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 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.

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

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 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

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