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 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

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

The paper from Silva et al. (2023) provides new insights into the genetic bases of natural resistance of rice to the Rice Hoja Blanca (RHB) disease, one of its most serious diseases in tropical countries of the American continent and the Caribbean. This disease is caused by the Rice Hoja Blanca Virus, or RHBV, the vector of which is the planthopper insect Tagosodes orizicolus Müir. It is responsible for serious damage to the rice crop (Morales and Jennings 2010). The authors take a Quantitative Trait Loci (QTL) detection approach to find genomic regions statistically associated with the resistant phenotype. To this aim, they use four resistant x susceptible crosses (the susceptible parent being the same in all four crosses) to maximize the chances to find new QTLs. The F2 populations derived from the crosses are genotyped using Single Nucleotide Polymorphisms (SNPs) extracted from whole-genome sequencing (WGS) data of the resistant parents, and the F3 families derived from the F2 individuals are scored for disease symptoms. For this, they use a computer-aided image analysis protocol that they designed so they can estimate the severity of the damages in the plant. They find several new QTLs, some being apparently more associated with disease severity, others with disease incidence. They also find that a previously identified QTL of Oryza sativa ssp. japonica origin is also present in the indica cluster (Romero et al. 2014). Finally, they discuss the candidate genes that could underlie the QTLs and provide a simple model for resistance.

It has to be noted that scoring symptoms of a viral disease such as RHB is very challenging. It requires maintaining populations of viruliferous insect vectors, mastering times and conditions for infestation by nymphs, and precise symptom scoring. It also requires the preparation of segregating populations, their genotyping with enough genetic markers, and mastering QTL detection methods. All these aspects are present in this work. In particular, the phenotyping of symptom severity implemented using computer-aided image processing represents an impressive, enormous amount of work.

From the genomics side, the fine-scale genotyping is based on the WGS of the parental lines (resistant and susceptible), followed by the application of suitable bioinformatic tools for SNP extraction and primers prediction that can be used on their Fluidigm platform. It also required implementing data correction algorithms to achieve precise genetic maps in the four crosses. The QTL detection itself required careful statistical pre-processing of phenotypic data. The authors then used a combination of several QTL detection methods, including an original meta-QTL method they developed in the software MapDisto. 

The authors then perform a very complete and convincing analysis of candidate genes, which includes genes already identified for a similar disease (RSV) on chromosome 11 of rice. What remains to elucidate is whether the candidate genes are actually involved or not in the disease resistance process. The team has already started implementing gene knockout strategies to study some of them in more detail. It will be interesting to see whether those genes act against the virus itself, or against the insect vector. 

Overall the work is of high quality and represents an important advance in the knowledge of disease resistance. In addition, it has many implications for crop breeding, allowing the setup of large-scale, marker-assisted strategies, for new resistant elite varieties of rice.

References

Morales F and Jennings P (2010) Rice hoja blanca: a complex plant-virus-vector pathosystem. CAB Reviews. https://doi.org/10.1079/PAVSNNR20105043

Romero LE, Lozano I, Garavito A, et al (2014) Major QTLs control resistance to Rice hoja blanca virus and its vector Tagosodes orizicolus. G3 | Genes, Genomes, Genetics 4:133–142. https://doi.org/10.1534/g3.113.009373

Silva A, Montoya ME, Quintero C, Cuasquer J, Tohme J, Graterol E, Cruz M, Lorieux M (2023) Genetic bases of resistance to the rice hoja blanca disease deciphered by a QTL approach. bioRxiv, 2022.11.07.515427, ver. 2 peer-reviewed and recommended by Peer Community in Genomics https://doi.org/10.1101/2022.11.07.515427

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