DefenseFinder in 2021 (...Bacteria and archaea, Bioinformatics, Evolutionary genomics, Viruses and transposable elementsSishuo Wang2024-04-17 18:30:32 View
06 Aug 2024
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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Unveiling transposon dynamics: Advancing TE expression analysis in Drosophila with long-read sequencing

Recommended by based on reviews by Silke Jensen, Christophe Antoniewski and 1 anonymous reviewer

Transposable elements (TEs) are mobile genetic elements with an intrinsic mutagenic potential that influences the physiology of any cell type, whether somatic or germinal. Measuring TE expression is a fundamental prerequisite for analysing the processes leading to the activity of TE-derived sequences. This applies to both old and recent TEs, as even if they are deficient in mobilisation, transcription of TE sequences alone can impact neighbouring gene expression and other cellular activities.

In terms of TE physiology, transcription is crucial for mobilisation activity. The transcription of some TEs can be tissue-specific and associated with splicing events, as exemplified by the P-element isoforms in the fruit fly (Laski et al. 1986). Regarding host cell physiology, TE transcripts can include nearby exons, with or without splicing, and such chimeric transcripts can significantly alter gene activity. Thus, quantitative and qualitative analyses must be conducted to assess TE function and how they can modify genomic activities. Yet, due to the polymorphic, interspersed, and repetitive nature of TE sequences, the quantitative and qualitative analysis of TE transcript levels using short-read sequencing remains challenging (Lanciano and Cristofari 2020).

In this context, Rebollo et al. (2024) employed nanopore long-read sequencing to analyse cDNAs derived from Drosophila melanogaster germline RNAs. The authors constructed two long-read cDNA libraries from pooled ovaries and testes using a protocol to obtain full-length cDNAs and sequenced them separately. They carefully compared their results with their short-read datasets. Overall, their observations corroborate known patterns of germline-specific expression of certain TEs and provide initial evidence of novel spliced TE transcript isoforms in Drosophila.

Rebollo and colleagues have provided a well-documented and detailed analysis of their results, which will undoubtedly benefit the scientific community. They presented the challenges and limitations of their approach, such as the length of the transcripts, and provided a reproducible analysis workflow that will enable better characterisation of TE expression using long-read technology.

Despite the small number of samples and limited sequencing depth, this pioneering study strikingly demonstrates the potential of long-read sequencing for the quantitative and qualitative analysis of TE transcription, a technology that will facilitate a better understanding of the transposon landscape.

              
References

Lanciano S, Cristofari G (2020) Measuring and interpreting transposable element expression. Nature Reviews Genetics, 21, 721–736. https://doi.org/10.1038/s41576-020-0251-y

Laski FA, Rio DC, Rubin GM (1986) Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing. Cell, 44, 7–19. https://doi.org/10.1016/0092-8674(86)90480-0

Rebollo R, Gerenton P, Cumunel E, Mary A, Sabot F, Burlet N, Gillet B, Hughes S, Oliveira DS, Goubert C, Fablet M, Vieira C, Lacroix V (2024) Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues. bioRxiv, ver.4 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2023.05.27.542554

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissuesRita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet, Benjamin Gillet, Sandrine Hughes, Daniel Siqueira Oliveira, Clément Goubert, Marie Fablet, Cristina Vieira, Vincent Lacroix<p>Transposable elements (TEs) are repeated DNA sequences potentially able to move throughout the genome. In addition to their inherent mutagenic effects, TEs can disrupt nearby genes by donating their intrinsic regulatory sequences, for instance,...Arthropods, Bioinformatics, Viruses and transposable elementsNicolas Pollet2023-06-13 14:46:20 View
05 Aug 2024
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LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins

A protein database to study the origin of metazoans

Recommended by ORCID_LOGO based on reviews by Giacomo Mutti and 2 anonymous reviewers

Sobala (2024) introduces a new, comprehensive, and curated eukaryotic database. It consolidates information from EukProt (Richter et al. 2022) and various other resources to enhance Metazoa representation in existing protein databases. The preprint is of significant interest to the phylogenomics and comparative genomics communities, and I commend the author for their work.

LukProt, the expanded database, significantly increases the taxon sampling within holozoans. It integrates data from the previously assembled EukProt and AniProtDB (Barreira et al. 2021) databases, with additional datasets from early-diverging animal lineages such as ctenophores, sponges, and cnidarians. This effort will undoubtedly be useful for researchers investigating these clades and their origins, as well as for the broader field of comparative genomics.

The author provides both web-portal and command-line versions of the database, making it accessible to users with varying degrees of bioinformatic proficiency. The curation effort is commendable, and I believe the comparative genomics community, especially those interested in animal origins, will find LukProt to be a valuable resource.

           

References

Barreira SN, Nguyen A-D, Fredriksen MT, Wolfsberg TG, Moreland RT, Baxevanis AD (2021) AniProtDB: A collection of consistently generated metazoan proteomes for comparative genomics studies. Molecular Biology and Evolution 38, 4628–4633. https://doi.org/10.1093/molbev/msab165

Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C (2022) EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community Journal 2, e56. https://doi.org/10.24072/pcjournal.173

Sobala ŁF (2024) LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2024.01.30.577650

LukProt: A database of eukaryotic predicted proteins designed for investigations of animal originsŁukasz F. Sobala<p>The origins and early evolution of animals is a subject with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database of sequences from non-bilaterians. Publicly available dat...Bioinformatics, Evolutionary genomics, Marine invertebratesJavier del CampoAnonymous, Giacomo Mutti , Anonymous2024-02-02 13:04:31 View