Fekete et al. (2024) generated a chromosome-level reference genome assembly for the mountain hare (Lepus timidus). This represents a significant advancement in genomic research for non-model organisms, achieving high quality through advanced sequencing and curation techniques. This achievement serves as a foundational blueprint for future efforts in other species, particularly those with ecological or evolutionary importance. The assembly has high continuity and completeness, with an N50 scaffold length of 125.8 Mb and a contig N50 of 4.9 Mb, meeting the Earth BioGenome Project's stringent criteria for reference-grade genomes (Mc Cartney et al., 2024). The combination of PacBio HiFi sequencing and Hi-C scaffolding techniques enabled robust assembly and chromosomal scaffolding of all 23 autosomes and the X and Y sex chromosomes. Additionally, manual curation enhanced the assembly quality, accurately representing genomic sequences. Although the genome provides valuable structural insights, the limited functional annotations highlight a need for further investigation into the genetic underpinnings of the ecological and adaptive traits of the mountain hare.

The ecological and evolutionary implications of resolving this genome are considerable, particularly given the mountain hare’s adaptations to cold, snowy environments and its role in boreal ecosystems. The assembly facilitates the study of adaptations, such as camouflage and snowshoe-like feet, which are critical for survival in its rapidly changing habitat. Comparative genomic analyses reveal the evolutionary relationship between Lepus timidus and closely related species, such as the brown hare (L. europaeus) and Irish hare (L. t. hibernicus), providing insights into gene flow, hybridization, and speciation. These findings have practical implications for conservation genetics, particularly for subspecies threatened by habitat loss and climate change. However, the study does not identify specific adaptive loci or functional variants, limiting its immediate applicability to understanding the molecular basis of traits crucial for survival in extreme environments. Expanding the functional annotation of this genome would significantly enhance its utility in conservation and ecological genomics. Moreover, the high repetitive element content (42.35%) underscores the need for detailed annotation to facilitate downstream studies. These issues suggest that additional refinement and validation are warranted. Despite these limitations, the assembly is invaluable for studying genetic adaptations, hybridization, and hare conservation. Future research should focus on functional annotation, population-level comparisons, and targeted studies of ecological traits to fully realize the potential of this high-quality reference genome.

References

Fekete Z, Absolon DE, Michell C, Wood JMD, Goffart S, Pohjoismäki JLO (2024) Chromosome-level reference genome assembly for the mountain hare (Lepus timidus). bioRxiv, ver. 2 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2024.06.10.598177

Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitão HG, Diedericks G, Kirangwa J, Morselli M, Salces-Ortiz J, Escudero N, Iannucci A, Natali C, Svardal H, Fernández R, De Pooter T, Joris G, Strazisar M, Wood JMD, Herron KE, …, Mazzoni CJ (2024) The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj Biodiversity, 3, 28. https://doi.org/10.1038/s44185-024-00054-6

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 ant species Cataglyphis hispanica is remarkably well adapted to arid habitats of the Iberian Peninsula where two hybridogenetic lineages co-occur, i.e., queens mating with males from the other lineage produce only non-reproductive hybrid workers whereas reproductive males and females are produced by parthenogenesis (Lavanchy and Schwander, 2019). For these two reasons, the genomes of these lineages, Chis1 and Chis2, are potential gold mines to explore the genetic bases of thermal adaptation and the evolution of alternative reproductive modes.

Nowadays, sequencing technology enables assembling all kinds of genomes provided genomic DNA can be extracted. More difficult to achieve is high-quality assemblies with just as high-quality annotations that are readily available to the community to be used and re-used at will (Byrne et al., 2019; Salzberg, 2019). The challenge was successfully completed by Darras and colleagues, the generated resource being fully available to the community, including scripts and command lines used to obtain the proposed results.

The authors particularly describe that lineage Chis2 has 27 chromosomes, against 26 or 27 for lineage Chis1, with a Robertsonian translocation identified by chromosome conformation capture (Duan et al., 2010, 2012) in the two Queens sequenced. Transcript-supported gene annotation provided 11,290 high-quality gene models. In addition, an ant-tailored annotation pipeline identified 56 different families of repetitive elements in both Chis1 and Chis2 lineages of C. hispanica spread in a little over 15 % of the genome. Altogether, the genomes of Chis1 and Chis2 are highly similar and syntenic, with some level of polymorphism raising questions about their evolutionary story timeline. In particular, the uniform distribution of polymorphisms along the genomes shakes up a previous hypothesis of hybridogenetic lineage pairs determined by ancient non-recombining regions (Linksvayer, Busch and Smith, 2013).

I recommend this paper because the science behind is both solid and well-explained. The provided resource is of high quality, and accompanied by a critical exploration of the perspectives brought by the results. These genomes are excellent resources to now go further in exploring the possible events at the genome level that accompanied the remarkable thermal adaptation of the ants Cataglyphis, as well as insights into the genetics of hybridogenetic lineages.

Beyond the scientific value of the resources and insights provided by the work performed, I also recommend this article because it is an excellent example of Open Science (Allen and Mehler, 2019; Sarabipour et al., 2019), all data methods and tools being fully and easily accessible to whoever wants/needs it. 

References

Allen C, Mehler DMA (2019) Open science challenges, benefits and tips in early career and beyond. PLOS Biology, 17, e3000246. https://doi.org/10.1371/journal.pbio.3000246

Byrne A, Cole C, Volden R, Vollmers C (2019) Realizing the potential of full-length transcriptome sequencing. Philosophical Transactions of the Royal Society B: Biological Sciences, 374, 20190097. https://doi.org/10.1098/rstb.2019.0097

Darras H, de Souza Araujo N, Baudry L, Guiglielmoni N, Lorite P, Marbouty M, Rodriguez F, Arkhipova I, Koszul R, Flot J-F, Aron S (2022) Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants. bioRxiv, 2022.01.07.475286, ver. 3 peer-reviewed and recommended by Peer community in Genomics. https://doi.org/10.1101/2022.01.07.475286

Duan Z, Andronescu M, Schutz K, Lee C, Shendure J, Fields S, Noble WS, Anthony Blau C (2012) A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes. Methods, 58, 277–288. https://doi.org/10.1016/j.ymeth.2012.06.018

Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS (2010) A three-dimensional model of the yeast genome. Nature, 465, 363–367. https://doi.org/10.1038/nature08973

Lavanchy G, Schwander T (2019) Hybridogenesis. Current Biology, 29, R9–R11. https://doi.org/10.1016/j.cub.2018.11.046

Linksvayer TA, Busch JW, Smith CR (2013) Social supergenes of superorganisms: Do supergenes play important roles in social evolution? BioEssays, 35, 683–689. https://doi.org/10.1002/bies.201300038

Salzberg SL (2019) Next-generation genome annotation: we still struggle to get it right. Genome Biology, 20, 92. https://doi.org/10.1186/s13059-019-1715-2

Sarabipour S, Debat HJ, Emmott E, Burgess SJ, Schwessinger B, Hensel Z (2019) On the value of preprints: An early career researcher perspective. PLOS Biology, 17, e3000151. https://doi.org/10.1371/journal.pbio.3000151

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​

Parasitic worms infect billions of animals worldwide. While parasitism is now considered a context-dependent relation along a symbiosis continuum, most of these parasitic worms, also known as helminths, can cause diseases that have a significant impact (Hopkins et al. 2017; Selzer, Epe 2021). When considering livestock animals, these impacts have a high economic cost, and therefore, prophylactic drugs are widely used (Selzer and Epe 2021). Consequently, drug resistance has become increasingly common across all parasites and concerns about drug effects on non-target organisms have been raised (de Souza and Guimarães 2022). This is why understanding the relationship between parasitic worms and their animal hosts and the diseases they cause at the genetic and molecular level is high on the agenda of parasitologists (Doyle 2022). The development of genomics resources plays a pivotal role in this agenda and is at the origin of Sallé and colleagues' article (2025).

The most common intestinal parasites in equids are helminths of the cyathostomin nematode complex. These are the primary parasitic cause of death in young horses and also exhibit a reduced sensitivity to anthelmintic drugs. Therefore, Sallé and colleagues embarked on the arduous journey to build a reference annotated genome of the Cylicocylus nassatus nematode. They used cutting-edge molecular genetics methods to amplify and sequence the genome of a single individual and obtained chromosomal-level contiguity using Hi-C technology for six chromosomes and an assembly of 514.7 Mbp. Remarkably, transposable elements occupy more than half of the C. nassatus genome and may have led to an increase in genome size in this nematode. In parallel, the authors built a gene catalogue using transcriptomic data, reaching a BUSCO gene completion score of 94.1% with 22,718 protein-coding genes. They quantified allele frequencies based on the resequencing of nine populations, including an ancient Egyptian worm from the 19th century, indicating a recent loss of genetic diversity in European cyathostomin even if geographical sampling  was limited. They also analysed transcriptomic differences between sexes and found differences linked with drug treatment. While there may be confounding effects due to global differences between sex that could explain this finding, these results will likely fuel future transcriptomic analyses investigating the response to antiparasitic drugs.

The Cylicocylus nassatus genome assembly obtained will be invaluable for studying nematode genome evolution and analysing the genetic and molecular basis of drug resistance in these parasites. 

References

Doyle SR (2022) Improving helminth genome resources in the post-genomic era. Trends in Parasitology, 38, 831–840. https://doi.org/10.1016/j.pt.2022.06.002

Hopkins SR, Wojdak JM, Belden LK (2017) Defensive symbionts mediate host–parasite interactions at multiple scales. Trends in Parasitology, 33, 53–64. https://doi.org/10.1016/j.pt.2016.10.003

Sallé G, Courtot É, Cabau C, Parrinello H, Serreau D, Reigner F, Gesbert A, Jacquinot L, Lenhof O, Aimé A, Picandet V, Kuzmina T, Holovachov O, Bellaw J, Nielsen MK, Samson-Himmelstjerna G von, Valière S, Gislard M, Lluch J, Kuchly C, Klopp C (2024) Spatio-temporal diversity and genetic architecture of pyrantel resistance in Cylicocyclus nassatus, the most abundant horse parasite. bioRxiv, ver. 2 peer-reviewed and recommended by PCI Genomics https://doi.org/10.1101/2023.07.19.549683

Selzer PM, Epe C (2021) Antiparasitics in animal health: quo vadis? Trends in Parasitology, 37, 77–89. https://doi.org/10.1016/j.pt.2020.09.004

de Souza RB, Guimarães JR (2022) Effects of avermectins on the environment based on its toxicity to plants and soil invertebrates–a review. Water, Air, and Soil Pollution, 233, 259. https://doi.org/10.1007/s11270-022-05744-0