Xenoturbella is a genus of morphologically simple bilaterians inhabiting benthic environments. Until very recently, only one species was known from the genus, Xenoturbella bocki Westblad 1949 [1]. Less than a decade ago, five more species were discovered (X. churro, X. monstrosa, X. profunda, X. hollandorum [2] and X. japonica [3]). These enigmatic animals lack an anus, a coelom, reproductive organs, nephrocytes and a centralized nervous system [1]. The systematic classification of the genus has substantially changed in the last decades, with first being considered as its own phylum (Xenoturbellida) and then being clustered together with acoels and nemertodermatids into the phylum Xenacoelomorpha [4,5]. The phylogenetic position of the xenacoelomorphs has been recalcitrant to resolution, with its position ranging from being the sister group to Nephrozoa (ie, protostomes and deuterostomes [6]) to the sister group to Ambulacraria (ie, Hemichordata and Echinodermata) in a clade called Xenambulacraria [4]. Recent studies based on expanded datasets and more refined analyses support either topology [7,8]. Either way, it is clear that additional studies on Xenoturbella could provide important insights into the origins of bilaterian traits such as the anus, the nephrons and the evolution of a centralized nervous system. 

Small but mighty genome - In this work [9], the authors present the chromosome-level genome of X. bocki - the first one for xenoturbellids - and explore their genomic idiosyncrasies in the context of other animal phyla. The first thing they discuss is the complexity of the genome, with X. bocki having a similar number of genes to other bilaterians (despite its small size of 111Mb), retained ancestral metazoan synteny, conserved clusters of Hox genes, largely complete signaling pathways and most bilaterian miRNAs present. This is not a surprise, though, as we know that the relationship between genomic and morphological complexity is far from straightforward - for instance, protist lineages closely related to animals share many gene families with us [10], and it is not the presence or absence of these gene families but their evolutionary dynamics what defines complexity in each animal phyla (eg [11]). However, the relationship between both is far from well-understood, and having a high-quality genome is the first crucial step towards a holistic understanding of genome evolution, allowing us to ask questions about how and when genes are regulated, how they interact in 3D space, or how their epigenetic landscape is shaped, for instance.

Xenacoelomorphs: deuterostomes or not? - The authors also discuss the phylogenetic position of xenacoelomorphs (including the newly generated high-quality genome of X. bocki) based on a gene presence/absence matrix. Although there is much more to be done to robustly assess the phylogenetic position of the phylum, these analyses represent a first attempt to investigate what the phylogeny looks like after the addition of the new high-quality data. The new analyses reflected once more the previously recovered phylogenies mentioned above, but this time with a twist: X. bocki was recovered as the sister group to echinoderms, yet acoels appeared as sister to all deuterostomes, hence not recovering Xenacoelomorpha as monophyletic. Thus, it is clear that much remains to be explored to disentangle the phylogenetic position of these mysterious lineages, where more sophisticated methodologies such as synteny-based orthology inference or models of evolution accounting for heterotachy probably have an important role to play. 

In any case, we are approaching a qualitative jump in how we understand phylogenomics thanks to efforts derived from the availability of chromosome-level genome assemblies for a growing number of species. Exciting times are ahead for us, evolutionary biologists, to explore what high-quality genomes - in combination with multiomics datasets - will reveal about animal evolution. I am personally really looking forward to it.  

References

1. Westblad E. (1949). Xenoturbella bocki n.g., n.sp., a peculiar, primitive Turbellarian type. Arkiv för Zoologi 1, 3-29 (1949).

2. Rouse, G. W., Wilson, N. G., Carvajal, J. I. & Vrijenhoek, R. C. New deep-sea species of Xenoturbella and the position of Xenacoelomorpha. Nature 530, 94–97 (2016). https://doi.org/10.1038/nature16545

3. Nakano, H. et al. Correction to: A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella. BMC Evol. Biol. 18, 1–2 (2018). https://doi.org/10.1186/s12862-018-1190-5​https://doi.org/10.1186/s12862-018-1190-5​

4. Philippe, H. et al. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470, 255–258 (2011). https://doi.org/10.1038/nature09676

5. Hejnol, A. et al. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. Biol. Sci. 276, 4261–4270 (2009). https://doi.org/10.1098/rspb.2009.0896

6. Cannon, J. T. et al. Xenacoelomorpha is the sister group to Nephrozoa. Nature 530, 89–93 (2016). https://doi.org/10.1038/nature16520

7. Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. Biol. Sci. 286, 20190831 (2019). https://doi.org/10.1098/rspb.2019.0831

8. Philippe, H. et al. Mitigating anticipated effects of systematic errors supports sister-group relationship between Xenacoelomorpha and Ambulacraria. Curr. Biol. 29, 1818–1826.e6 (2019). https://doi.org/10.1016/j.cub.2019.04.009

9. Schiffer, P. H., Natsidis, P., Leite D. J., Robertson, H., Lapraz, F., Marlétaz, F., Fromm, B., Baudry, L., Simpson, F., Høye, E., Zakrzewski, A-C., Kapli, P., Hoff, K. J., Mueller, S., Marbouty, M., Marlow, H., Copley, R. R., Koszul, R., Sarkies, P. & Telford, M .J. The slow evolving genome of the xenacoelomorph worm Xenoturbella bocki. bioRxiv (2023), ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.06.24.497508

10. Suga, H. et al. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat. Commun. 4, 2325 (2013). https://doi.org/10.1038/ncomms3325

11. Fernández, R. & Gabaldón, T. Gene gain and loss across the metazoan tree of life. Nat Ecol Evol 4, 524–533 (2020). https://doi.org/10.1038/s41559-019-1069-x

Transposable elements (TEs) are important components of genomes. Indeed, they are now recognized as having a major role in gene and genome evolution (Biémont 2010). In particular, several examples have shown that the presence of TEs near genes may influence their functioning, either by recruiting particular epigenetic modifications (Guio et al. 2018) or by directly providing new regulatory sequences allowing new expression patterns (Chung et al. 2007; Sundaram et al. 2014). Therefore, the study of the interaction between TEs and their host genome requires tools to easily cross-annotate both types of entities. In particular, one needs to be able to identify all TEs located in the close vicinity of genes or inside them. Such task may not always be obvious for many biologists, as it requires informatics knowledge to develop their own script codes.

In their work, Meguerdichian et al. (2021) propose a command-line pipeline that takes as input the annotations of both genes and TEs for a given genome, then detects and reports the positional relationships between each TE insertion and their closest genes. The results are processed into an R script to provide tables displaying some statistics and graphs to visualize these relationships. 

This tool has the potential to be very useful for performing preliminary analyses before studying the impact of TEs on gene functioning, especially for biologists. Indeed, it makes it possible to identify genes close to TE insertions. These identified genes could then be specifically considered in order to study in more detail the link between the presence of TEs and their functioning. For example, the identification of TEs close to genes may allow to determine their potential role on gene expression.

References

Biémont C (2010). A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics, 186, 1085–1093. https://doi.org/10.1534/genetics.110.124180

Chung H, Bogwitz MR, McCart C, Andrianopoulos A, ffrench-Constant RH, Batterham P, Daborn PJ (2007). Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics, 175, 1071–1077. https://doi.org/10.1534/genetics.106.066597

Guio L, Vieira C, González J (2018). Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster. Scientific Reports, 8, 12197. https://doi.org/10.1038/s41598-018-30491-w

Meguerditchian C, Ergun A, Decroocq V, Lefebvre M, Bui Q-T (2021). A pipeline to detect the relationship between transposable elements and adjacent genes in host genomes. bioRxiv, 2021.02.25.432867, ver. 4 peer-reviewed and recommended by Peer Community In Genomics. https://doi.org/10.1101/2021.02.25.432867

Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T (2014). Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Research, 24, 1963–1976. https://doi.org/10.1101/gr.168872.113

Parasitoid wasps lay their eggs inside another arthropod, whose body is physically consumed by the parasitoid larvae. Phylogenetic inference suggests that Parasitoida are monophyletic, and that this clade underwent a strong radiation shortly after branching off from the Apocrita stem, some 236 million years ago (Peters et al. 2017). The increase in taxonomic diversity during evolutionary radiations is usually concurrent with an increase in genetic/genomic diversity, and is often associated with an increase in phenotypic diversity. Gene (or genome) duplication provides the evolutionary potential for such increase of genomic diversity by neo/subfunctionalisation of one of the gene paralogs, and is often proposed to be related to evolutionary radiations (Ohno 1970; Francino 2005).

In their recent preprint, Dominique Colinet and coworkers have explored the genetic and functional diversity of a Rho GTPase activating protein (RhoGAP) multigene family in two very divergent wasp clades within Parasitoida, namely Leptopilina (Figitidae) and Venturia (Ichneumonidae) (Colinet et al. 2024). Some members of the RhoGAP family are present in the venom of the parasitoid wasp Leptopilina boulardi as well as in other Leptopilina species, and are probably involved in the parasitic lifestyle by binding and inactivating host’s Rho GTPases, thereby interfering with the host’s immune response (Colinet et al. 2007).

Venom protein composition is highly variable, even between very closely related species, and is subject to rapid evolutionary changes. Although gene duplication and subsequent neo/subfunctionalisation have been frequently proposed as the main mechanism underlying this evolutionary diversification, observations are often compatible with alternative explanations, such as horizontal gene transfer, gene co-option or multifunctionalisation (Martinson et al. 2017; Alvarado et al. 2020; Huang et al. 2021; Undheim and Jenner 2021). Furthermore, high mutation rates in venom protein-encoding genes hinder phylogenetic hypothesis testing, and venom proteomics can be needed to verify transcriptomic predictions (Smith and Undheim 2018; von Reumont et al. 2022).

Colinet and coworkers (2024) have applied a combined transcriptomic, proteomic and functional approach to i) identify potential transcripts of the RhoGAP family in Leptopilina species using experimental and bioinformatic approaches; ii) experimentally identify proteins of the RhoGAP family in the venom of three Leptopilina species; iii) identify transcripts and proteins of the RhoGAP family in the ovarian calyx of Venturia canescens; and iv) perform phylogenetic and selection analyses on the extant sequences of these RhoGAP family genes to propose an evolutionary scenario for their origin and diversification. The most striking results are first the large diversity of RhoGAP sequences retrieved in the transcriptomes and proteomes of Leptopilina and of V. canescens, and second the high number of branches and positions identified to have evolved under positive selection. All the retrieved hits share a RhoGAP domain, either alone or in tandem, preceded in the case of Leptopilina RhoGAPs by a signal peptide that may be responsible for protein vehiculation for venom secretion. Further, for some of the protein positions identified to have evolved under positive selection, the authors have experimentally verified the functional impact of the changes by reverse genetic engineering.

The authors propose an evolutionary scenario to interpret the phylogenetic relationships among extant RhoGAP diversity in the clades under study. They posit that two independent, incomplete duplication events from the respectively ancestral RacGAP gene, followed by subsequent, lineage- and paralog-specific duplication events, lie at the origin of the wealth of diversity of in the Leptopilina venom RhoGAPs and of V. canescens ovarian calyx RhoGAPs. Notwithstanding, the global relationships presented in the work are not systematically consistent with this interpretation, e.g. regarding the absence of monophyly for Leptopilina RhoGAPs and Leptopilina RacGAP, and the same holds true for the respective V. canescens sequences. It may very well be that the high evolutionary rate of these genes has eroded the phylogenetic signal and prevented proper reconstruction, as the large differences between codon-based and amino acid-based phylogenies and the low support suggest. Explicit hypothesis testing, together with additional data from other taxa, may shed light onto the evolution of this gene family.

The work by Colinet and coworkers communicates sound, novel transcriptomic, proteomic and functional data from complex gene targets, consolidated from an important amount of experimental and bioinformatic work, and related to evolutionarily intriguing and complex phenotypes. These results, and the evolutionary hypothesis proposed to account for them, will be instrumental for our understanding of the evolution and diversity of vesicle-associated RhoGAPs in divergent parasitoid wasps.

References

Alvarado, G., Holland, S., R., DePerez-Rasmussen, J., Jarvis, B., A., Telander, T., Wagner, N., Waring, A., L., Anast, A., Davis, B., Frank, A., et al. (2020). Bioinformatic analysis suggests potential mechanisms underlying parasitoid venom evolution and function. Genomics 112(2), 1096–1104. https://doi.org/10.1016/j.ygeno.2019.06.022

Colinet, D., Cavigliasso, F., Leobold, M., Pichon, A., Urbach, S., Cazes, D., Poullet, M., Belghazi, M., Volkoff, A-N., Drezen, J-M., Gatti, J-L., and Poirié, M. (2024). Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.06.05.543686

Colinet, D., Schmitz, A., Depoix, D., Crochard, D., and Poirié, M. (2007). Convergent Use of RhoGAP Toxins by eukaryotic parasites and bacterial pathogens. PLoS Pathogens 3(12), e203. https://doi.org/10.1371/journal.ppat.0030203

Francino, M.P. (2005). An adaptive radiation model for the origin of new gene functions. Nature Genetics 37, 573–577. https://doi.org/10.1038/ng1579

Huang, J., Chen, J., Fang, G., Pang, L., Zhou, S., Zhou, Y., Pan, Z., Zhang, Q., Sheng, Y., Lu, Y., et al. (2021). Two novel venom proteins underlie divergent parasitic strategies between a generalist and a specialist parasite. Nature Communications 12, 234. https://doi.org/10.1038/s41467-020-20332-8

Martinson, E., O., Mrinalini, Kelkar, Y. D., Chang, C-H., and Werren, J., H. 2017. The evolution of venom by co-option of single-copy genes. Current Biololgy 27(13), 2007-2013.e8. https://doi.org/10.1016/j.cub.2017.05.032

Ohno, S. (1970). Evolution by gene duplication. New-York: Springer-Verlag.

Peters, R., S., Krogmann, L., Mayer, C., Donath, A., Gunkel, S., Meusemann, K., Kozlov, A., Podsiadlowski, L., Petersen, M., Lanfear, R., et al. (2017). Evolutionary history of the Hymenoptera. Current Biology 27(7), 1013–1018. https://doi.org/10.1016/j.cub.2017.01.027

von Reumont, B., M., Anderluh, G., Antunes, A., Ayvazyan, N., Beis, D., Caliskan, F., Crnković, A., Damm, M., Dutertre, S., Ellgaard, L., et al. (2022). Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research. GigaScience 11, giac048. https://doi.org/10.1093/gigascience/giac048

Smith, J., J., and Undheim, E., A., B. (2018). True lies: using proteomics to assess the accuracy of transcriptome-based venomics in centipedes uncovers false positives and reveals startling intraspecific variation in Scolopendra subspinipes. Toxins 10(3), 96. https://doi.org/10.3390/toxins10030096

Undheim, E., A., B., and Jenner, R., A. (2021). Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer. Nature Communications 12, 818. https://doi.org/10.1038/s41467-021-21093-8

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 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