Böhne et al. (2024) do not present a classical scientific paper per se but a report on how the European Reference Genome Atlas (ERGA) aims to deal with sampling and sample information, i.e. metadata.

As the goal of ERGA is to provide an almost fully representative set of reference genomes representative of European biodiversity to serve many research areas in biology, they have to be really exhaustive. In this regard, in addition to providing sample metadata recording guidelines, they also discuss the biases existing in sampling and sequencing projects.

The first task for such a project is to be sure that the data they generate will be usable and available in the future (“[in] perpetuity", Böhne et al. 2024). The authors deployed a very efficient pipeline for conserving information on sampling: location, physical information, copies of tissues and of DNA, shipping, legal/ethical aspects regarding the Nagoya Protocol, etc., alongside a best-practice manual. This effort is linked to practical guides for the DNA extraction of specific taxa. More generally, these details enable “Findable, Accessible, Interoperable, and Reusable” (FAIR) principles (Wilkinson et al. 2016) to be followed.

An important aspect of this paper, in addition to practical points, is the reflection upon the different biases inherent to the choice of sequenced samples. Acknowledging their own biases with regards to DNA extraction protocol efficiency, small genome size choice, as well as the availability of material (Nagoya Protocol aspects) and material transfer efficiency, the authors recommend in the future to not survey biodiversity by selecting one’s favorite samples or species, but also considering "orphan" taxa. Some of these "orphan" taxonomic groups belong to non-arthropod invertebrates but internal disparities are also prominent within other taxa. Finally, the implementation of the "Collective benefit, Authority to control, Responsibility, and Ethics" (CARE) principles (Carroll et al. 2021) will allow Indigenous rights to be considered when prioritizing samples, and to enable their "knowledge systems to permeate throughout the process of reference genome production and beyond" (Böhne et al. 2024).

Last, but not least, as ERGA, including its Sampling and Sample Processing committee, is a large collective effort, it is very refreshing to read a paper starting with the acknowledgements and the roles of each member.

References

Böhne A, Fernández R, Leonard JA, McCartney AM, McTaggart S, Melo-Ferreira J, Monteiro R, Oomen RA, Pettersson OV, Struck TH (2024) Contextualising samples: Supporting reference genomes of European biodiversity through sample and associated metadata collection. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.06.28.546652

Carroll SR, Herczog E, Hudson M, Russell K, Stall S (2021) Operationalizing the CARE and FAIR Principles for Indigenous data futures. Scientific Data, 8, 108. https://doi.org/10.1038/s41597-021-00892-0

Wilkinson MD, Dumontier M, Aalbersberg IjJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S-A, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B (2016) The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18

The advent of High Throughput Sequencing (HTS) since the last decade has revealed previously unsuspected diversity of viruses as well as their (sometimes) unexpected presence in some healthy individuals. These results demonstrate that genomics offers a powerful tool for studying viruses at the individual level, allowing an in-depth inventory of those that are infecting an organism. Such approaches make it possible to study viromes with an unprecedented level of detail, both qualitative and quantitative, which opens new venues for analyses of viruses of humans, animals and plants. Consequently, the diagnostic field is using more and more HTS, fueling the need for efficient and reliable bioinformatics tools. 

Many such tools have already been developed, but in plant disease diagnostics, validation of the bioinformatics pipelines used for the detection of viruses in HTS datasets is still in its infancy. There is an urgent need for benchmarking the different tools and algorithms using well-designed reference datasets generated for this purpose. This is a crucial step to move forward and to improve existing solutions toward well-standardized bioinformatics protocols. This context has led to the creation of the Plant Health Bioinformatics Network (PHBN), a Euphresco network project aiming to build a bioinformatics community working on plant health. One of their objectives is to provide researchers with open-access reference datasets allowing to compare and validate virus detection pipelines. 

In this framework, Tamisier et al. [1] present real, semi-artificial, and completely artificial datasets, each aimed at addressing challenges that could affect virus detection. These datasets comprise real RNA-seq reads from virus-infected plants as well as simulated virus reads. Such a work, providing open-access datasets for benchmarking bioinformatics tools, should be encouraged as they are key to software improvement as demonstrated by the well-known success story of the protein structure prediction community: their pioneer community-wide effort, called Critical Assessment of protein Structure Prediction (CASP)[2], has been providing research groups since 1994 with an invaluable way to objectively test their structure prediction methods, thereby delivering an independent assessment of state-of-art protein-structure modelling tools. Following this success, many other bioinformatic community developed similar “competitions”, such as RNA-puzzles [3] to predict RNA structures, Critical Assessment of Function Annotation [4] to predict gene functions, Critical Assessment of Prediction of Interactions [5] to predict protein-protein interactions, Assemblathon [6] for genome assembly, etc. These are just a few examples from a long list of successful initiatives. Such efforts enable rigorous assessments of tools, stimulate the developers’ creativity, but also provide user communities with a state-of-art evaluation of available tools.

Inspired by these success stories, the authors propose a “VIROMOCK challenge” [7], asking researchers in the field to test their tools and to provide feedback on each dataset through a repository. This initiative, if well followed, will undoubtedly improve the field of virus detection in plants, but also probably in many other organisms. This will be a major contribution to the field of viruses, leading to better diagnostics and, consequently, a better understanding of viral diseases, thus participating in promoting human, animal and plant health.   

References

[1] Tamisier, L., Haegeman, A., Foucart, Y., Fouillien, N., Al Rwahnih, M., Buzkan, N., Candresse, T., Chiumenti, M., De Jonghe, K., Lefebvre, M., Margaria, P., Reynard, J.-S., Stevens, K., Kutnjak, D. and Massart, S. (2021) Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection. Zenodo, 4273791, version 4 peer-reviewed and recommended by Peer community in Genomics. doi: https://doi.org/10.5281/zenodo.4273791

[2] Critical Assessment of protein Structure Prediction” (CASP) - https://en.wikipedia.org/wiki/CASP

[3] RNA-puzzles - https://www.rnapuzzles.org

[4] Critical Assessment of Function Annotation (CAFA) - https://en.wikipedia.org/wiki/Critical_Assessment_of_Function_Annotation

[5] Critical Assessment of Prediction of Interactions (CAPI) - https://en.wikipedia.org/wiki/Critical_Assessment_of_Prediction_of_Interactions

[6] Assemblathon - https://assemblathon.org

[7] VIROMOCK challenge - https://gitlab.com/ilvo/VIROMOCKchallenge

Transposable elements (TEs) are mobile genetic elements with an intrinsic mutagenic potential that influences the physiology of any cell type, whether somatic or germinal. Measuring TE expression is a fundamental prerequisite for analysing the processes leading to the activity of TE-derived sequences. This applies to both old and recent TEs, as even if they are deficient in mobilisation, transcription of TE sequences alone can impact neighbouring gene expression and other cellular activities.

In terms of TE physiology, transcription is crucial for mobilisation activity. The transcription of some TEs can be tissue-specific and associated with splicing events, as exemplified by the P-element isoforms in the fruit fly (Laski et al. 1986). Regarding host cell physiology, TE transcripts can include nearby exons, with or without splicing, and such chimeric transcripts can significantly alter gene activity. Thus, quantitative and qualitative analyses must be conducted to assess TE function and how they can modify genomic activities. Yet, due to the polymorphic, interspersed, and repetitive nature of TE sequences, the quantitative and qualitative analysis of TE transcript levels using short-read sequencing remains challenging (Lanciano and Cristofari 2020).

In this context, Rebollo et al. (2024) employed nanopore long-read sequencing to analyse cDNAs derived from Drosophila melanogaster germline RNAs. The authors constructed two long-read cDNA libraries from pooled ovaries and testes using a protocol to obtain full-length cDNAs and sequenced them separately. They carefully compared their results with their short-read datasets. Overall, their observations corroborate known patterns of germline-specific expression of certain TEs and provide initial evidence of novel spliced TE transcript isoforms in Drosophila.

Rebollo and colleagues have provided a well-documented and detailed analysis of their results, which will undoubtedly benefit the scientific community. They presented the challenges and limitations of their approach, such as the length of the transcripts, and provided a reproducible analysis workflow that will enable better characterisation of TE expression using long-read technology.

Despite the small number of samples and limited sequencing depth, this pioneering study strikingly demonstrates the potential of long-read sequencing for the quantitative and qualitative analysis of TE transcription, a technology that will facilitate a better understanding of the transposon landscape.

              
References

Lanciano S, Cristofari G (2020) Measuring and interpreting transposable element expression. Nature Reviews Genetics, 21, 721–736. https://doi.org/10.1038/s41576-020-0251-y

Laski FA, Rio DC, Rubin GM (1986) Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing. Cell, 44, 7–19. https://doi.org/10.1016/0092-8674(86)90480-0

Rebollo R, Gerenton P, Cumunel E, Mary A, Sabot F, Burlet N, Gillet B, Hughes S, Oliveira DS, Goubert C, Fablet M, Vieira C, Lacroix V (2024) Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues. bioRxiv, ver.4 peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2023.05.27.542554

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

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