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

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

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

The genomics era has pushed forward our understanding of fungal biology. Much progress has been made in unraveling new gene functions and pathways, as well as the evolution or adaptation of fungi to their hosts or environments through population studies (Hartmann et al. 2019; Gladieux et al. 2018). Closing gaps more systematically in draft genomes using the most recent long-read technologies now seems the new standard, even with fungal species presenting complex genome structures (e.g. large and highly repetitive dikaryotic genomes; Duan et al. 2022). Understanding the genomic dynamics underlying host specialization in phytopathogenic fungi is of utmost importance as it may open new avenues to combat diseases. A strong host specialization is commonly observed for biotrophic and hemi-biotrophic fungal species or for necrotrophic fungi with a narrow host range, whereas necrotrophic fungi with broad host range are considered generalists (Liang and Rollins, 2018; Newman and Derbyshire, 2020). However, some degrees of specialization towards given hosts have been reported in generalist fungi and the underlying mechanisms remain to be determined.

Botrytis cinerea is a polyphagous necrotrophic phytopathogen with a particularly wide host range and it is notably responsible for grey mould disease on many fruits, such as tomato and grapevine. Because of its importance as a plant pathogen, its relatively small genome size and its taxonomical position, it has been targeted for early genome sequencing and a first reference genome was provided in 2011 (Amselem et al. 2011). Other genomes were subsequently sequenced for other strains, and most importantly a gapless assembled version of the initial reference genome B05.10 was provided to the community (van Kan et al. 2017). This genomic resource has supported advances in various aspects of the biology of B. cinerea such as the production of specialized metabolites, which plays an important role in host-plant colonization, or more recently in the production of small RNAs which interfere with the host immune system, representing a new class of non-proteinaceous virulence effectors (Dalmais et al. 2011; Weiberg et al. 2013).

In the present study, Simon et al. (2022) use PacBio long-read sequencing for Sl3 and Vv3 strains, which represent genetic clusters in B. cinerea populations found on tomato and grapevine. The authors combined these complete and high-quality genome assemblies with the B05.10 reference genome and population sequencing data to perform a comparative genomic analysis of specialization towards the two host plants. Transposable elements generate genomic diversity due to their mobile and repetitive nature and they are of utmost importance in the evolution of fungi as they deeply reshape the genomic landscape (Lorrain et al. 2021). Accessory chromosomes are also known drivers of adaptation in fungi (Möller and Stukenbrock, 2017). Here, the authors identify several genomic features such as the presence of different sets of accessory chromosomes, the presence of differentiated repertoires of transposable elements, as well as related small RNAs in the tomato and grapevine populations, all of which may be involved in host specialization. Whereas core chromosomes are highly syntenic between strains, an accessory chromosome validated by pulse-field electrophoresis is specific of the strains isolated from grapevine. Particularly, they show that two particular retrotransposons are discriminant between the strains and that they allow the production of small RNAs that may act as effectors. The discriminant accessory chromosome of the Vv3 strain harbors one of the unraveled retrotransposons as well as new genes of yet unidentified function.

I recommend this article because it perfectly illustrates how efforts put into generating reference genomic sequences of higher quality can lead to new discoveries and allow to build strong hypotheses about biology and evolution in fungi. Also, the study combines an up-to-date genomics approach with a classical methodology such as pulse-field electrophoresis to validate the presence of accessory chromosomes. A major input of this investigation of the genomic determinants of B. cinerea is that it provides solid hints for further analysis of host-specialization at the population level in a broad-scale phytopathogenic fungus.

References

Amselem J, Cuomo CA, Kan JAL van, Viaud M, Benito EP, Couloux A, Coutinho PM, Vries RP de, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier J-M, Quévillon E, Sharon A, Simon A, Have A ten, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Silva CD, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun M-H, Dickman M (2011) Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLOS Genetics, 7, e1002230. https://doi.org/10.1371/journal.pgen.1002230

Dalmais B, Schumacher J, Moraga J, Le Pêcheur P, Tudzynski B, Collado IG, Viaud M (2011) The Botrytis cinerea phytotoxin botcinic acid requires two polyketide synthases for production and has a redundant role in virulence with botrydial. Molecular Plant Pathology, 12, 564–579. https://doi.org/10.1111/j.1364-3703.2010.00692.x

Duan H, Jones AW, Hewitt T, Mackenzie A, Hu Y, Sharp A, Lewis D, Mago R, Upadhyaya NM, Rathjen JP, Stone EA, Schwessinger B, Figueroa M, Dodds PN, Periyannan S, Sperschneider J (2022) Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data. Genome Biology, 23, 84. https://doi.org/10.1186/s13059-022-02658-2

Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun M-H, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E (2018) Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio, 9, e01219-17. https://doi.org/10.1128/mBio.01219-17

Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T (2019) Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. Annual Review of Phytopathology, 57, 431–457. https://doi.org/10.1146/annurev-phyto-082718-095947

Liang X, Rollins JA (2018) Mechanisms of Broad Host Range Necrotrophic Pathogenesis in Sclerotinia sclerotiorum. Phytopathology®, 108, 1128–1140. https://doi.org/10.1094/PHYTO-06-18-0197-RVW

Lorrain C, Oggenfuss U, Croll D, Duplessis S, Stukenbrock E (2021) Transposable Elements in Fungi: Coevolution With the Host Genome Shapes, Genome Architecture, Plasticity and Adaptation. In: Encyclopedia of Mycology (eds Zaragoza Ó, Casadevall A), pp. 142–155. Elsevier, Oxford. https://doi.org/10.1016/B978-0-12-819990-9.00042-1

Möller M, Stukenbrock EH (2017) Evolution and genome architecture in fungal plant pathogens. Nature Reviews Microbiology, 15, 756–771. https://doi.org/10.1038/nrmicro.2017.76

Newman TE, Derbyshire MC (2020) The Evolutionary and Molecular Features of Broad Host-Range Necrotrophy in Plant Pathogenic Fungi. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.591733

Simon A, Mercier A, Gladieux P, Poinssot B, Walker A-S, Viaud M (2022) Botrytis cinerea strains infecting grapevine and tomato display contrasted repertoires of accessory chromosomes, transposons and small RNAs. bioRxiv, 2022.03.07.483234, ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.03.07.483234

Van Kan JAL, Stassen JHM, Mosbach A, Van Der Lee TAJ, Faino L, Farmer AD, Papasotiriou DG, Zhou S, Seidl MF, Cottam E, Edel D, Hahn M, Schwartz DC, Dietrich RA, Widdison S, Scalliet G (2017) A gapless genome sequence of the fungus Botrytis cinerea. Molecular Plant Pathology, 18, 75–89. https://doi.org/10.1111/mpp.12384

Weiberg A, Wang M, Lin F-M, Zhao H, Zhang Z, Kaloshian I, Huang H-D, Jin H (2013) Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways. Science, 342, 118–123. https://doi.org/10.1126/science.1239705

Nonhost resistance is a common form of disease resistance exhibited by plants against microorganisms that are pathogenic to other plant species [1]. Apples and pears are two closely related species belonging to Rosaceae family, both affected by scab disease caused by fungal pathogens in the Venturia genus. These pathogens appear to be highly host-specific. While apples are nonhosts for Venturia pyrina, pears are nonhosts for Venturia inaequalis. To date, the molecular bases of scab nonhost resistance in apple and pear have not been elucidated.

This preprint by Vergne, et al (2022) [2] analyzed nonhost resistance symptoms in apple/V. pyrina and pear/V. inaequalis interactions as well as their transcriptomic responses. Interestingly, the author demonstrated that the nonhost apple/V. pyrina interaction was almost symptomless while hypersensitive reactions were observed for pear/V. inaequalis interaction. The transcriptomic analyses also revealed a number of differentially expressed genes (DEGs) that corresponded to the severity of the interactions, with very few DEGs observed during the apple/V. pyrina interaction and a much higher number of DEGs during the pear/V. inaequalis interaction.

This type of reciprocal host-pathogen interaction study is valuable in gaining new insights into how plants interact with microorganisms that are potential pathogens in related species. A few processes appeared to be involved in the pear resistance against the nonhost pathogen V. inaequalis at the transcriptomic level, such as stomata closure, modification of cell wall and production of secondary metabolites as well as phenylpropanoids. Based on the transcriptomics changes during the nonhost interaction, the author compared the responses to those of host-pathogen interactions and revealed some interesting findings. They proposed a series of cascading effects in pear induced by the presence of V. inaequalis, which I believe helps shed some light on the basic mechanism for nonhost resistance.

I am recommending this study because it provides valuable information that will strengthen our understanding of nonhost resistance in the Rosaceae family and other plant species. The knowledge gained here may be applied to genetically engineer plants for a broader resistance against a number of pathogens in the future.​

References

1. Senthil-Kumar M, Mysore KS (2013) Nonhost Resistance Against Bacterial Pathogens: Retrospectives and Prospects. Annual Review of Phytopathology, 51, 407–427. https://doi.org/10.1146/annurev-phyto-082712-102319

2. Vergne E, Chevreau E, Ravon E, Gaillard S, Pelletier S, Bahut M, Perchepied L (2022) Phenotypic and transcriptomic analyses reveal major differences between apple and pear scab nonhost resistance. bioRxiv, 2021.06.01.446506, ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2021.06.01.446506