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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
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
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
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
07 Sep 2023
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The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches

Natural variation and adaptation in Brachypodium distachyon

Recommended by based on reviews by Thibault Leroy and 1 anonymous reviewer

Identifying the genetic factors that allow plant adaptation is a major scientific question that is particularly relevant in the face of the climate change that we are already experiencing. To address this, it is essential to have genetic information on a high number of accessions (i.e., plants registered with unique accession numbers) growing under contrasting environmental conditions. There is already an important number of studies addressing these issues in the plant Arabidopsis thaliana, but there is a need to expand these analyses to species that play key roles in wild ecosystems and are close to very relevant crops, as is the case of grasses.

The work of Minadakis, Roulin and co-workers (1) presents a Brachypodium distachyon panel of 332 fully sequences accessions that covers the whole species distribution across a wide range of bioclimatic conditions, which will be an invaluable tool to fill this gap. In addition, the authors use this data to start analyzing the population structure and demographic history of this plant, suggesting that the species experienced a shift of its distribution following the Last Glacial Maximum, which may have forced the species into new habitats. The authors also present a modeling of the niches occupied by B. distachyon together with an analysis of the genetic clades found in each of them, and start analyzing the different adaptive loci that may have allowed the species’ expansion into different bioclimatic areas.

In addition to the importance of the resources made available by the authors for the scientific community, the analyses presented are well done and carefully discussed, and they highlight the potential of these new resources to investigate the genetic bases of plant adaptation. 

References

1. Nikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin. The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches. bioRxiv, 2023.06.01.543285, ver. 5 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.06.01.543285

The demographic history of the wild crop relative *Brachypodium distachyon* is shaped by distinct past and present ecological nichesNikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin<p style="text-align: justify;">Closely related to economically important crops, the grass <em>Brachypodium distachyon</em> has been originally established as a pivotal species for grass genomics but more recently flourished as a model for develop...Evolutionary genomics, Functional genomics, Plants, Population genomicsJosep Casacuberta2023-06-14 15:28:30 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
09 Aug 2023
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Efficient k-mer based curation of raw sequence data: application in Drosophila suzukii

Decontaminating reads, not contigs

Recommended by based on reviews by Marie Cariou and Denis Baurain

Contamination, the presence of foreign DNA sequences in a sample of interest, is currently a major problem in genomics. Because contamination is often unavoidable at the experimental stage, it is increasingly recognized that the processing of high-throughput sequencing data must include a decontamination step. This is usually performed after the many sequence reads have been assembled into a relatively small number of contigs. Dubious contigs are then discarded based on their composition (e.g. GC-content) or because they are highly similar to a known piece of DNA from a foreign species.

Here [1], Mathieu Gautier explores a novel strategy consisting in decontaminating reads, not contigs. Why is this promising? Assembly programs and algorithms are complex, and it is not easy to predict, or monitor, how they handle contaminant reads. Ideally, contaminant reads will be assembled into obvious contaminant contigs. However, there might be more complex situations, such as chimeric contigs with alternating genuine and contaminant segments. Decontaminating at the read level, if possible, should eliminate such unfavorable situations where sequence information from contaminant and target samples are intimately intertwined by an assembler.

To achieve this aim, Gautier proposes to use methods initially designed for the analysis of metagenomic data. This is pertinent since the decontamination process involves considering a sample as a mixture of different sources of DNA. The programs used here, CLARK and CLARK-L, are based on so-called k-mer analysis, meaning that the similarity between a read to annotate and a reference sequence is measured by how many sub-sequences (of length 31 base pairs for CLARK and 27 base pairs for CLARK-L) they share. This is notoriously more efficient than traditional sequence alignment algorithms when it comes to comparing a very large number of (most often unrelated) sequences. This is, therefore, a reference-based approach, in which the reads from a sample are assigned to previously sequenced genomes based on k-mer content.

This original approach is here specifically applied to the case of Drosophila suzukii, an invasive pest damaging fruit production in Europe and America. Fortunately, Drosophila is a genus of insects with abundant genomic resources, including high-quality reference genomes in dozens of species. Having calibrated and validated his pipeline using data sets of known origins, Gautier quantifies in each of 258 presumed D. suzukii samples the proportion of reads that likely belong to other species of fruit flies, or to fruit fly-associated microbes. This proportion is close to one in 16 samples, which clearly correspond to mis-labelled individuals. It is non-negligible in another ~10 samples, which really correspond to D. suzukii individuals. Most of these reads of unexpected origin are contaminants and should be filtered out. Interestingly, one D. suzukii sample contains a substantial proportion of reads from the closely related D. subpulchera, which might instead reflect a recent episode of gene flow between these two species. The approach, therefore, not only serves as a crucial technical step, but also has the potential to reveal biological processes.

Gautier's thorough, well-documented work will clearly benefit the ongoing and future research on D. suzuki, and Drosophila genomics in general. The author and reviewers rightfully note that, like any reference-based approach, this method is heavily dependent on the availability and quality of reference genomes - Drosophila being a favorable case. Building the reference database is a key step, and the interpretation of the output can only be made in the light of its content and gaps, as illustrated by Gautier's careful and detailed discussion of his numerous results. 

This pioneering study is a striking demonstration of the potential of metagenomic methods for the decontamination of high-throughput sequence data at the read level. The pipeline requires remarkably few computing resources, ensuring low carbon emission. I am looking forward to seeing it applied to a wide range of taxa and samples.

 

Reference

[1] Gautier Mathieu. Efficient k-mer based curation of raw sequence data: application in Drosophila suzukii. bioRxiv, 2023.04.18.537389​, ver. 2, peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.04.18.537389​

Efficient k-mer based curation of raw sequence data: application in *Drosophila suzukii*Gautier Mathieu<p>Several studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient kmer-based approach to assess th...Bioinformatics, Population genomicsNicolas Galtier2023-04-20 22:05:13 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
02 Jun 2023
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Near-chromosome level genome assembly of devil firefish, Pterois miles

The genome of a dangerous invader (fish) beauty

Recommended by based on reviews by Maria Recuerda and 1 anonymous reviewer

High-quality genomes are currently being generated at an unprecedented speed powered by long-read sequencing technologies. However, sequencing effort is concentrated unequally across the tree of life and several key evolutionary and ecological groups remain largely unexplored. So is the case for fish species of the family Scorpaenidae (Perciformes). Kitsoulis et al. present the genome of the devil firefish, Pterois miles (1). Following current best practices, the assembly relies largely on Oxford Nanopore long reads, aided by Illumina short reads for polishing to increase the per-base accuracy. PacBio’s IsoSeq was used to sequence RNA from a variety of tissues as direct evidence for annotating genes. The reconstructed genome is 902 Mb in size and has high contiguity (N50=14.5 Mb; 660 scaffolds, 90% of the genome covered by the 83 longest scaffolds) and completeness (98% BUSCO completeness). The new genome is used to assess the phylogenetic position of P. miles, explore gene synteny against zebrafish, look at orthogroup expansion and contraction patterns in Perciformes, as well as to investigate the evolution of toxins in scorpaenid fish (2). In addition to its value for better understanding the evolution of scorpaenid and teleost fishes, this new genome is also an important resource for monitoring its invasiveness through the Mediterranean Sea (3) and the Atlantic Ocean, in the latter case forming the invasive lionfish complex with P. volitans (4).

REFERENCES

1. Kitsoulis CV, Papadogiannis V, Kristoffersen JB, Kaitetzidou E, Sterioti E, Tsigenopoulos CS, Manousaki T. (2023) Near-chromosome level genome assembly of devil firefish, Pterois miles. BioRxiv, ver. 6 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.01.10.523469

2. Kiriake A, Shiomi K. (2011) Some properties and cDNA cloning of proteinaceous toxins from two species of lionfish (Pterois antennata and Pterois volitans). Toxicon, 58(6-7):494–501.  https://doi.org/10.1016/j.toxicon.2011.08.010

3. Katsanevakis S, et al. (2020) Un- published Mediterranean records of marine alien and cryptogenic species. BioInvasions Records, 9:165–182. https://doi.org/10.3391/bir.2020.9.2.01

4. Lyons TJ, Tuckett QM, Hill JE. (2019) Data quality and quantity for invasive species: A case study of the lionfishes. Fish and Fisheries, 20:748–759. https://doi.org/10.1111/faf.12374

Near-chromosome level genome assembly of devil firefish, *Pterois miles*Christos V. Kitsoulis, Vasileios Papadogiannis, Jon B. Kristoffersen, Elisavet Kaitetzidou, Aspasia Sterioti, Costas S. Tsigenopoulos, Tereza Manousaki<p style="text-align: justify;">Devil firefish (<em>Pterois miles</em>), a member of Scorpaenidae family, is one of the most successful marine non-native species, dominating around the world, that was rapidly spread into the Mediterranean Sea, thr...Evolutionary genomicsIker Irisarri2023-01-17 12:37:20 View
07 Aug 2023
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Genomic data suggest parallel dental vestigialization within the xenarthran radiation

What does dental gene decay tell us about the regressive evolution of teeth in South American mammals?

Recommended by based on reviews by Juan C. Opazo, Régis Debruyne and Nicolas Pollet

A group of mammals, Xenathra, evolved and diversified in South America during its long period of isolation in the early to mid Cenozoic era. More recently, as a result of the Great Faunal Interchange between South America and North America, many xenarthran species went extinct. The thirty-one extant species belong to three groups: armadillos, sloths and anteaters. They share dental degeneration. However, the level of degeneration is variable. Anteaters entirely lack teeth, sloths have intermediately regressed teeth and most armadillos have a toothless premaxilla, as well as peg-like, single-rooted teeth that lack enamel in adult animals (Vizcaíno 2009). This diversity raises a number of questions about the evolution of dentition in these mammals. Unfortunately, the fossil record is too poor to provide refined information on the different stages of regressive evolution in these clades. In such cases, the identification of loss-of-function mutations and/or relaxed selection in genes related to a character regression can be very informative (Emerling and Springer 2014; Meredith et al. 2014; Policarpo et al. 2021). Indeed, shared and unique pseudogenes/relaxed selection can tell us to what extent regression has occurred in common ancestors and whether some changes are lineage-specific. In addition, the distribution of pseudogenes/relaxed selection on the branches of a phylogenetic tree is related to the evolutionary processes involved. A much higher density of pseudogenes in the most internal branches indicates that degeneration took place early and over a short period of time, consistent with selection against the presence of the morphological character with which they are associated, while pseudogenes distributed evenly in many internal and external branches suggest a more gradual process over many millions of years, in line with relaxed selection and fixation of loss-of-function mutations by genetic drift.

In this paper (Emerling et al. 2023), the authors examined the dynamics of decay of 11 dental genes that may parallel teeth regression. The analyses of the data reported in this paper clearly point to xenarthran teeth having repeatedly regressed in parallel in the three clades. In fact, no loss-of-function mutation is shared by all species examined. However, more genes should be studied to confirm the hypothesis that the common ancestor of extant xenarthrans had normal dentition. There are distinct patterns of gene loss in different lineages that are associated with the variation in dentition observed across the clades. These patterns of gene loss suggest that regressive evolution took place both gradually and in relatively rapid, discrete phases during the diversification of xenarthrans. This study underscores the utility of using pseudogenes to reconstruct evolutionary history of morphological characters when fossils are sparse.

References

Emerling CA, Gibb GC, Tilak M-K, Hughes JJ, Kuch M, Duggan AT, Poinar HN, Nachman MW, Delsuc F. 2023. Genomic data suggest parallel dental vestigialization within the xenarthran radiation. bioRxiv, 2022.12.09.519446, ver 2, peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2022.12.09.519446

Emerling CA, Springer MS. 2014. Eyes underground: Regression of visual protein networks in subterranean mammals. Molecular Phylogenetics and Evolution 78: 260-270. https://doi.org/10.1016/j.ympev.2014.05.016

Meredith RW, Zhang G, Gilbert MTP, Jarvis ED, Springer MS. 2014. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science 346: 1254390. https://doi.org/10.1126/science.1254390

Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, Dechaud C, Volff J-N, Cabau C, Klopp C, et al. 2021. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Molecular Biology and Evolution 38: 589-605. https://doi.org/10.1093/molbev/msaa249

Vizcaíno SF. 2009. The teeth of the “toothless”: novelties and key innovations in the evolution of xenarthrans (Mammalia, Xenarthra). Paleobiology 35: 343-366. https://doi.org/10.1666/0094-8373-35.3.343

Genomic data suggest parallel dental vestigialization within the xenarthran radiationChristopher A Emerling, Gillian C Gibb, Marie-Ka Tilak, Jonathan J Hughes, Melanie Kuch, Ana T Duggan, Hendrik N Poinar, Michael W Nachman, Frederic Delsuc<p style="text-align: justify;">The recent influx of genomic data has provided greater insights into the molecular basis for regressive evolution, or vestigialization, through gene loss and pseudogenization. As such, the analysis of gene degradati...Evolutionary genomics, VertebratesDidier Casane2022-12-12 16:01:57 View