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 development (and standardization) of high-throughput sequencing techniques has revolutionized evolutionary biology, to the point that we almost see as normal fine-detail studies of genome architecture evolution (Robert et al., 2022), adaptation to new habitats (Rahi et al., 2019), or the development of key evolutionary novelties (Hilgers et al., 2018), to name three examples. One of the fields that has benefited the most is phylogenomics, i.e. the use of genome-wide data for inferring the evolutionary relationships among organisms. Dealing with such amount of data, however, has come with important analytical and computational challenges. Likewise, although the steady generation of genomic data from virtually any organism opens exciting opportunities for comparative analyses, it also creates a sort of “information fog”, where it is hard to find the most appropriate and/or the higher quality data. I have personally experienced this not so long ago, when I had to spend several weeks selecting the most complete transcriptomes from several phyla, moving back and forth between the NCBI SRA repository and the relevant literature.

In an attempt to deal with this issue, some research labs have committed their time and resources to the generation of taxa- and topic-specific databases (Lathe et al., 2008), such as MolluscDB (Liu et al., 2021), focused on mollusk genomics, or EukProt (Richter et al., 2022), a protein repository representing the diversity of eukaryotes. A new database that promises to become an important resource in the near future is MATEdb (Fernández et al., 2022), a repository of high-quality genomic data from Metazoa. MATEdb has been developed from publicly available and newly generated transcriptomes and genomes, prioritizing quality over quantity. Upon download, the user has access to both raw data and the related datasets: assemblies, several quality metrics, the set of inferred protein-coding genes, and their annotation. Although it is clear to me that this repository has been created with phylogenomic analyses in mind, I see how it could be generalized to other related problems such as analyses of gene content or evolution of specific gene families. In my opinion, the main strengths of MATEdb are threefold:

1. Rosa Fernández and her team have carefully scrutinized the genomic data available in several repositories to retrieve only the most complete transcriptomes and genomes, saving a lot of time in data mining to the user.
2. These data have been analyzed to provide both the assembly and the set of protein-coding genes, easing the computational burden that usually accompanies these pipelines. Interestingly, all the data have been analyzed with the same software and parameters, facilitating comparisons among taxa.
3. Genomic analysis can be intimidating, and even more for inexperienced users. That is particularly important when it comes to transcriptome and genome assembly because it has an effect in all downstream analyses. I believe that having access to already analyzed data softens this transition. The users can move forward on their research while they learn how to generate and analyze their data at their own pace.

On a negative note, I see two main drawbacks. First, as of today (September 16th, 2022) this database is in an early stage and it still needs to incorporate a lot of animal groups. This has been discussed during the revision process and the authors are already working on it, so it is only a matter of time until all major taxa are represented. Second, there is a scalability issue. In its current format it is not possible to select the taxa of interest and the full database has to be downloaded, which will become more and more difficult as it grows. Nonetheless, with the appropriate resources it would be easy to find a better solution. There are plenty of examples that could serve as inspiration, so I hope this does not become a big problem in the future.

Altogether, I and the researchers that participated in the revision process believe that MATEdb has the potential to become an important and valuable addition to the metazoan phylogenomics community. Personally, I wish it was available just a few months ago, it would have saved me so much time.

References

Fernández R, Tonzo V, Guerrero CS, Lozano-Fernandez J, Martínez-Redondo GI, Balart-García P, Aristide L, Eleftheriadi K, Vargas-Chávez C (2022) MATEdb, a data repository of high-quality metazoan transcriptome assemblies to accelerate phylogenomic studies. bioRxiv, 2022.07.18.500182, ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.07.18.500182

Hilgers L, Hartmann S, Hofreiter M, von Rintelen T (2018) Novel Genes, Ancient Genes, and Gene Co-Option Contributed to the Genetic Basis of the Radula, a Molluscan Innovation. Molecular Biology and Evolution, 35, 1638–1652. https://doi.org/10.1093/molbev/msy052

Lathe W, Williams J, Mangan M, Karolchik, D (2008). Genomic data resources: challenges and promises. Nature Education, 1(3), 2.

Liu F, Li Y, Yu H, Zhang L, Hu J, Bao Z, Wang S (2021) MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. Nucleic Acids Research, 49, D988–D997. https://doi.org/10.1093/nar/gkaa918

Rahi ML, Mather PB, Ezaz T, Hurwood DA (2019) The Molecular Basis of Freshwater Adaptation in Prawns: Insights from Comparative Transcriptomics of Three Macrobrachium Species. Genome Biology and Evolution, 11, 1002–1018. https://doi.org/10.1093/gbe/evz045

Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, Vargas C de (2022) EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes. bioRxiv, 2020.06.30.180687, ver. 5 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2020.06.30.180687

Robert NSM, Sarigol F, Zimmermann B, Meyer A, Voolstra CR, Simakov O (2022) Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions. BMC Genomics, 23, 143. https://doi.org/10.1186/s12864-022-08304-2

Third-generation sequencing has revolutionised de novo genome assembly. Thanks to this technology, genome reference sequences have evolved from fragmented drafts to gapless, telomere-to-telomere genome assemblies. Long reads produced by Oxford Nanopore and PacBio technologies can span structural variants and resolve complex repetitive regions such as centromeres, unlocking previously inaccessible genomic information. Nowadays, many research groups can afford to sequence the genome of their working model using long reads. Nevertheless, genome assembly poses a significant computational challenge. Read length, quality, coverage and genomic features such as repeat content can affect assembly contiguity, accuracy, and completeness in almost unpredictable ways. Consequently, there is no best universal software or protocol for this task. Producing a high-quality assembly requires chaining several tools into pipelines and performing extensive comparisons between the assemblies obtained by different tool combinations to decide which one is the best. This task can be extremely challenging, as the number of tools available rises very rapidly, and thorough benchmarks cannot be updated and published at such a fast pace. 

In their paper, Orjuela and collaborators present CulebrONT [1], a universal pipeline that greatly contributes to overcoming these challenges and facilitates long-read genome assembly for all taxonomic groups. CulebrONT incorporates six commonly used assemblers and allows to perform assembly, circularization (if needed), polishing, and evaluation in a simple framework. One important aspect of CulebrONT is its modularity, which allows the activation or deactivation of specific tools, giving great flexibility to the user. Nevertheless, possibly the best feature of CulebrONT is the opportunity to benchmark the selected tool combinations based on the excellent report generated by the pipeline. This HTML report aggregates the output of several tools for quality evaluation of the assemblies (e.g. BUSCO [2] or QUAST [3]) generated by the different assemblers, in addition to the running time and configuration parameters. Such information is of great help to identify the best-suited pipeline, as exemplified by the authors using four datasets of different taxonomic origins. Finally, CulebrONT can handle multiple samples in parallel, which makes it a good solution for laboratories looking for multiple assemblies on a large scale. 

References

1. Orjuela J, Comte A, Ravel S, Charriat F, Vi T, Sabot F, Cunnac S (2022) CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes. bioRxiv, 2021.07.19.452922, ver. 5 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2021.07.19.452922

2. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210–3212. https://doi.org/10.1093/bioinformatics/btv351

3. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29, 1072–1075. https://doi.org/10.1093/bioinformatics/btt086

A group of mammals, Xenathra, evolved and diversified in South America during its long period of isolation in the early to mid Cenozoic era. More recently, as a result of the Great Faunal Interchange between South America and North America, many xenarthran species went extinct. The thirty-one extant species belong to three groups: armadillos, sloths and anteaters. They share dental degeneration. However, the level of degeneration is variable. Anteaters entirely lack teeth, sloths have intermediately regressed teeth and most armadillos have a toothless premaxilla, as well as peg-like, single-rooted teeth that lack enamel in adult animals (Vizcaíno 2009). This diversity raises a number of questions about the evolution of dentition in these mammals. Unfortunately, the fossil record is too poor to provide refined information on the different stages of regressive evolution in these clades. In such cases, the identification of loss-of-function mutations and/or relaxed selection in genes related to a character regression can be very informative (Emerling and Springer 2014; Meredith et al. 2014; Policarpo et al. 2021). Indeed, shared and unique pseudogenes/relaxed selection can tell us to what extent regression has occurred in common ancestors and whether some changes are lineage-specific. In addition, the distribution of pseudogenes/relaxed selection on the branches of a phylogenetic tree is related to the evolutionary processes involved. A much higher density of pseudogenes in the most internal branches indicates that degeneration took place early and over a short period of time, consistent with selection against the presence of the morphological character with which they are associated, while pseudogenes distributed evenly in many internal and external branches suggest a more gradual process over many millions of years, in line with relaxed selection and fixation of loss-of-function mutations by genetic drift.

In this paper (Emerling et al. 2023), the authors examined the dynamics of decay of 11 dental genes that may parallel teeth regression. The analyses of the data reported in this paper clearly point to xenarthran teeth having repeatedly regressed in parallel in the three clades. In fact, no loss-of-function mutation is shared by all species examined. However, more genes should be studied to confirm the hypothesis that the common ancestor of extant xenarthrans had normal dentition. There are distinct patterns of gene loss in different lineages that are associated with the variation in dentition observed across the clades. These patterns of gene loss suggest that regressive evolution took place both gradually and in relatively rapid, discrete phases during the diversification of xenarthrans. This study underscores the utility of using pseudogenes to reconstruct evolutionary history of morphological characters when fossils are sparse.

References

Emerling CA, Gibb GC, Tilak M-K, Hughes JJ, Kuch M, Duggan AT, Poinar HN, Nachman MW, Delsuc F. 2023. Genomic data suggest parallel dental vestigialization within the xenarthran radiation. bioRxiv, 2022.12.09.519446, ver 2, peer-reviewed and recommended by PCI Genomics. https://doi.org/10.1101/2022.12.09.519446

Emerling CA, Springer MS. 2014. Eyes underground: Regression of visual protein networks in subterranean mammals. Molecular Phylogenetics and Evolution 78: 260-270. https://doi.org/10.1016/j.ympev.2014.05.016

Meredith RW, Zhang G, Gilbert MTP, Jarvis ED, Springer MS. 2014. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science 346: 1254390. https://doi.org/10.1126/science.1254390

Policarpo M, Fumey J, Lafargeas P, Naquin D, Thermes C, Naville M, Dechaud C, Volff J-N, Cabau C, Klopp C, et al. 2021. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Molecular Biology and Evolution 38: 589-605. https://doi.org/10.1093/molbev/msaa249

Vizcaíno SF. 2009. The teeth of the “toothless”: novelties and key innovations in the evolution of xenarthrans (Mammalia, Xenarthra). Paleobiology 35: 343-366. https://doi.org/10.1666/0094-8373-35.3.343

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