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11 May 2024
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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Informed Choices, Cohesive Future: Decisions and Recommendations for ERGA

Recommended by ORCID_LOGO based on reviews by Justin Ideozu and Eric Crandall

The European Reference Genome Atlas (ERGA) (Mc Cartney et al, 2024, Mazzoni et al, 2023) demonstrates the collaborative spirit and intellectual abilities of researchers from 33 European countries. This ambitious project, which is part of the Earth BioGenome Project (Lewin et al., 2018) Phase II, has embarked on an unprecedented mission: to decipher the genetic makeup of 150,000 species over a span of four years. At the heart of ERGA is a decentralized pilot infrastructure specifically built to assist the production of high-quality reference genomes. This structure acts as a scaffold for the massive task of genome sequencing, giving the necessary framework to manage the complexity of genomic research. The research paper under consideration offers a comprehensive narrative of ERGA's evolution, outlining both successes and challenges encountered along the road. 

One of the most significant issues addressed in the manuscript is the equitable distribution of resources and expertise among participating laboratories and countries. In a project of this magnitude, it is critical to leverage the pooled talents and capacities of researchers from across Europe. ERGA's pan-European network promotes communications and collaboration, creating an environment in which knowledge flows freely and barriers are overcome. This adoption of strong coordination and communication tactics will be essential to ERGA's success. Scientific collaboration depends on efficient communication channels because they allow researchers to share resources, collaborate on new initiatives, and exchange ideas. Through a diverse range of gatherings, courses, and virtual discussion boards, ERGA fosters an environment of transparency and cooperation among members, enabling scientists to overcome challenges and make significant discoveries. The importance ERGA places on training and information transfer programmes is a pillar of its strategy. Understanding the importance of capacity development, ERGA invests in providing researchers with the knowledge and abilities necessary for effectively navigating the complicated terrain of genomic research. A wide range of subjects are covered in training programmes (Larivière et al. 2023), from sample preparation and collection to data processing methods and sequencing technology. Through the development of a group of highly qualified experts, ERGA creates the foundation for continued advancement and creativity in the genomics sector.

This manuscript also covers in detail the technological workflows and sequencing techniques used in ERGA's pilot infrastructure. With the aid of cutting-edge sequencing technologies based on both long-read and short-read sequencing, they are working to unravel the complex structure of the genetic code with a level of accuracy and precision never before possible. To guarantee the accuracy of genetic data and prevent mistakes and flaws that can jeopardize the findings' integrity, quality control methods are put in place. Despite having a focus on genome sequencing due to its technological complexities, ERGA also remains firm in its dedication to metadata collection and sample validation. Metadata serves as a critical link between raw genetic data and useful scientific insights, giving necessary context and allowing researchers to draw practical findings from their investigations. Sample validation approaches improve the reliability and reproducibility of the results, providing users confidence in the quality of the genetic data provided by ERGA.​

Looking ahead, ERGA envisions its decentralized infrastructure serving as a model for global collaborative research efforts. By embracing diversity, encouraging cooperation, and pushing for open access to data and resources, ERGA hopes to catalyze scientific discovery and generate positive change in the field of biodiversity genomics. ERGA aims to promote a more equitable and sustainable future for all by ongoing interaction with stakeholders, intensive outreach and education activities, and policy change advocacy. In addition to its immediate goals, ERGA considers the long-term implications of its work. As genomic technology progresses, the potential application of high-quality reference genomes will continue to grow. From informing conservation efforts and illuminating evolutionary histories to revolutionizing healthcare and agriculture, it is likely that ERGA's contributions will have far-reaching consequences for people and the planet as a whole.​

Furthermore, ERGA understands the importance of interdisciplinary collaboration in addressing the difficult challenges of the twenty-first century. ERGA aims to integrate genetic research into larger initiatives to promote sustainability and biodiversity conservation by forming relationships with stakeholders from other areas, such as policymakers, conservationists, and indigenous groups. Through shared knowledge and community action, ERGA seeks to create a future in which mankind coexists peacefully with the natural world, guided by a thorough grasp of its genetic legacy and ecological interconnectivity.

Finally, the manuscript exemplifies ERGA's collaborative ambitions and achievements, capturing the spirit of creativity and collaboration that defines this ground-breaking effort. As ERGA continues to push the boundaries of genetic research, it remains dedicated to scientific excellence, inclusivity, and the quest of knowledge for the benefit of society. I wholeheartedly recommend the publication of this groundbreaking initiative, offering my enthusiastic endorsement for its valuable contribution to the scientific community.​​

References
Larivière, D., Abueg, L., Brajuka, N. et al. (2024). Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology 42, 367-370. https://doi.org/10.1038/s41587-023-02100-3

Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., Durbin, R., Edwards, S. V., Forest, F., Gilbert, M. T. P., Goldstein, M. M., Grigoriev, I. V., Hackett, K. J., Haussler, D., Jarvis, E. D., Johnson, W. E., Patrinos, A., Richards, S., Castilla-Rubio, J. C., … Zhang, G. (2018). Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences, 115(17), 4325–4333. https://doi.org/10.1073/pnas.1720115115

Mazzoni, C. J., Claudio, C.i, Waterhouse, R. M. (2023). Biodiversity: an atlas of European reference genomes. Nature 619 : 252-252. https://doi.org/10.1038/d41586-023-02229-w

Mc Cartney, A. M., Formenti, G., Mouton, A., Panis, D. de, Marins, L. S., Leitão, H. G., Diedericks, G., Kirangwa, J., Morselli, M., Salces-Ortiz, J., Escudero, N., Iannucci, A., Natali, C., Svardal, H., Fernández, R., Pooter, T. de, Joris, G., Strazisar, M., Wood, J., … Mazzoni, C. J. (2024). The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.09.25.559365

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomicsAnn M Mc Cartney, Giulio Formenti, Alice Mouton, Claudio Ciofi, Robert M Waterhouse, Camila J Mazzoni, Diego De Panis, Luisa S Schlude Marins, Henrique G Leitao, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces, Nuria Escudero, ...<p>English: A global genome database of all of Earth's species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic...Bioinformatics, ERGA PilotJitendra Narayan Justin Ideozu, Eric Crandall2023-10-01 01:03:58 View
01 May 2024
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Evolution of ion channels in cetaceans: A natural experiment in the tree of life

Positive selection acted upon cetacean ion channels during the aquatic transition

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

The transition of cetaceans (whales, dolphins, and porpoises) from terrestrial to aquatic lifestyles is a striking example of natural selection driving major phenotypic changes (Figure 1). For instance, cetaceans have evolved the ability to withstand high pressure and to store oxygen for long periods, among other adaptations (Das et al. 2023). Many phenotypic changes, such as shifts in organ structure, have been well-characterized through fossils (Thewissen et al. 2009). Although such phenotypic transitions are now well understood, we have only a partial understanding of the underlying genetic mechanisms. Scanning for signatures of adaptation in genes related to phenotypes of interest is one approach to better understand these mechanisms. This was the focus of Uribe and colleagues’ (2024) work, who tested for such signatures across cetacean protein-coding genes.

 

Cetacean fossils

Figure 1: The skeletons of Ambulocetus (an early whale; top) and Pakicetus (the earliest known cetacean, which lived about 50 million years ago; bottom). Copyright: J. G. M. Thewissen. Displayed here with permission from the copyright holder.

 

The authors were specifically interested in investigating the evolution of ion channels, as these proteins play fundamental roles in physiological processes. An important aspect of their work was to develop a bioinformatic pipeline to identify orthologous ion channel genes across a set of genomes. After applying their bioinformatic workflow to 18 mammalian species (including nine cetaceans), they conducted tests to find out whether these genes showed signatures of positive selection in the cetacean lineage. For many ion channel genes, elevated ratios of non-synonymous to synonymous substitution rates were detected (for at least a subset of sites, and not necessarily the entire coding region of the genes). The genes concerned were enriched for several functions, including heart and nervous system-related phenotypes.

One top gene hit among the putatively selected genes was SCN5A, which encodes a sodium channel expressed in the heart. Interestingly, the authors noted a specific amino acid replacement, which is associated with sensitivity to the toxin tetrodotoxin in other lineages. This substitution appears to have occurred in the common ancestor of toothed whales, and then was reversed in the ancestor of bottlenose dolphins. The authors describe known bottlenose dolphin interactions with toxin-producing pufferfish that could result in high tetrodotoxin exposure, and thus perhaps higher selection for tetrodotoxin resistance. Although this observation is intriguing, the authors emphasize it requires experimental confirmation.

The authors also recapitulated the previously described observation (Yim et al. 2014; Huelsmann et al. 2019) that cetaceans have fewer protein-coding genes compared to terrestrial mammals, on average. This signal has previously been hypothesized to partially reflect adaptive gene loss. For example, specific gene loss events likely decreased the risk of developing blood clots while diving (Huelsmann et al. 2019). Uribe and colleagues also considered overall gene turnover rate, which encompasses gene copy number variation across lineages, and found the cetacean gene turnover rate to be three times higher than that of terrestrial mammals. Finally, they found that cetaceans have a higher proportion of ion channel genes (relative to all protein-coding genes in a genome) compared to terrestrial mammals. 

Similar investigations of the relative non-synonymous to synonymous substitution rates across cetacean and terrestrial mammal orthologs have been conducted previously, but these have primarily focused on dolphins as the sole cetacean representative (McGowen et al. 2012; Nery et al. 2013; Sun et al. 2013). These projects have also been conducted across a large proportion of orthologous genes, rather than a subset with a particular function. Performing proteome-wide investigations can be valuable in that they summarize the genome-wide signal, but can suffer from a high multiple testing burden. More generally, investigating a more targeted question, such as the extent of positive selection acting on ion channels in this case, or on genes potentially linked to cetaceans’ increased brain sizes (McGowen et al. 2011) or hypoxia tolerance (Tian et al. 2016), can be easier to interpret, as opposed to summarizing broader signals. However, these smaller-scale studies can also experience a high multiple testing burden, especially as similar tests are conducted across numerous studies, which often is not accounted for (Ioannidis 2005). In addition, integrating signals across the entire genome will ultimately be needed given that many genetic changes undoubtedly underlie cetaceans’ phenotypic diversification. As highlighted by the fact that past genome-wide analyses have produced some differing biological interpretations (McGowen et al. 2012; Nery et al. 2013; Sun et al. 2013), this is not a trivial undertaking. 

Nonetheless, the work performed in this preprint, and in related research, is valuable for (at least) three reasons. First, although it is a challenging task, a better understanding of the genetic basis of cetacean phenotypes could have benefits for many aspects of cetacean biology, including conservation efforts. In addition, the remarkable phenotypic shifts in cetaceans make the question of what genetic mechanisms underlie these changes intrinsically interesting to a wide audience. Last, since the cetacean fossil record is especially well-documented (Thewissen et al. 2009), cetaceans represent an appealing system to validate and further develop statistical methods for inferring adaptation from genetic data. Uribe and colleagues’ (2024) analyses provide useful insights relevant to each of these points, and have generated intriguing hypotheses for further investigation.


References

Das, K., Sköld, H., Lorenz, A., Parmentier, E. 2023. Who are the marine mammals? In: “Marine Mammals: A Deep Dive into the World of Science”. Brennecke, D., Knickmeier, K., Pawliczka, I., Siebert, U., Wahlberg, M (editors). Springer, Cham. p. 1–14. https://doi.org/10.1007/978-3-031-06836-2_1

Huelsmann, M., Hecker, N., Springer, M., S., Gatesy, J., Sharma, V., Hiller, M. 2019. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. Science Advances. 5(9):eaaw6671. https://doi.org/10.1126/sciadv.aaw6671

Ioannidis, J., P., A. 2005. Why most published research findings are false. PLOS Medicine. 2(8):e124. https://doi.org/10.1371/journal.pmed.0020124

McGowen MR, Montgomery SH, Clark C, Gatesy J. 2011. Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans. BMC Evolutionary Biology. 11(1):98. https://doi.org/10.1186/1471-2148-11-98

McGowen MR, Grossman LI, Wildman DE. 2012. Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown. Proceedings of the Royal Society B: Biological Sciences. 279(1743):3643–3651. https://doi.org/10.1098/rspb.2012.0869

Nery, M., F., González, D., J., Opazo, J., C. 2013. How to make a dolphin: molecular signature of positive selection in cetacean genome. PLOS ONE. 8(6):e65491. https://doi.org/10.1371/journal.pone.0065491

Sun, Y.-B., Zhou, W.-P., Liu, H.-Q., Irwin, D., M., Shen, Y.-Y., Zhang, Y.-P. 2013. Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins. Genome Biology and Evolution. 5(1):130–139. https://doi.org/10.1093/gbe/evs123

Tian, R., Wang, Z., Niu, X., Zhou, K., Xu, S., Yang, G. 2016. Evolutionary genetics of hypoxia tolerance in cetaceans during diving. Genome Biology and Evolution. 8(3):827–839. https://doi.org/10.1093/gbe/evw037

Thewissen, J., G., M., Cooper, L., N., George, J., C., Bajpai, S. 2009. From land to water: the origin of whales, dolphins, and porpoises. Evolution: Education and Outreach. 2(2):272–288. https://doi.org/10.1007/s12052-009-0135-2

Uribe, C., Nery, M., Zavala, K., Mardones, G., Riadi, G., Opazo, J. 2024. Evolution of ion channels in cetaceans: A natural experiment in the tree of life. bioRxiv, ver. 8 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.06.15.545160

Yim, H.-S., Cho, Y., S., Guang, X., Kang, S., G., Jeong, J.-Y., Cha, S.-S., Oh, H.-M., Lee, J.-H., Yang, E., C., Kwon, K., K., et al. 2014. Minke whale genome and aquatic adaptation in cetaceans. Nature Genetics. 46(1):88–92. https://doi.org/10.1038/ng.2835

 

Evolution of ion channels in cetaceans: A natural experiment in the tree of lifeCristóbal Uribe, Mariana F. Nery, Kattina Zavala, Gonzalo A. Mardones, Gonzalo Riadi & Juan C. Opazo<p>Cetaceans could be seen as a natural experiment within the tree of life in which a mammalian lineage changed from terrestrial to aquatic habitats. This shift involved extensive phenotypic modifications, which represent an opportunity to explore...Evolutionary genomicsGavin Douglas2023-07-04 20:53:46 View
15 Mar 2024
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Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps

Using transcriptomics and proteomics to understand the expansion of a secreted poisonous armoury in parasitoid wasps genomes

Recommended by ORCID_LOGO based on reviews by Inacio Azevedo and 2 anonymous reviewers

Parasitoid wasps lay their eggs inside another arthropod, whose body is physically consumed by the parasitoid larvae. Phylogenetic inference suggests that Parasitoida are monophyletic, and that this clade underwent a strong radiation shortly after branching off from the Apocrita stem, some 236 million years ago (Peters et al. 2017). The increase in taxonomic diversity during evolutionary radiations is usually concurrent with an increase in genetic/genomic diversity, and is often associated with an increase in phenotypic diversity. Gene (or genome) duplication provides the evolutionary potential for such increase of genomic diversity by neo/subfunctionalisation of one of the gene paralogs, and is often proposed to be related to evolutionary radiations (Ohno 1970; Francino 2005).


In their recent preprint, Dominique Colinet and coworkers have explored the genetic and functional diversity of a Rho GTPase activating protein (RhoGAP) multigene family in two very divergent wasp clades within Parasitoida, namely Leptopilina (Figitidae) and Venturia (Ichneumonidae) (Colinet et al. 2024). Some members of the RhoGAP family are present in the venom of the parasitoid wasp Leptopilina boulardi as well as in other Leptopilina species, and are probably involved in the parasitic lifestyle by binding and inactivating host’s Rho GTPases, thereby interfering with the host’s immune response (Colinet et al. 2007).


Venom protein composition is highly variable, even between very closely related species, and is subject to rapid evolutionary changes. Although gene duplication and subsequent neo/subfunctionalisation have been frequently proposed as the main mechanism underlying this evolutionary diversification, observations are often compatible with alternative explanations, such as horizontal gene transfer, gene co-option or multifunctionalisation (Martinson et al. 2017; Alvarado et al. 2020; Huang et al. 2021; Undheim and Jenner 2021). Furthermore, high mutation rates in venom protein-encoding genes hinder phylogenetic hypothesis testing, and venom proteomics can be needed to verify transcriptomic predictions (Smith and Undheim 2018; von Reumont et al. 2022).


Colinet and coworkers (2024) have applied a combined transcriptomic, proteomic and functional approach to i) identify potential transcripts of the RhoGAP family in Leptopilina species using experimental and bioinformatic approaches; ii) experimentally identify proteins of the RhoGAP family in the venom of three Leptopilina species; iii) identify transcripts and proteins of the RhoGAP family in the ovarian calyx of Venturia canescens; and iv) perform phylogenetic and selection analyses on the extant sequences of these RhoGAP family genes to propose an evolutionary scenario for their origin and diversification. The most striking results are first the large diversity of RhoGAP sequences retrieved in the transcriptomes and proteomes of Leptopilina and of V. canescens, and second the high number of branches and positions identified to have evolved under positive selection. All the retrieved hits share a RhoGAP domain, either alone or in tandem, preceded in the case of Leptopilina RhoGAPs by a signal peptide that may be responsible for protein vehiculation for venom secretion. Further, for some of the protein positions identified to have evolved under positive selection, the authors have experimentally verified the functional impact of the changes by reverse genetic engineering.


The authors propose an evolutionary scenario to interpret the phylogenetic relationships among extant RhoGAP diversity in the clades under study. They posit that two independent, incomplete duplication events from the respectively ancestral RacGAP gene, followed by subsequent, lineage- and paralog-specific duplication events, lie at the origin of the wealth of diversity of in the Leptopilina venom RhoGAPs and of V. canescens ovarian calyx RhoGAPs. Notwithstanding, the global relationships presented in the work are not systematically consistent with this interpretation, e.g. regarding the absence of monophyly for Leptopilina RhoGAPs and Leptopilina RacGAP, and the same holds true for the respective V. canescens sequences. It may very well be that the high evolutionary rate of these genes has eroded the phylogenetic signal and prevented proper reconstruction, as the large differences between codon-based and amino acid-based phylogenies and the low support suggest. Explicit hypothesis testing, together with additional data from other taxa, may shed light onto the evolution of this gene family.


The work by Colinet and coworkers communicates sound, novel transcriptomic, proteomic and functional data from complex gene targets, consolidated from an important amount of experimental and bioinformatic work, and related to evolutionarily intriguing and complex phenotypes. These results, and the evolutionary hypothesis proposed to account for them, will be instrumental for our understanding of the evolution and diversity of vesicle-associated RhoGAPs in divergent parasitoid wasps.

  

 

References


Alvarado, G., Holland, S., R., DePerez-Rasmussen, J., Jarvis, B., A., Telander, T., Wagner, N., Waring, A., L., Anast, A., Davis, B., Frank, A., et al. (2020). Bioinformatic analysis suggests potential mechanisms underlying parasitoid venom evolution and function. Genomics 112(2), 1096–1104. https://doi.org/10.1016/j.ygeno.2019.06.022


Colinet, D., Cavigliasso, F., Leobold, M., Pichon, A., Urbach, S., Cazes, D., Poullet, M., Belghazi, M., Volkoff, A-N., Drezen, J-M., Gatti, J-L., and Poirié, M. (2024). Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.06.05.543686


Colinet, D., Schmitz, A., Depoix, D., Crochard, D., and Poirié, M. (2007). Convergent Use of RhoGAP Toxins by eukaryotic parasites and bacterial pathogens. PLoS Pathogens 3(12), e203. https://doi.org/10.1371/journal.ppat.0030203


Francino, M.P. (2005). An adaptive radiation model for the origin of new gene functions. Nature Genetics 37, 573–577. https://doi.org/10.1038/ng1579


Huang, J., Chen, J., Fang, G., Pang, L., Zhou, S., Zhou, Y., Pan, Z., Zhang, Q., Sheng, Y., Lu, Y., et al. (2021). Two novel venom proteins underlie divergent parasitic strategies between a generalist and a specialist parasite. Nature Communications 12, 234. https://doi.org/10.1038/s41467-020-20332-8


Martinson, E., O., Mrinalini, Kelkar, Y. D., Chang, C-H., and Werren, J., H. 2017. The evolution of venom by co-option of single-copy genes. Current Biololgy 27(13), 2007-2013.e8. https://doi.org/10.1016/j.cub.2017.05.032


Ohno, S. (1970). Evolution by gene duplication. New-York: Springer-Verlag.


Peters, R., S., Krogmann, L., Mayer, C., Donath, A., Gunkel, S., Meusemann, K., Kozlov, A., Podsiadlowski, L., Petersen, M., Lanfear, R., et al. (2017). Evolutionary history of the Hymenoptera. Current Biology 27(7), 1013–1018. https://doi.org/10.1016/j.cub.2017.01.027


von Reumont, B., M., Anderluh, G., Antunes, A., Ayvazyan, N., Beis, D., Caliskan, F., Crnković, A., Damm, M., Dutertre, S., Ellgaard, L., et al. (2022). Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research. GigaScience 11, giac048. https://doi.org/10.1093/gigascience/giac048


Smith, J., J., and Undheim, E., A., B. (2018). True lies: using proteomics to assess the accuracy of transcriptome-based venomics in centipedes uncovers false positives and reveals startling intraspecific variation in Scolopendra subspinipes. Toxins 10(3), 96. https://doi.org/10.3390/toxins10030096


Undheim, E., A., B., and Jenner, R., A. (2021). Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer. Nature Communications 12, 818. https://doi.org/10.1038/s41467-021-21093-8

Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid waspsDominique Colinet, Fanny Cavigliasso, Matthieu Leobold, Appoline Pichon, Serge Urbach, Dominique Cazes, Marine Poullet, Maya Belghazi, Anne-Nathalie Volkoff, Jean-Michel Drezen, Jean-Luc Gatti, and Marylène Poirié<p>Animal venoms and other protein-based secretions that perform a variety of functions, from predation to defense, are highly complex cocktails of bioactive compounds. Gene duplication, accompanied by modification of the expression and/or functio...Evolutionary genomicsIgnacio Bravo2023-06-12 11:08:31 View
06 Feb 2024
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The need of decoding life for taking care of biodiversity and the sustainable use of nature in the Anthropocene - a Faroese perspective

Why sequence everything? A raison d’être for the Genome Atlas of Faroese Ecology

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

When discussing the Earth BioGenome Project with scientists and potential funding agencies, one common question is: why sequence everything? Whether sequencing a subset would be more optimal is not an unreasonable question given what we know about the mathematics of importance and Pareto’s 80:20 principle, that 80% of the benefits can come from 20% of the effort. However, one must remember that this principle is an observation made in hindsight and selecting the most effective 20% of experiments is difficult. As an example, few saw great applied value in comparative genomic analysis of the archaea Haloferax mediterranei, but this enabled the discovery of CRISPR/Cas9 technology (1). When discussing whether or not to sequence all life on our planet, smaller countries such as the Faroe Islands are seldom mentioned. 
 
Mikalsen and co-authors (2) provide strong arguments to appreciate, investigate and steward genetic diversity, from a Faroese viewpoint, a fishery viewpoint, and a global viewpoint. As readers, we learn to cherish the Faroe Islands, the Faroese, and perhaps by extension all of nature and the people of the world. The manuscript describes the proposed Faroese participation in the European Reference Genome Atlas (ERGA) consortium through Gen@FarE – the Genome Atlas of Faroese Ecology. Gen@FarE aims to: i) generate high-quality reference genomes for all eukaryotes on the islands and in its waters; ii) establish population genetics of all species of commercial or ecological interest; and iii) establish a “databank” for all Faroese species with citizen science tools for participation.


In the background section of the manuscript, the authors argue that as caretakers of the earth (and responsible for the current rapid decrease in biodiversity), humanity must be aware of the biodiversity and existing genetic diversity, to protect these for future generations. Thus, it is necessary to have reference genomes for as many species as possible, enabling estimation of population sizes and gene flow between ecosystem locations. Without this the authors note that “…it is impossible to make relevant management plans for a species, an ecosystem or a geographical area…”. Gen@FarE is important. The Faroe nation has a sizable economic zone in the North Atlantic and large fisheries. In terms of biodiversity and conservation, the authors list some species endemic to other Faroe islands, especially sea birds. The article discusses ongoing marine environmental-DNA-based monitoring programs that started in 2018, and how new reference genome databases will help these efforts to track and preserve marine biodiversity. They point to the lack of use of population genomics information for Red List decisions on which species are endangered, and the need for these techniques to inform sustainable harvesting of fisheries, given collapses in critical food species such as Northwest Atlantic cod and herring. In one example, they highlight how the herring chromosome 12 inversion contains a “supergene” collection of tightly linked genes associated with ecological adaptation. Genetic tools may also help enable the identification and nurturing of feeding grounds for young individuals. Critically, the Faroe Islands have a significant role to play in protecting the millions of tons of seafood caught annually upon which humanity relies. As the authors note, population genomics based on high-quality reference sequences is “likely the best tool” to monitor and protect commercial fisheries. There is an important section discussing the role of interactions between visible and “invisible" species in the marine ecosystem on which we all depend. Examples of “invisible” species include a wide range of morphologically similar planktonic algae, and invasive species transported by ballast water or ship hulls.​ As biologists, I believe we forget that our population studies of life on the earth have so far been mostly in the dark. Gen@FarE is but one light that can be switched on. 


The authors conclude by discussing Gen@FarE plans for citizen science and education, perhaps the most important part of this project if humanity is to learn to cherish and care for the earth. Where initiatives such as the Human Genome Project did not need the collaborative efforts of the world for sample access, the Earth BioGenome Project most certainly does. In the same way, at a smaller scale, Gen@FarE requires the support and determination of the Faroese. 
 


References    

1          Mojica, F. J., Díez-Villaseñor, C. S., García-Martínez, J. & Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60, 174-182 (2005).

2          Mikalsen, S-O., Hjøllum, J. í., Salter, I., Djurhuus, A. & Kongsstovu, S. í. The need of decoding life for taking care of biodiversity and the sustainable use of nature in the Anthropocene – a Faroese perspective. EcoEvoRxiv (2024), ver. 3 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.32942/X21S4C

The need of decoding life for taking care of biodiversity and the sustainable use of nature in the Anthropocene - a Faroese perspectiveSvein-Ole Mikalsen, Jari í Hjøllum, Ian Salter, Anni Djurhuus, Sunnvør í Kongsstovu<p>Biodiversity is under pressure, mainly due to human activities and climate change. At the international policy level, it is now recognised that genetic diversity is an important part of biodiversity. The availability of high-quality reference g...ERGA, ERGA Pilot, Population genomics, VertebratesStephen Richards2023-07-31 16:59:33 View
24 Jan 2024
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High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding

A high quality reference genome of the brown hare

Recommended by ORCID_LOGO based on reviews by Merce Montoliu-Nerin and 1 anonymous reviewer

The brown hare, or European hare, Lupus europaeus, is a widespread mammal whose natural range spans western Eurasia. At the northern limit of its range, it hybridises with the mountain hare (L. timidis), and humans have introduced it into other continents. It represents a particularly interesting mammal to study for its population genetics, extensive hybridisation zones, and as an invasive species.

This study (Michell et al. 2024) has generated a high-quality assembly of a genome from a brown hare from Finland using long PacBio HiFi sequencing reads and Hi-C scaffolding. The contig N50 of this new genome is 43 Mb, and completeness, assessed using BUSCO, is 96.1%. The assembly comprises 23 autosomes, and an X chromosome and Y chromosome, with many chromosomes including telomeric repeats, indicating the high level of completeness of this assembly.

While the genome of the mountain hare has previously been assembled, its assembly was based on a short-read shotgun assembly, with the rabbit as a reference genome. The new high-quality brown hare genome assembly allows a direct comparison with the rabbit genome assembly. For example, the assembly addresses the karyotype difference between the hare (n=24) and the rabbit (n=22). Chromosomes 12 and 17 of the hare are equivalent to chromosome 1 of the rabbit, and chromosomes 13 and 16 of the hare are equivalent to chromosome 2 of the rabbit. The new assembly also provides a hare Y-chromosome, as the previous mountain hare genome was from a female.

This new genome assembly provides an important foundation for population genetics and evolutionary studies of lagomorphs.

References

Michell, C., Collins, J., Laine, P. K., Fekete, Z., Tapanainen, R., Wood, J. M. D., Goffart, S., Pohjoismäki, J. L. O. (2024). High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.08.29.555262

High quality genome assembly of the brown hare (*Lepus europaeus*) with chromosome-level scaffoldingCraig Michell, Joanna Collins, Pia K. Laine, Zsofia Fekete, Riikka Tapanainen, Jonathan M. D. Wood, Steffi Goffart, Jaakko L. O. Pohjoismaki<p style="text-align: justify;">We present here a high-quality genome assembly of the brown hare (Lepus europaeus Pallas), based on a fibroblast cell line of a male specimen from Liperi, Eastern Finland. This brown hare genome represents the first...ERGA Pilot, VertebratesEd Hollox2023-10-16 20:46:39 View
15 Jan 2024
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The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution

Embarking on a novel journey in Metazoa evolution through the pioneering sequencing of a key underrepresented lineage

Recommended by ORCID_LOGO based on reviews by Gonzalo Riadi and 2 anonymous reviewers

Whole genome sequences are revolutionizing our understanding across various biological fields. They not only shed light on the evolution of genetic material but also uncover the genetic basis of phenotypic diversity. The sequencing of underrepresented lineages, such as the one presented in this study, is of critical importance. It is crucial in filling significant gaps in our understanding of Metazoa evolution. Despite the wealth of genome sequences in public databases, it is crucial to acknowledge that some lineages across the Tree of Life are underrepresented or absent. This research represents a significant step towards addressing this imbalance, contributing to the collective knowledge of the global scientific community.

In this genome note, as part of the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity (Mc Cartney et al. 2023), Klara Eleftheriadi and colleagues (Eleftheriadi et al. 2023) make a significant effort to add a genome sequence of an unrepresented group in the animal Tree of Life. More specifically, they present a taxonomic description and chromosome-level genome assembly of a newly described species of horsehair worm (Gordionus montsenyensis). Their sequence methodology gave rise to an assembly of 396 scaffolds totaling 288 Mb, with an N50 value of 64.4 Mb, where 97% of this assembly is grouped into five pseudochromosomes. The nuclear genome annotation predicted 10,320 protein-coding genes, and they also assembled the circular mitochondrial genome into a 15-kilobase sequence.

The selection of a species representing the phylum Nematomorpha, a group of parasitic organisms belonging to the Ecdysozoa lineage, is good, since today, there is only one publicly available genome for this animal phylum (Cunha et al. 2023). Interestingly, this article shows, among other things, that the species analyzed has lost ∼30% of the universal Metazoan genes. Efforts, like the one performed by Eleftheriadi and colleagues, are necessary to gain more insights, for example, on the evolution of this massive gene lost in this group of animals.


References

Cunha, T. J., de Medeiros, B. A. S, Lord, A., Sørensen, M. V., and Giribet, G. (2023). Rampant Loss of Universal Metazoan Genes Revealed by a Chromosome-Level Genome Assembly of the Parasitic Nematomorpha. Current Biology, 33 (16): 3514–21.e4. https://doi.org/10.1016/j.cub.2023.07.003

Eleftheriadi, K., Guiglielmoni, N., Salces-Ortiz, J., Vargas-Chavez, C., Martínez-Redondo, G. I., Gut, M., Flot, J.-F., Schmidt-Rhaesa, A., and Fernández, R. (2023). The Genome Sequence of the Montseny Horsehair worm, Gordionus montsenyensis sp. Nov., a Key Resource to Investigate Ecdysozoa Evolution. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.06.26.546503

Mc Cartney, A. M., Formenti, G., Mouton, A., De Panis, D., Marins, L. S., Leitão, H. G., Diedericks, G., et al. (2023). The European Reference Genome Atlas: Piloting a Decentralised Approach to Equitable Biodiversity Genomics. bioRxiv. https://doi.org/10.1101/2023.09.25.559365

The genome sequence of the Montseny horsehair worm, *Gordionus montsenyensis* sp. nov., a key resource to investigate Ecdysozoa evolutionEleftheriadi Klara, Guiglielmoni Nadège, Salces-Ortiz Judit, Vargas-Chávez Carlos, Martínez-Redondo Gemma I, Gut Marta, Flot Jean François, Schmidt-Rhaesa Andreas, Fernández Rosa<p>Nematomorpha, also known as Gordiacea or Gordian worms, are a phylum of parasitic organisms that belong to the Ecdysozoa, a clade of invertebrate animals characterized by molting. They are one of the less scientifically studied animal phyla, an...ERGA PilotJuan C. Opazo2023-06-29 10:31:36 View
22 Nov 2023
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The slow evolving genome of the xenacoelomorph worm Xenoturbella bocki

Genomic idiosyncrasies of Xenoturbella bocki: morphologically simple yet genetically complex

Recommended by based on reviews by Christopher Laumer and 1 anonymous reviewer

Xenoturbella is a genus of morphologically simple bilaterians inhabiting benthic environments. Until very recently, only one species was known from the genus, Xenoturbella bocki Westblad 1949 [1]. Less than a decade ago, five more species were discovered (X. churro, X. monstrosa, X. profunda, X. hollandorum [2] and X. japonica [3]). These enigmatic animals lack an anus, a coelom, reproductive organs, nephrocytes and a centralized nervous system [1]. The systematic classification of the genus has substantially changed in the last decades, with first being considered as its own phylum (Xenoturbellida) and then being clustered together with acoels and nemertodermatids into the phylum Xenacoelomorpha [4,5]. The phylogenetic position of the xenacoelomorphs has been recalcitrant to resolution, with its position ranging from being the sister group to Nephrozoa (ie, protostomes and deuterostomes [6]) to the sister group to Ambulacraria (ie, Hemichordata and Echinodermata) in a clade called Xenambulacraria [4]. Recent studies based on expanded datasets and more refined analyses support either topology [7,8]. Either way, it is clear that additional studies on Xenoturbella could provide important insights into the origins of bilaterian traits such as the anus, the nephrons and the evolution of a centralized nervous system. 


Small but mighty genome - In this work [9], the authors present the chromosome-level genome of X. bocki - the first one for xenoturbellids - and explore their genomic idiosyncrasies in the context of other animal phyla. The first thing they discuss is the complexity of the genome, with X. bocki having a similar number of genes to other bilaterians (despite its small size of 111Mb), retained ancestral metazoan synteny, conserved clusters of Hox genes, largely complete signaling pathways and most bilaterian miRNAs present. This is not a surprise, though, as we know that the relationship between genomic and morphological complexity is far from straightforward - for instance, protist lineages closely related to animals share many gene families with us [10], and it is not the presence or absence of these gene families but their evolutionary dynamics what defines complexity in each animal phyla (eg [11]). However, the relationship between both is far from well-understood, and having a high-quality genome is the first crucial step towards a holistic understanding of genome evolution, allowing us to ask questions about how and when genes are regulated, how they interact in 3D space, or how their epigenetic landscape is shaped, for instance.


Xenacoelomorphs: deuterostomes or not? - The authors also discuss the phylogenetic position of xenacoelomorphs (including the newly generated high-quality genome of X. bocki) based on a gene presence/absence matrix. Although there is much more to be done to robustly assess the phylogenetic position of the phylum, these analyses represent a first attempt to investigate what the phylogeny looks like after the addition of the new high-quality data. The new analyses reflected once more the previously recovered phylogenies mentioned above, but this time with a twist: X. bocki was recovered as the sister group to echinoderms, yet acoels appeared as sister to all deuterostomes, hence not recovering Xenacoelomorpha as monophyletic. Thus, it is clear that much remains to be explored to disentangle the phylogenetic position of these mysterious lineages, where more sophisticated methodologies such as synteny-based orthology inference or models of evolution accounting for heterotachy probably have an important role to play. 

In any case, we are approaching a qualitative jump in how we understand phylogenomics thanks to efforts derived from the availability of chromosome-level genome assemblies for a growing number of species. Exciting times are ahead for us, evolutionary biologists, to explore what high-quality genomes - in combination with multiomics datasets - will reveal about animal evolution. I am personally really looking forward to it.  

References

1. Westblad E. (1949). Xenoturbella bocki n.g., n.sp., a peculiar, primitive Turbellarian type. Arkiv för Zoologi 1, 3-29 (1949).

2. Rouse, G. W., Wilson, N. G., Carvajal, J. I. & Vrijenhoek, R. C. New deep-sea species of Xenoturbella and the position of Xenacoelomorpha. Nature 530, 94–97 (2016). https://doi.org/10.1038/nature16545

3. Nakano, H. et al. Correction to: A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella. BMC Evol. Biol. 18, 1–2 (2018). https://doi.org/10.1186/s12862-018-1190-5​https://doi.org/10.1186/s12862-018-1190-5

4. Philippe, H. et al. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470, 255–258 (2011). https://doi.org/10.1038/nature09676

5. Hejnol, A. et al. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. Biol. Sci. 276, 4261–4270 (2009). https://doi.org/10.1098/rspb.2009.0896

6. Cannon, J. T. et al. Xenacoelomorpha is the sister group to Nephrozoa. Nature 530, 89–93 (2016). https://doi.org/10.1038/nature16520

7. Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. Biol. Sci. 286, 20190831 (2019). https://doi.org/10.1098/rspb.2019.0831

8. Philippe, H. et al. Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria. Curr. Biol. 29, 1818–1826.e6 (2019). https://doi.org/10.1016/j.cub.2019.04.009

9. Schiffer, P. H., Natsidis, P., Leite D. J., Robertson, H., Lapraz, F., Marlétaz, F., Fromm, B., Baudry, L., Simpson, F., Høye, E., Zakrzewski, A-C., Kapli, P., Hoff, K. J., Mueller, S., Marbouty, M., Marlow, H., Copley, R. R., Koszul, R., Sarkies, P. & Telford, M .J. The slow evolving genome of the xenacoelomorph worm Xenoturbella bocki. bioRxiv (2023), ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.06.24.497508

10. Suga, H. et al. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat. Commun. 4, 2325 (2013). https://doi.org/10.1038/ncomms3325

11. Fernández, R. & Gabaldón, T. Gene gain and loss across the metazoan tree of life. Nat Ecol Evol 4, 524–533 (2020). https://doi.org/10.1038/s41559-019-1069-x

The slow evolving genome of the xenacoelomorph worm *Xenoturbella bocki*Philipp H. Schiffer, Paschalis Natsidis, Daniel J. Leite, Helen Robertson, François Lapraz, Ferdinand Marlétaz, Bastian Fromm, Liam Baudry, Fraser Simpson, Eirik Høye, Anne-C. Zakrzewski, Paschalia Kapli, Katharina J. Hoff, Steven Mueller, Martial...<p style="text-align: justify;">The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part o...Evolutionary genomicsRosa Fernández2022-11-01 12:31:53 View
20 Nov 2023
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Building a Portuguese Coalition for Biodiversity Genomics

The Portuguese genomics community teams up with iconic species to understand the destruction of biodiversity

Recommended by based on reviews by Svein-Ole Mikalsen and 1 anonymous reviewer

This manuscript describes the ongoing work and plans of Biogenome Portugal: a new network of researchers in the Portuguese biodiversity genomics community. The aims of this network are to jointly train scientists in ecology and evolution, generate new knowledge and understanding of Portuguese biodiversity, and better engage with the public and with international researchers, so as to advance conservation efforts in the region. In collaboration across disciplines and institutions, they are also contributing to the European Reference Genome Atlas (ERGA): a massive scientific effort, seeking to eventually produce reference-quality genomes for all species in the European continent (Mc Cartney et al. 2023).

The manuscript centers around six iconic and/or severely threatened species, whose range extends across parts of what is today considered Portuguese territory. Via the Portugal chapter of ERGA (ERGA-Portugal), the researchers will generate high-quality genome sequences from these species. The species are the Iberian hare, the Azores laurel, the Black wheatear, the Portuguese crowberry, the Cave ground beetle and the Iberian minnowcarp. In ignorance of human-made political borders, some of these species also occupy large parts of the rest of the Iberian peninsula, highlighting the importance of transnational collaboration in biodiversity efforts. The researchers extracted samples from members of each of these species, and are building reference genome sequences from them. In some cases, these sequences will also be co-analyzed with additional population genomic data from the same species or genetic data from cohabiting species. The researchers aim to answer a variety of ecological and evolutionary questions using this information, including how genetic diversity is being affected by the destruction of their habitat, and how they are being forced to adapt as a consequence of the climate emergency.

The authors did a very good job in providing a justification for the choice of pilot species, a thorough methodological overview of current work, and well thought-out plans for future analyses once the genome sequences are available for study. The authors also describe plans for networking and training activities to foster a well-connected Portuguese biodiversity genomics community.

Applying a genomic analysis lens is important for understanding the ever faster process of devastation of our natural world. Governments and corporations around the globe are destroying nature at ever larger scales (Diaz et al. 2019). They are also destabilizing the climatic conditions on which life has existed for thousands of years (Trisos et al. 2020). Thus, genetic diversity is decreasing faster than ever in human history, even when it comes to non-threatened species (Exposito-Alonso et al. 2022), and these decreases are disrupting ecological processes worldwide (Richardson et al. 2023). This, in turn, is threatening the conditions on which the stability of our societies rest (Gardner and Bullock 2021). The efforts of Biogenome Portal and ERGA-Portugal will go a long way in helping us understand in greater detail how this process is unfolding in Portuguese territories.

 

 

References

Díaz, Sandra, et al. "Pervasive human-driven decline of life on Earth points to the need for transformative change." Science 366.6471 (2019): eaax3100. https://doi.org/10.1126/science.aax3100

Exposito-Alonso, Moises, et al. "Genetic diversity loss in the Anthropocene." Science 377.6613 (2022): 1431-1435. https://doi.org/10.1126/science.abn5642

Gardner, Charlie J., and James M. Bullock. "In the climate emergency, conservation must become survival ecology." Frontiers in Conservation Science 2 (2021): 659912. https://doi.org/10.3389/fcosc.2021.659912

Mc Cartney, Ann M., et al. "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics." bioRxiv (2023): 2023-09, ver. 2 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.32942/X20W3Q

Richardson, Katherine, et al. "Earth beyond six of nine planetary boundaries." Science Advances 9.37 (2023): eadh2458. https://doi.org/10.1126/sciadv.adh2458

Trisos, Christopher H., Cory Merow, and Alex L. Pigot. "The projected timing of abrupt ecological disruption from climate change." Nature 580.7804 (2020): 496-501. https://doi.org/10.1038/s41586-020-2189-9

Building a Portuguese Coalition for Biodiversity GenomicsJoão Pedro Marques, Paulo Célio Alves, Isabel R. Amorim, Ricardo J. Lopes, Mónica Moura, Gene Meyers, Manuela Sim-Sim, Carla Sousa-Santos, Maria Judite Alves, Paulo AV Borges, Thomas Brown, Miguel Carneiro, Carlos Carrapato, Luís Ceríaco, Claudio ...<p style="text-align: justify;">The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene gla...ERGA, ERGA PilotFernando Racimo2023-07-14 11:24:22 View
14 Sep 2023
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Expression of cell-wall related genes is highly variable and correlates with sepal morphology

The same but different: How small scale hidden variations can have large effects

Recommended by ORCID_LOGO based on reviews by Sandra Corjito and 1 anonymous reviewer

For ages, we considered only single genes, or just a few, in order to understand the relationship between phenotype and genotype in response to environmental challenges. Recently, the use of meaningful groups of genes, e.g. gene regulatory networks, or modules of co-expression, allowed scientists to have a larger view of gene regulation. However, all these findings were based on contrasted genotypes, e.g. between wild-types and mutants, as the implicit assumption often made is that there is little transcriptomic variability within the same genotype context. 

Hartasànchez and collaborators (2023) decided to challenge both views: they used a single genotype instead of two, the famous A. thaliana Col0, and numerous plants, and considered whole gene networks related to sepal morphology and its variations. They used a clever approach, combining high-level phenotyping and gene expression to better understand phenomena and regulations underlying sepal morphologies. Using multiple controls, they showed that basic variations in the expression of genes related to the cell wall regulation, as well as the ones involved in chloroplast metabolism, influenced the global transcriptomic pattern observed in sepal while being in near-identical genetic background and controlling for all other experimental conditions. 

The paper of Hartasànchez et al. is thus a tremendous call for humility in biology, as we saw in their work that we just understand the gross machinery. However, the Devil is in the details: understanding those very small variations that may have a large influence on phenotypes, and thus on local adaptation to environmental challenges, is of great importance in these times of climatic changes.

References

Hartasánchez DA, Kiss A, Battu V, Soraru C, Delgado-Vaquera A, Massinon F, Brasó-Vives M, Mollier C, Martin-Magniette M-L, Boudaoud A, Monéger F. 2023. Expression of cell-wall related genes is highly variable and correlates with sepal morphology. bioRxiv, ver. 4, peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.04.26.489498

Expression of cell-wall related genes is highly variable and correlates with sepal morphologyDiego A. Hartasánchez, Annamaria Kiss, Virginie Battu, Charline Soraru, Abigail Delgado-Vaquera, Florian Massinon, Marina Brasó-Vives, Corentin Mollier, Marie-Laure Martin-Magniette, Arezki Boudaoud, Françoise Monéger<p style="text-align: justify;">Control of organ morphology is a fundamental feature of living organisms. There is, however, observable variation in organ size and shape within a given genotype. Taking the sepal of Arabidopsis as a model, we inves...Bioinformatics, Epigenomics, PlantsFrancois Sabot2023-03-14 19:10:15 View
11 Sep 2023
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COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences

A pipeline to select SARS-CoV-2 sequences for reliable phylodynamic analyses

Recommended by based on reviews by Gabriel Wallau and Bastien Boussau

Phylodynamic approaches enable viral genetic variation to be tracked over time, providing insight into pathogen phylogenetic relationships and epidemiological dynamics. These are important methods for monitoring viral spread, and identifying important parameters such as transmission rate, geographic origin and duration of infection [1]. This knowledge makes it possible to adjust public health measures in real-time and was important in the case of the COVID-19 pandemic [2]. However, these approaches can be complicated to use when combining a very large number of sequences. This was particularly true during the COVID-19 pandemic, when sequencing data representing millions of entire viral genomes was generated, with associated metadata enabling their precise identification.

Danesh et al. [3] present a bioinformatics pipeline, CovFlow, for selecting relevant sequences according to user-defined criteria to produce files that can be used directly for phylodynamic analyses. The selection of sequences first involves a quality filter on the size of the sequences and the absence of unresolved bases before being able to make choices based on the associated metadata. Once the sequences are selected, they are aligned and a time-scaled phylogenetic tree is inferred. An output file in a format directly usable by BEAST 2 [4] is finally generated.

To illustrate the use of the pipeline, Danesh et al. [3] present an analysis of the Delta variant in two regions of France. They observed a delay in the start of the epidemic depending on the region. In addition, they identified genetic variation linked to the start of the school year and the extension of vaccination, as well as the arrival of a new variant. This tool will be of major interest to researchers analysing SARS-CoV-2 sequencing data, and a number of future developments are planned by the authors.

References

[1] Baele G, Dellicour S, Suchard MA, Lemey P, Vrancken B. 2018. Recent advances in computational phylodynamics. Curr Opin Virol. 31:24-32. https://doi.org/10.1016/j.coviro.2018.08.009

[2] Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. 2022. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet. 23:547-562. https://doi.org/10.1038/s41576-022-00483-8

[3] Danesh G, Boennec C, Verdurme L, Roussel M, Trombert-Paolantoni S, Visseaux B, Haim-Boukobza S, Alizon S. 2023. COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences. bioRxiv, ver. 7 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.06.17.496544

[4] Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H et al. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10: e1003537. https://doi.org/10.1371/journal.pcbi.1003537

COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequencesGonché Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert-Paolantoni, Benoit Visseaux, Stephanie Haim-Boukobza, Samuel Alizon<p style="text-align: justify;">Phylodynamic analyses generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and...Bioinformatics, Evolutionary genomicsEmmanuelle Lerat2022-12-12 09:04:01 View