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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
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 MS, 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, eaaw6671. https://doi.org/10.1126/sciadv.aaw6671

Ioannidis JPA (2005) Why most published research findings are false. PLOS Medicine, 2, 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, 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, 3643–3651. https://doi.org/10.1098/rspb.2012.0869

Nery MF, González DJ, Opazo JC (2013) How to make a dolphin: molecular signature of positive selection in cetacean genome. PLOS ONE, 8, e65491. https://doi.org/10.1371/journal.pone.0065491

Sun YB, Zhou WP, Liu HQ, Irwin DM, Shen YY, Zhang YP (2013) Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins. Genome Biology and Evolution, 5, 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, 827–839. https://doi.org/10.1093/gbe/evw037

Thewissen JGM, Cooper LN, George JC, Bajpai  (2009) From land to water: the origin of whales, dolphins, and porpoises. Evolution: Education and Outreach, 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 HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK, et al. (2014) Minke whale genome and aquatic adaptation in cetaceans. Nature Genetics, 46, 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
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
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
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High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4

Reference genome for the lichen-forming green alga Coccomyxa viridis SAG 216–4

Recommended by ORCID_LOGO based on reviews by Elisa Goldbecker, Fabian Haas and 2 anonymous reviewers

Green algae of the genus Coccomyxa (family Trebouxiophyceae) are extremely diverse in their morphology, habitat (i.e., in marine, freshwater, and terrestrial environments) and lifestyle, including free-living and mutualistic forms. Coccomyxa viridis (strain SAG 216–4) is a photobiont in the lichen Peltigera aphthosa, which was isolated in Switzerland more than 70 years ago (cf. SAG, the Culture Collection of Algae at the University of Göttingen, Germany). Despite the high diversity and plasticity in Coccomyxa, integrative taxonomic analyses led Darienko et al. (2015) to propose clear species boundaries. These authors also showed that symbiotic strains that form lichens evolved multiple times independently in Coccomyxa.

Using state-of-the-art sequencing data and bioinformatic methods, including Pac-Bio HiFi and ONT long reads, as well as Hi-C chromatin conformation information, Kraege et al. (2024) generated a high-quality genome assembly for the Coccomyxa viridis strain SAG 216–4. They reconstructed 19 complete nuclear chromosomes, flanked by telomeric regions, totaling 50.9 Mb, plus the plastid and mitochondrial genomes. The performed quality controls leave no doubt of the high quality of the genome assemblies and structural annotations. An interesting observation is the lack of conserved synteny with the close relative Coccomyxa subellipsoidea, but further comparative studies with additional Coccomyxa strains will be required to grasp the genomic evolution in this genus of green algae. This project is framed within the ERGA pilot project, which aims to establish a pan-European genomics infrastructure and contribute to cataloging genomic biodiversity and producing resources that can inform conservation strategies (Formenti et al. 2022). This complete reference genome represents an important step towards this goal, in addition to contributing to future genomic analyses of Coccomyxa more generally.

                                

References

Darienko T, Gustavs L, Eggert A, Wolf W, Pröschold T (2015) Evaluating the species boundaries of green microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) using integrative taxonomy and DNA barcoding with further implications for the species identification in environmental samples. PLOS ONE, 10, e0127838. https://doi.org/10.1371/journal.pone.0127838

Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel A-M, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M, European Reference Genome Atlas Consortium (2022) The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, 37, 197–202. https://doi.org/10.1016/j.tree.2021.11.008

Kraege A, Chavarro-Carrero EA, Guiglielmoni N, Schnell E, Kirangwa J, Heilmann-Heimbach S, Becker K, Köhrer K, WGGC Team, DeRGA Community, Schiffer P, Thomma BPHJ, Rovenich H (2024) High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga Coccomyxa viridis SAG 216-4. bioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.07.11.548521

High quality genome assembly and annotation (v1) of the eukaryotic terrestrial microalga *Coccomyxa viridis* SAG 216-4Anton Kraege, Edgar Chavarro-Carrero, Nadège Guiglielmoni, Eva Schnell, Joseph Kirangwa, Stefanie Heilmann-Heimbach, Kerstin Becker, Karl Köhrer, Philipp Schiffer, Bart P. H. J. Thomma, Hanna Rovenich<p>Unicellular green algae of the genus Coccomyxa are recognized for their worldwide distribution and ecological versatility. Most species described to date live in close association with various host species, such as in lichen associations. Howev...ERGA PilotIker Irisarri2023-11-09 11:54:43 View
03 Jul 2024
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T7 DNA polymerase treatment improves quantitative sequencing of both double-stranded and single-stranded DNA viruses

Improving the sequencing of single-stranded DNA viruses: Another brick for building Earth's complete virome encyclopedia

Recommended by based on reviews by Philippe Roumagnac and 3 anonymous reviewers

The wide adoption of high-throughput sequencing technologies has uncovered an astonishing diversity of viruses in most biosphere habitats. Among them, single-stranded DNA viruses are prevalent, infecting diverse hosts from all three domains of life (Malathi et al. 2014) with some species being highly pathogenic to animals or plants.

Sequencing of single-stranded DNA viruses requires a specific approach that usually leads to their over-representation compared to double-stranded DNA. The article from Billaud et al. (2024) addresses this challenge. It presents a novel and efficient method for converting single-stranded DNA to double-stranded DNA using T7 DNA polymerase before high-throughput virome sequencing. It compares this new method with the Phi29 polymerase method, demonstrating its advantages in the representation and accuracy of viral DNA content in well-defined synthetic phage mixtures and complex human virome samples from the stool. This T7 DNA polymerase treatment significantly improved the richness and abundance of the Microviridae fraction in their samples, suggesting a more comprehensive representation of viral diversity.

The article presents a compelling case for testing and adopting the T7 DNA polymerase methodology in preparing virome samples for shotgun sequencing. This novel approach, supported by comparative analysis with existing methodologies, represents a valuable contribution to metagenomics for characterizing virome diversity.

                       

References

Billaud M, Theodorou I, Lamy-Besnier Q, Shah SA, Lecointe F, Sordi LD, Paepe MD, Petit M-A (2024) T7 DNA polymerase treatment improves quantitative sequencing of both double-stranded and single-stranded DNA viruses. bioRxiv, ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.12.12.520144

Malathi VG, Renuka Devi P. (2019) ssDNA viruses: key players in global virome. Virus disease. 30: 3–12. https://doi.org/10.1007/s13337-019-00519-4 

 

T7 DNA polymerase treatment improves quantitative sequencing of both double-stranded and single-stranded DNA virusesMaud Billaud, Ilias Theodorou, Quentin Lamy-Besnier, Shiraz Shah, François Lecointe, Luisa De Sordi, Marianne De Paepe, Marie-Agnès Petit<p>Background: Bulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular s...Viruses and transposable elementsSebastien Massart2023-12-20 16:50:00 View
08 Nov 2022
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Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks

How to best call the somatic mosaic tree?

Recommended by based on reviews by 2 anonymous reviewers

Any multicellular organism is a molecular mosaic with some somatic mutations accumulated between cell lineages. Big long-lived trees have nourished this imaginary of a somatic mosaic tree, from the observation of spectacular phenotypic mosaics and also because somatic mutations are expected to potentially be passed on to gametes in plants (review in Schoen and Schultz 2019). The lower cost of genome sequencing now offers the opportunity to tackle the issue and identify somatic mutations in trees.

However, when it comes to characterizing this somatic mosaic from genome sequences, things become much more difficult than one would think in the first place. What separates cell lineages ontogenetically, in cell division number, or in time? How to sample clonal cell populations? How do somatic mutations distribute in a population of cells in an organ or an organ sample? Should they be fixed heterozygotes in the sample of cells sequenced or be polymorphic? Do we indeed expect somatic mutations to be fixed? How should we identify and count somatic mutations?

To date, the detection of somatic mutations has mostly been done with a single variant caller in a given study, and we have little perspective on how different callers provide similar or different results. Some studies have used standard SNP callers that assumed a somatic mutation is fixed at the heterozygous state in the sample of cells, with an expected allele coverage ratio of 0.5, and less have used cancer callers, designed to detect mutations in a fraction of the cells in the sample. However, standard SNP callers detect mutations that deviate from a balanced allelic coverage, and different cancer callers can have different characteristics that should affect their outcomes.

In order to tackle these issues, Schmitt et al. (2022) conducted an extensive simulation analysis to compare different variant callers. Then, they reanalyzed two large published datasets on pedunculate oak, Quercus robur.  The analysis of in silico somatic mutations allowed the authors to evaluate the performance of different variant callers as a function of the allelic fraction of somatic mutations and the sequencing depth. They found one of the seven callers to provide better and more robust calls for a broad set of allelic fractions and sequencing depths. The reanalysis of published datasets in oaks with the most effective cancer caller of the in silico analysis allowed them to identify numerous low-frequency mutations that were missed in the original studies.

I recommend the study of Schmitt et al. (2022) first because it shows the benefit of using cancer callers in the study of somatic mutations, whatever the allelic fraction you are interested in at the end. You can select fixed heterozygotes if this is your ultimate target, but cancer callers allow you to have in addition a valuable overview of the allelic fractions of somatic mutations in your sample, and most do as well as SNP callers for fixed heterozygous mutations. In addition, Schmitt et al. (2022) provide the pipelines that allow investigating in silico data that should correspond to a given study design, encouraging to compare different variant callers rather than arbitrarily going with only one. We can anticipate that the study of somatic mutations in non-model species will increasingly attract attention now that multiple tissues of the same individual can be sequenced at low cost, and the study of Schmitt et al. (2022) paves the way for questioning and choosing the best variant caller for the question one wants to address.

References

Schoen DJ, Schultz ST (2019) Somatic Mutation and Evolution in Plants. Annual Review of Ecology, Evolution, and Systematics, 50, 49–73. https://doi.org/10.1146/annurev-ecolsys-110218-024955

Schmitt S, Leroy T, Heuertz M, Tysklind N (2022) Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks. bioRxiv, 2021.10.11.462798. ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2021.10.11.462798

Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaksSylvain Schmitt, Thibault Leroy, Myriam Heuertz, Niklas Tysklind<p style="text-align: justify;">1. Mutation, the source of genetic diversity, is the raw material of evolution; however, the mutation process remains understudied, especially in plants. Using both a simulation and reanalysis framework, we set out ...Bioinformatics, PlantsNicolas BierneAnonymous, Anonymous2022-04-28 13:24:19 View
26 Jun 2024
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Transposable element expression with variation in sex chromosome number supports a toxic Y effect on human longevity

The number of Y chromosomes is positively associated with transposable element expression in humans, in line with the toxic Y hypothesis

Recommended by ORCID_LOGO based on reviews by 3 anonymous reviewers

The study of human longevity has long been a source of fascination for scientists, particularly in relation to the genetic factors that contribute to differences in lifespan between the sexes. One particularly intriguing area of research concerns the Y chromosome and its impact on male longevity. The Y chromosome expresses genes that are essential for male development and reproduction. However, it may also influence various physiological processes and health outcomes. It is therefore of great importance to investigate the impact of the Y chromosome on longevity. This may assist in elucidating the biological mechanisms underlying sex-specific differences in aging and disease susceptibility. As longevity research progresses, the Y chromosome's role presents a promising avenue for elucidating the complex interplay between genetics and aging.

Transposable elements (TEs), often referred to as "jumping genes", are DNA sequences that can move within the genome, potentially causing mutations and genomic instability. In young, healthy cells, various mechanisms, including DNA methylation and histone modifications, suppress TE activity to maintain genomic integrity. However, as individuals age, these regulatory mechanisms may deteriorate, leading to increased TE activity. This dysregulation could contribute to age-related genomic instability, cellular dysfunction, and the onset of diseases such as cancer. Understanding how TE repression changes with age is crucial for uncovering the molecular underpinnings of aging (De Cecco et al. 2013; Van Meter et al. 2014).

The lower recombination rates observed on Y chromosomes result in the accumulation of TE insertions, which in turn leads to an enrichment of TEs and potentially higher TE activity. To ascertain whether the number of Y chromosomes is associated with TE activity in humans, Teoli et al. (2024) studied the TE expression level, as a proxy of the TE activity, in several karyotype compositions (i.e. with differing numbers of Y chromosomes). They used transcriptomic data from blood samples collected in 24 individuals (six females 46,XX, six males 46,XY, eight males 47,XXY and four males 47,XYY). Even though they did not observe a significant correlation between the number of Y chromosomes and TE expression, their results suggest an impact of the presence of the Y chromosome on the overall TE expression. The presence of Y chromosomes also affected the type (family) of TE present/expressed. To ensure that the TE expression level was not biased by the expression of a gene in proximity due to intron retention or pervasive intragenic transcription, the authors also tested whether the TE expression variation observed between the different karyotypes could be explained by gene (i.e. here non-TE gene) expression. 

As TE repression mechanisms are known to decrease over time, the authors also tested whether TE repression is weaker in older individuals, which would support a compelling link between genomic stability and aging. They investigated the TE expression differently between males and females, hypothesizing that old males should exhibit a stronger TE activity than old females. Using selected 45 males (47,XY) and 35 females (46,XX) blood samples of various ages (from 20 to 70) from the Genotype-Tissue Expression (GTEx) project, the authors studied the effect of age on TE expression using 10-year range to group the study subjects. Based on these data, they fail to find an overall increase of TE expression in old males compared to old females.

Notwithstanding the small number of samples, the study is well-designed and innovative, and its findings are highly promising. It marks an initial step towards understanding the impact of Y-chromosome ‘toxicity’ on human longevity. Despite the relatively small sample size, which is a consequence of the difficulty of obtaining samples from individuals with sex chromosome aneuploidies, the results are highly intriguing and will be of interest to a broad range of biologists.

                                             

References

De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, Peterson AL, Kreiling JA, Neretti N, Sedivy JM (2013) Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell, 12, 247–256. https://doi.org/10.1111/acel.12047

Teoli J, Merenciano M, Fablet M, Necsulea A, Siqueira-de-Oliveira D, Brandulas-Cammarata A, Labalme A, Lejeune H, Lemaitre J-F, Gueyffier F,  Sanlaville D, Bardel C, Vieira C, Marais GAB, Plotton I (2024) Transposable element expression with variation in sex chromosome number supports a toxic Y effect on human longevity. bioRxiv, ver. 5 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.08.03.550779

Van Meter M, Kashyap M, Rezazadeh S, Geneva AJ, Morello TD, Seluanov A,  Gorbunova V (2014) SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age. Nature Communications, 5, 5011. https://doi.org/10.1038/ncomms6011

 

 

Transposable element expression with variation in sex chromosome number supports a toxic Y effect on human longevityJordan Teoli, Miriam Merenciano, Marie Fablet, Anamaria Necsulea, Daniel Siqueira-de-Oliveira, Alessandro Brandulas-Cammarata, Audrey Labalme, Hervé Lejeune, Jean-François Lemaitre, François Gueyffier, Damien Sanlaville, Claire Bardel, Cristina Vi...<p>Why women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic ...Evolutionary genomicsAnna-Sophie Fiston-LavierAnonymous, Igor Rogozin , Paul Jay , Anonymous2023-08-18 15:01:38 View
18 Feb 2021
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Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks

Using small fragments to discover old TE remnants: the Duster approach empowers the TE detection

Recommended by ORCID_LOGO based on reviews by Josep Casacuberta and 1 anonymous reviewer

Transposable elements are the raw material of the dark matter of the genome, the foundation of the next generation of genes and regulation networks". This sentence could be the essence of the paper of Baud et al. (2021). Transposable elements (TEs) are endogenous mobile genetic elements found in almost all genomes, which were discovered in 1948 by Barbara McClintock (awarded in 1983 the only unshared Medicine Nobel Prize so far). TEs are present everywhere, from a single isolated copy for some elements to more than millions for others, such as Alu. They are founders of major gene lineages (HET-A, TART and telomerases, RAG1/RAG2 proteins from mammals immune system; Diwash et al, 2017), and even of retroviruses (Xiong & Eickbush, 1988). However, most TEs appear as selfish elements that replicate, land in a new genomic region, then start to decay and finally disappear in the midst of the genome, turning into genomic ‘dark matter’ (Vitte et al, 2007). The mutations (single point, deletion, recombination, and so on) that occur during this slow death erase some of their most notable features and signature sequences, rendering them completely unrecognizable after a few million years. Numerous TE detection tools have tried to optimize their detection (Goerner-Potvin & Bourque, 2018), but further improvement is definitely challenging. This is what Baud et al. (2021) accomplished in their paper. They used a simple, elegant and efficient k-mer based approach to find small signatures that, when accumulated, allow identifying very old TEs. Using this method, called Duster, they improved the amount of annotated TEs in the model plant Arabidopsis thaliana by 20%, pushing the part of this genome occupied by TEs up from 40 to almost 50%. They further observed that these very old Duster-specific TEs (i.e., TEs that are only detected by Duster) are, among other properties, close to genes (much more than recent TEs), not targeted by small RNA pathways, and highly associated with conserved regions across the rosid family. In addition, they are highly associated with flowering or stress response genes, and may be involved through exaptation in the evolution of responses to environmental changes. TEs are not just selfish elements: more and more studies have shown their key role in the evolution of their hosts, and tools such as Duster will help us better understand their impact.
 

References

Baud, A., Wan, M., Nouaud, D., Francillonne, N., Anxolabéhère, D. and Quesneville, H. (2021). Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks. bioRxiv, 547877, ver. 5 peer-reviewed and recommended by PCI Genomics.doi: https://doi.org/10.1101/547877
 
Bourque, G., Burns, K.H., Gehring, M. et al. (2018) Ten things you should know about transposable elements. Genome Biology 19:199. doi: https://doi.org/10.1186/s13059-018-1577-z
 
Goerner-Potvin, P., Bourque, G. Computational tools to unmask transposable elements. Nature Reviews Genetics 19:688–704 (2018) https://doi.org/10.1038/s41576-018-0050-x
 
Jangam, D., Feschotte, C. and Betrán, E. (2017) Transposable element domestication as an adaptation to evolutionary conflicts. Trends in Genetics 33:817-831. doi: https://doi.org/10.1016/j.tig.2017.07.011
 
Vitte, C., Panaud, O. and Quesneville, H. (2007) LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics 8:218. doi: https://doi.org/10.1186/1471-2164-8-218
 
Xiong, Y. and Eickbush, T. H. (1988) Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Molecular Biology and Evolution 5: 675–690. doi: https://doi.org/10.1093/oxfordjournals.molbev.a040521

Traces of transposable element in genome dark matter co-opted by flowering gene regulation networksAgnes Baud, Mariene Wan, Danielle Nouaud, Nicolas Francillonne, Dominique Anxolabehere, Hadi Quesneville<p>Transposable elements (TEs) are mobile, repetitive DNA sequences that make the largest contribution to genome bulk. They thus contribute to the so-called 'dark matter of the genome', the part of the genome in which nothing is immediately recogn...Bioinformatics, Evolutionary genomics, Functional genomics, Plants, Structural genomics, Viruses and transposable elementsFrancois SabotAnonymous, Josep Casacuberta2020-04-07 17:12:12 View