|Id||Title||Authors||Abstract||Picture||Thematic fields||Recommender▲||Reviewers||Submission date|
06 May 2022
A deep dive into genome assemblies of non-vertebrate animalsNadège Guiglielmoni, Ramón Rivera-Vicéns, Romain Koszul, Jean-François Flot https://doi.org/10.20944/preprints202111.0170.v3
Diving, and even digging, into the wild jungle of annotation pathways for non-vertebrate animalsRecommended by Francois Sabot based on reviews by Yann Bourgeois, Cécile Monat, Valentina Peona and Benjamin Istace
In their paper, Guiglielmoni et al. propose we pick up our snorkels and palms and take "A deep dive into genome assemblies of non-vertebrate animals" (1). Indeed, while numerous assembly-related tools were developed and tested for human genomes (or at least vertebrates such as mice), very few were tested on non-vertebrate animals so far. Moreover, most of the benchmarks are aimed at raw assembly tools, and very few offer a guide from raw reads to an almost finished assembly, including quality control and phasing.
This huge and exhaustive review starts with an overview of the current sequencing technologies, followed by the theory of the different approaches for assembly and their implementation. For each approach, the authors present some of the most representative tools, as well as the limits of the approach.
The authors additionally present all the steps required to obtain an almost complete assembly at a chromosome-scale, with all the different technologies currently available for scaffolding, QC, and phasing, and the way these tools can be applied to non-vertebrates animals. Finally, they propose some useful advice on the choice of the different approaches (but not always tools, see below), and advocate for a robust genome database with all information on the way the assembly was obtained.
This review is a very complete one for now and is a very good starting point for any student or scientist interested to start working on genome assembly, from either model or non-model organisms. However, the authors do not provide a list of tools or a benchmark of them as a recommendation. Why? Because such a proposal may be obsolete in less than a year.... Indeed, with the explosion of the 3rd generation of sequencing technology, assembly tools (from different steps) are constantly evolving, and their relative performance increases on a monthly basis. In addition, some tools are really efficient at the time of a review or of an article, but are not further developed later on, and thus will not evolve with the technology. We have all seen it with wonderful tools such as Chiron (2) or TopHat (3), which were very promising ones, but cannot be developed further due to the stop of the project, the end of the contract of the post-doc in charge of the development, or the decision of the developer to switch to another paradigm. Such advice would, therefore, need to be constantly updated.
Thus, the manuscript from Guiglielmoni et al will be an almost intemporal one (up to the next sequencing revolution at last), and as they advocated for a more informed genome database, I think we should consider a rolling benchmarking system (tools, genome and sequence dataset) allowing to keep the performance of the tools up-to-date, and to propose the best set of assembly tools for a given type of genome.
1. Guiglielmoni N, Rivera-Vicéns R, Koszul R, Flot J-F (2022) A Deep Dive into Genome Assemblies of Non-vertebrate Animals. Preprints, 2021110170, ver. 3 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.20944/preprints202111.0170
2. Teng H, Cao MD, Hall MB, Duarte T, Wang S, Coin LJM (2018) Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning. GigaScience, 7, giy037. https://doi.org/10.1093/gigascience/giy037
3. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105–1111. https://doi.org/10.1093/bioinformatics/btp120
|A deep dive into genome assemblies of non-vertebrate animals||Nadège Guiglielmoni, Ramón Rivera-Vicéns, Romain Koszul, Jean-François Flot||<p style="text-align: justify;">Non-vertebrate species represent about ∼95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expan...||Bioinformatics, Evolutionary genomics||Francois Sabot||Valentina Peona, Benjamin Istace, Cécile Monat, Yann Bourgeois||2021-11-10 17:47:31||View|
14 Sep 2023
Expression of cell-wall related genes is highly variable and correlates with sepal morphologyDiego A. Hartasánchez, Annamaria Kiss, Virginie Battu, Charline Soraru, Abigail Delgado-Vaquera, Florian Massinon, Marina Brasó-Vives, Corentin Mollier, Marie-Laure Martin-Magniette, Arezki Boudaoud, Françoise Monéger https://doi.org/10.1101/2022.04.26.489498
The same but different: How small scale hidden variations can have large effectsRecommended by Francois Sabot based on reviews by Sandra Corjito and 1 anonymous reviewer
For ages, we considered only single genes, or just a few, in order to understand the relationship between phenotype and genotype in response to environmental challenges. Recently, the use of meaningful groups of genes, e.g. gene regulatory networks, or modules of co-expression, allowed scientists to have a larger view of gene regulation. However, all these findings were based on contrasted genotypes, e.g. between wild-types and mutants, as the implicit assumption often made is that there is little transcriptomic variability within the same genotype context.
Hartasànchez and collaborators (2023) decided to challenge both views: they used a single genotype instead of two, the famous A. thaliana Col0, and numerous plants, and considered whole gene networks related to sepal morphology and its variations. They used a clever approach, combining high-level phenotyping and gene expression to better understand phenomena and regulations underlying sepal morphologies. Using multiple controls, they showed that basic variations in the expression of genes related to the cell wall regulation, as well as the ones involved in chloroplast metabolism, influenced the global transcriptomic pattern observed in sepal while being in near-identical genetic background and controlling for all other experimental conditions.
The paper of Hartasànchez et al. is thus a tremendous call for humility in biology, as we saw in their work that we just understand the gross machinery. However, the Devil is in the details: understanding those very small variations that may have a large influence on phenotypes, and thus on local adaptation to environmental challenges, is of great importance in these times of climatic changes.
Hartasánchez DA, Kiss A, Battu V, Soraru C, Delgado-Vaquera A, Massinon F, Brasó-Vives M, Mollier C, Martin-Magniette M-L, Boudaoud A, Monéger F. 2023. Expression of cell-wall related genes is highly variable and correlates with sepal morphology. bioRxiv, ver. 4, peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.04.26.489498
|Expression of cell-wall related genes is highly variable and correlates with sepal morphology||Diego A. Hartasánchez, Annamaria Kiss, Virginie Battu, Charline Soraru, Abigail Delgado-Vaquera, Florian Massinon, Marina Brasó-Vives, Corentin Mollier, Marie-Laure Martin-Magniette, Arezki Boudaoud, Françoise Monéger||<p style="text-align: justify;">Control of organ morphology is a fundamental feature of living organisms. There is, however, observable variation in organ size and shape within a given genotype. Taking the sepal of Arabidopsis as a model, we inves...||Bioinformatics, Epigenomics, Plants||Francois Sabot||2023-03-14 19:10:15||View|
07 Feb 2023
RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomesFrederic Bertels, Julia von Irmer, Carsten Fortmann-Grote https://doi.org/10.1101/2022.05.22.493013
A workflow for studying enigmatic non-autonomous transposable elements across bacteriaRecommended by Gavin Douglas based on reviews by Sophie Abby and 1 anonymous reviewer
Repetitive extragenic palindromic sequences (REPs) are common repetitive elements in bacterial genomes (Gilson et al., 1984; Stern et al., 1984). In 2011, Bertels and Rainey identified that REPs are overrepresented in pairs of inverted repeats, which likely form hairpin structures, that they referred to as “REP doublets forming hairpins” (REPINs). Based on bioinformatics analyses, they argued that REPINs are likely selfish elements that evolved from REPs flanking particular transposes (Bertels and Rainey, 2011). These transposases, so-called REP-associated tyrosine transposases (RAYTs), were known to be highly associated with the REP content in a genome and to have characteristic upstream and downstream flanking REPs (Nunvar et al., 2010). The flanking REPs likely enable RAYT transposition, and their horizontal replication is physically linked to this process. In contrast, Bertels and Rainey hypothesized that REPINs are selfish elements that are highly replicated due to the similarity in arrangement to these RAYT-flanking REPs, but independent of RAYT transposition and generally with no impact on bacterial fitness (Bertels and Rainey, 2011).
This last point was especially contentious, as REPINs are highly conserved within species (Bertels and Rainey, 2023), which is unusual for non-beneficial bacterial DNA (Mira et al., 2001). Bertels and Rainey have since refined their argument to be that REPINs must provide benefits to host cells, but that there are nonetheless signatures of intragenomic conflict in genomes associated with these elements (Bertels and Rainey, 2023). These signatures reflect the divergent levels of selections driving REPIN distribution: selection at the level of each DNA element and selection on each individual bacterium. I found this observation particularly interesting as I and my colleague recently argued that these divergent levels of selection, and the interaction between them, is key to understanding bacterial pangenome diversity (Douglas and Shapiro, 2021). REPINs could be an excellent system for investigating these levels of selection across bacteria more generally.
The problem is that REPINs have not been widely characterized in bacterial genomes, partially because no bioinformatic workflow has been available for this purpose. To address this problem, Fortmann-Grote et al. (2023) developed RAREFAN, which is a web server for identifying RAYTs and associated REPINs in a set of input genomes. The authors showcase their tool by applying it to 49 Stenotrophomonas maltophilia genomes and providing examples of how to identify and assess RAYT-REPIN hits. The workflow requires several manual steps, but nonetheless represents a straightforward and standardized approach. Overall, this workflow should enable RAYTs and REPINs to be identified across diverse bacterial species, which will facilitate further investigation into the mechanisms driving their maintenance and spread.
Bertels F, Rainey PB (2023) Ancient Darwinian replicators nested within eubacterial genomes. BioEssays, 45, 2200085. https://doi.org/10.1002/bies.202200085
Bertels F, Rainey PB (2011) Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria. PLOS Genetics, 7, e1002132. https://doi.org/10.1371/journal.pgen.1002132
Douglas GM, Shapiro BJ (2021) Genic Selection Within Prokaryotic Pangenomes. Genome Biology and Evolution, 13, evab234. https://doi.org/10.1093/gbe/evab234
Fortmann-Grote C, Irmer J von, Bertels F (2023) RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes. bioRxiv, 2022.05.22.493013, ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.05.22.493013
Gilson E, Clément J m., Brutlag D, Hofnung M (1984) A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. The EMBO Journal, 3, 1417–1421. https://doi.org/10.1002/j.1460-2075.1984.tb01986.x
Mira A, Ochman H, Moran NA (2001) Deletional bias and the evolution of bacterial genomes. Trends in Genetics, 17, 589–596. https://doi.org/10.1016/S0168-9525(01)02447-7
Nunvar J, Huckova T, Licha I (2010) Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes. BMC Genomics, 11, 44. https://doi.org/10.1186/1471-2164-11-44
Stern MJ, Ames GF-L, Smith NH, Clare Robinson E, Higgins CF (1984) Repetitive extragenic palindromic sequences: A major component of the bacterial genome. Cell, 37, 1015–1026. https://doi.org/10.1016/0092-8674(84)90436-7
|RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes||Frederic Bertels, Julia von Irmer, Carsten Fortmann-Grote||<p style="text-align: justify;">Compared to eukaryotes, repetitive sequences are rare in bacterial genomes and usually do not persist for long. Yet, there is at least one class of persistent prokaryotic mobile genetic elements: REPINs. REPINs are ...||Bacteria and archaea, Bioinformatics, Evolutionary genomics, Viruses and transposable elements||Gavin Douglas||2022-06-07 08:21:34||View|
15 Sep 2022
EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotesDaniel J. Richter, Cédric Berney, Jürgen F. H. Strassert, Yu-Ping Poh, Emily K. Herman, Sergio A. Muñoz-Gómez, Jeremy G. Wideman, Fabien Burki, Colomban de Vargas https://doi.org/10.1101/2020.06.30.180687
EukProt enables reproducible Eukaryota-wide protein sequence analysesRecommended by Gavin Douglas based on reviews by 2 anonymous reviewers
Comparative genomics is a general approach for understanding how genomes differ, which can be considered from many angles. For instance, this approach can delineate how gene content varies across organisms, which can lead to novel hypotheses regarding what those organisms do. It also enables investigations into the sequence-level divergence of orthologous DNA, which can provide insight into how evolutionary forces differentially shape genome content and structure across lineages.
Burki F, Roger AJ, Brown MW, Simpson AGB (2020) The New Tree of Eukaryotes. Trends in Ecology & Evolution, 35, 43–55. https://doi.org/10.1016/j.tree.2019.08.008
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
Wilkinson MD, Dumontier M, Aalbersberg IjJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S-A, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B (2016) The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18
|EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes||Daniel J. Richter, Cédric Berney, Jürgen F. H. Strassert, Yu-Ping Poh, Emily K. Herman, Sergio A. Muñoz-Gómez, Jeremy G. Wideman, Fabien Burki, Colomban de Vargas||<p style="text-align: justify;">EukProt is a database of published and publicly available predicted protein sets selected to represent the breadth of eukaryotic diversity, currently including 993 species from all major supergroups as well as orpha...||Bioinformatics, Evolutionary genomics||Gavin Douglas||2022-06-08 14:19:28||View|
24 Feb 2023
MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomesBertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P. C. Rocha, Sophie S. Abby https://doi.org/10.1101/2022.09.02.506364
A unique and customizable approach for functionally annotating prokaryotic genomesRecommended by Gavin Douglas based on reviews by Kwee Boon Brandon Seah and Max Emil Schön
Macromolecular System Finder (MacSyFinder) v2 (Néron et al., 2023) is a newly updated approach for performing functional annotation of prokaryotic genomes (Abby et al., 2014). This tool parses an input file of protein sequences from a single genome (either ordered by genome location or unordered) and identifies the presence of specific cellular functions (referred to as “systems”). These systems are called based on two criteria: (1) that the "quorum" of a minimum set of core proteins involved is reached the “quorum” of a minimum set of core proteins being involved that are present, and (2) that the genes encoding these proteins are in the expected genomic organization (e.g., within the same order in an operon), when ordered data is provided. I believe the MacSyFinder approach represents an improvement over more commonly used methods exactly because it can incorporate such information on genomic organization, and also because it is more customizable.
Before properly appreciating these points, it is worth noting the norms and key challenges surrounding high-throughput functional annotation of prokaryotic genomes. Genome sequences are being added to online repositories at increasing rates, which has led to an enormous amount of bacterial genome diversity available to investigate (Altermann et al., 2022). A key aspect of understanding this diversity is the functional annotation step, which enables genes to be grouped into more biologically interpretable categories. For instance, gene calls can be mapped against existing Clusters of Orthologous Genes, which are themselves grouped into general categories such as ‘Transcription’ and ‘Lipid metabolism’ (Galperin et al., 2021).
This approach is valuable but is primarily used for global summaries of functional annotations within a genome: for example, it could be useful to know that a genome is particularly enriched for genes involved in lipid metabolism. However, knowing that a particular gene is involved in the general process of lipid metabolism is less likely to be actionable. In other words, the desired specificity of a gene’s functional annotation will depend on the exact question being investigated. There is no shortage of functional ontologies in genomics that can be applied for this purpose (Douglas and Langille, 2021), and researchers are often overwhelmed by the choice of which functional ontology to use. In this context, giving researchers the ability to precisely specify the gene families and operon structures they are interested in identifying across genomes provides useful control over what precise functions they are profiling. Of course, most researchers will lack the information and/or expertise to fully take advantage of MacSyFinder’s customizable features, but having this option for specialized purposes is valuable.
The other MacSyFinder feature that I find especially noteworthy is that it can incorporate genomic organization (e.g., of genes ordered in operons) when calling systems. This is a rare feature among commonly used tools for functional annotation and likely results in much higher specificity. As the authors note, this capability makes the co-occurrence of paralogs, and other divergent genes that share sequence similarity, to contribute less noise (i.e., they result in fewer false positive calls).
It is important to emphasize that these features are not new additions in MacSyFinder v2, but there are many other valuable changes. Most practically, this release is written in Python 3, rather than the obsolete Python 2.7, and was made more computationally efficient, which will enable MacSyFinder to be more widely used and more easily maintained moving forward. In addition, the search algorithm for analyzing individual proteins was fundamentally updated as well. The authors show that their improvements to the search algorithm result in an 8% and 20% increase in the number of identified calls for single and multi-locus secretion systems, respectively. Taken together, MacSyFinder v2 represents both practical and scientific improvements over the previous version, which will be of great value to the field.
Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC (2014) MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLOS ONE, 9, e110726. https://doi.org/10.1371/journal.pone.0110726
Altermann E, Tegetmeyer HE, Chanyi RM (2022) The evolution of bacterial genome assemblies - where do we need to go next? Microbiome Research Reports, 1, 15. https://doi.org/10.20517/mrr.2022.02
Douglas GM, Langille MGI (2021) A primer and discussion on DNA-based microbiome data and related bioinformatics analyses. Peer Community Journal, 1. https://doi.org/10.24072/pcjournal.2
Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D, Koonin EV (2021) COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Research, 49, D274–D281. https://doi.org/10.1093/nar/gkaa1018
Néron B, Denise R, Coluzzi C, Touchon M, Rocha EPC, Abby SS (2023) MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. bioRxiv, 2022.09.02.506364, ver. 2 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.09.02.506364
|MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes||Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P. C. Rocha, Sophie S. Abby||<p style="text-align: justify;">Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to mod...||Bacteria and archaea, Bioinformatics, Functional genomics||Gavin Douglas||Kwee Boon Brandon Seah, Max Emil Schön||2022-09-09 10:30:31||View|
02 Apr 2021
Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detectionLucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, Nihal Buzkan, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Marie Lefebvre, Paolo Margaria, Jean Sébastien Reynard, Kristian Stevens, Denis Kutnjak, Sébastien Massart https://doi.org/10.5281/zenodo.4584718
Toward a critical assessment of virus detection in plantsRecommended by Hadi Quesneville based on reviews by Alexander Suh and 1 anonymous reviewer
The advent of High Throughput Sequencing (HTS) since the last decade has revealed previously unsuspected diversity of viruses as well as their (sometimes) unexpected presence in some healthy individuals. These results demonstrate that genomics offers a powerful tool for studying viruses at the individual level, allowing an in-depth inventory of those that are infecting an organism. Such approaches make it possible to study viromes with an unprecedented level of detail, both qualitative and quantitative, which opens new venues for analyses of viruses of humans, animals and plants. Consequently, the diagnostic field is using more and more HTS, fueling the need for efficient and reliable bioinformatics tools.
Many such tools have already been developed, but in plant disease diagnostics, validation of the bioinformatics pipelines used for the detection of viruses in HTS datasets is still in its infancy. There is an urgent need for benchmarking the different tools and algorithms using well-designed reference datasets generated for this purpose. This is a crucial step to move forward and to improve existing solutions toward well-standardized bioinformatics protocols. This context has led to the creation of the Plant Health Bioinformatics Network (PHBN), a Euphresco network project aiming to build a bioinformatics community working on plant health. One of their objectives is to provide researchers with open-access reference datasets allowing to compare and validate virus detection pipelines.
In this framework, Tamisier et al.  present real, semi-artificial, and completely artificial datasets, each aimed at addressing challenges that could affect virus detection. These datasets comprise real RNA-seq reads from virus-infected plants as well as simulated virus reads. Such a work, providing open-access datasets for benchmarking bioinformatics tools, should be encouraged as they are key to software improvement as demonstrated by the well-known success story of the protein structure prediction community: their pioneer community-wide effort, called Critical Assessment of protein Structure Prediction (CASP), has been providing research groups since 1994 with an invaluable way to objectively test their structure prediction methods, thereby delivering an independent assessment of state-of-art protein-structure modelling tools. Following this success, many other bioinformatic community developed similar “competitions”, such as RNA-puzzles  to predict RNA structures, Critical Assessment of Function Annotation  to predict gene functions, Critical Assessment of Prediction of Interactions  to predict protein-protein interactions, Assemblathon  for genome assembly, etc. These are just a few examples from a long list of successful initiatives. Such efforts enable rigorous assessments of tools, stimulate the developers’ creativity, but also provide user communities with a state-of-art evaluation of available tools.
Inspired by these success stories, the authors propose a “VIROMOCK challenge” , asking researchers in the field to test their tools and to provide feedback on each dataset through a repository. This initiative, if well followed, will undoubtedly improve the field of virus detection in plants, but also probably in many other organisms. This will be a major contribution to the field of viruses, leading to better diagnostics and, consequently, a better understanding of viral diseases, thus participating in promoting human, animal and plant health.
 Tamisier, L., Haegeman, A., Foucart, Y., Fouillien, N., Al Rwahnih, M., Buzkan, N., Candresse, T., Chiumenti, M., De Jonghe, K., Lefebvre, M., Margaria, P., Reynard, J.-S., Stevens, K., Kutnjak, D. and Massart, S. (2021) Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection. Zenodo, 4273791, version 4 peer-reviewed and recommended by Peer community in Genomics. doi: https://doi.org/10.5281/zenodo.4273791
 Critical Assessment of protein Structure Prediction” (CASP) - https://en.wikipedia.org/wiki/CASP
 RNA-puzzles - https://www.rnapuzzles.org
 Critical Assessment of Function Annotation (CAFA) - https://en.wikipedia.org/wiki/Critical_Assessment_of_Function_Annotation
 Critical Assessment of Prediction of Interactions (CAPI) - https://en.wikipedia.org/wiki/Critical_Assessment_of_Prediction_of_Interactions
 Assemblathon - https://assemblathon.org
 VIROMOCK challenge - https://gitlab.com/ilvo/VIROMOCKchallenge
|Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection||Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, Nihal Buzkan, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Marie Lefebvre, Paolo Margaria, Jean Sébastien Reynard, Kristian Stevens, Denis Kutnjak, Séb...||<p>The widespread use of High-Throughput Sequencing (HTS) for detection of plant viruses and sequencing of plant virus genomes has led to the generation of large amounts of data and of bioinformatics challenges to process them. Many bioinformatics...||Bioinformatics, Plants, Viruses and transposable elements||Hadi Quesneville||2020-11-27 14:31:47||View|
13 Jul 2022
Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codonsBrandon Kwee Boon Seah, Aditi Singh, Estienne Carl Swart https://doi.org/10.1101/2022.04.12.488043
An accident frozen in time: the ambiguous stop/sense genetic code of karyorelict ciliatesRecommended by Iker Irisarri based on reviews by Vittorio Boscaro and 2 anonymous reviewers
Several variations of the “universal” genetic code are known. Among the most striking are those where a codon can either encode for an amino acid or a stop signal depending on the context. Such ambiguous codes are known to have evolved in eukaryotes multiple times independently, particularly in ciliates – eight different codes have so far been discovered (1). We generally view such genetic codes are rare ‘variants’ of the standard code restricted to single species or strains, but this might as well reflect a lack of study of closely related species. In this study, Seah and co-authors (2) explore the possibility of codon reassignment in karyorelict ciliates closely related to Parduczia sp., which has been shown to contain an ambiguous genetic code (1). Here, single-cell transcriptomics are used, along with similar available data, to explore the possibility of codon reassignment across the diversity of Karyorelictea (four out of the six recognized families). Codon reassignments were inferred from their frequencies within conserved Pfam (3) protein domains, whereas stop codons were inferred from full-length transcripts with intact 3’-UTRs.
Results show the reassignment of UAA and UAG stop codons to code for glutamine (Q) and the reassignment of the UGA stop codon into tryptophan (W). This occurs only within the coding sequences, whereas the end of transcription is marked by UGA as the main stop codon, and to a lesser extent by UAA. In agreement with a previous model proposed that explains the functioning of ambiguous codes (1,4), the authors observe a depletion of in-frame UGAs before the UGA codon that indicates the stop, thus avoiding premature termination of transcription. The inferred codon reassignments occur in all studied karyorelicts, including the previously studied Parduczia sp. Despite the overall clear picture, some questions remain. Data for two out of six main karyorelict lineages are so far absent and the available data for Cryptopharyngidae was inconclusive; the phylogenetic affinities of Cryptopharyngidae have also been questioned (5). This indicates the need for further study of this interesting group of organisms. As nicely discussed by the authors, experimental evidence could further strengthen the conclusions of this paper, including ribosome profiling, mass spectrometry – as done for Condylostoma (1) – or even direct genetic manipulation.
The uniformity of the ambiguous genetic code across karyorelicts might at first seem dull, but when viewed in a phylogenetic context character distribution strongly suggest that this genetic code has an ancient origin in the karyorelict ancestor ~455 Ma in the Proterozoic (6). This ambiguous code is also not a rarity of some obscure species, but it is shared by ciliates that are very diverse and ecologically important. The origin of the karyorelict code is also intriguing. Adaptive arguments suggest that it could confer robustness to mutations causing premature stop codons. However, we lack evidence for ambiguous codes being linked to specific habitats of lifestyles that could account for it. Instead, the authors favor the neutral view of an ancient “frozen accident”, fixed stochastically simply because it did not pose a significant selective disadvantage. Once a stop codon is reassigned to an amino acid, it is increasingly difficult to revert this without the deleterious effect of prematurely terminating translation. At the end, the origin of the genetic code itself is thought to be a frozen accident too (7).
1. Swart EC, Serra V, Petroni G, Nowacki M. Genetic codes with no dedicated stop codon: Context-dependent translation termination. Cell 2016;166: 691–702. https://doi.org/10.1016/j.cell.2016.06.020
2. Seah BKB, Singh A, Swart EC (2022) Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codons. bioRxiv, 2022.04.12.488043. ver. 4 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.04.12.488043
3. Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A. Pfam: The protein families database in 2021, Nuc Acids Res 2020;49: D412-D419. https://doi.org/10.1093/nar/gkaa913
4. Alkalaeva E, Mikhailova T. Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma. Bioessays. 2017;39. https://doi.org/10.1002/bies.201600213
5. Xu Y, Li J, Song W, Warren A. Phylogeny and establishment of a new ciliate family, Wilbertomorphidae fam. nov. (Ciliophora, Karyorelictea), a highly specialized taxon represented by Wilbertomorpha colpoda gen. nov., spec. nov. J Eukaryot Microbiol. 2013;60: 480–489. https://doi.org/10.1111/jeu.12055
6. Fernandes NM, Schrago CG. A multigene timescale and diversification dynamics of Ciliophora evolution. Mol Phylogenet Evol. 2019;139: 106521. https://doi.org/10.1016/j.ympev.2019.106521
7. Crick FH. The origin of the genetic code. J Mol Biol. 1968;38: 367–379. https://doi.org/10.1016/0022-2836(68)90392-6
|Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codons||Brandon Kwee Boon Seah, Aditi Singh, Estienne Carl Swart||<p style="text-align: justify;">In ambiguous stop/sense genetic codes, the stop codon(s) not only terminate translation but can also encode amino acids. Such codes have evolved at least four times in eukaryotes, twice among ciliates (<em>Condylost...||Bioinformatics, Evolutionary genomics||Iker Irisarri||2022-05-02 11:06:10||View|
02 Jun 2023
Near-chromosome level genome assembly of devil firefish, Pterois milesChristos V. Kitsoulis, Vasileios Papadogiannis, Jon B. Kristoffersen, Elisavet Kaitetzidou, Aspasia Sterioti, Costas S. Tsigenopoulos, Tereza Manousaki https://doi.org/10.1101/2023.01.10.523469
The genome of a dangerous invader (fish) beautyRecommended by Iker Irisarri based on reviews by Maria Recuerda and 1 anonymous reviewer
High-quality genomes are currently being generated at an unprecedented speed powered by long-read sequencing technologies. However, sequencing effort is concentrated unequally across the tree of life and several key evolutionary and ecological groups remain largely unexplored. So is the case for fish species of the family Scorpaenidae (Perciformes). Kitsoulis et al. present the genome of the devil firefish, Pterois miles (1). Following current best practices, the assembly relies largely on Oxford Nanopore long reads, aided by Illumina short reads for polishing to increase the per-base accuracy. PacBio’s IsoSeq was used to sequence RNA from a variety of tissues as direct evidence for annotating genes. The reconstructed genome is 902 Mb in size and has high contiguity (N50=14.5 Mb; 660 scaffolds, 90% of the genome covered by the 83 longest scaffolds) and completeness (98% BUSCO completeness). The new genome is used to assess the phylogenetic position of P. miles, explore gene synteny against zebrafish, look at orthogroup expansion and contraction patterns in Perciformes, as well as to investigate the evolution of toxins in scorpaenid fish (2). In addition to its value for better understanding the evolution of scorpaenid and teleost fishes, this new genome is also an important resource for monitoring its invasiveness through the Mediterranean Sea (3) and the Atlantic Ocean, in the latter case forming the invasive lionfish complex with P. volitans (4).
1. Kitsoulis CV, Papadogiannis V, Kristoffersen JB, Kaitetzidou E, Sterioti E, Tsigenopoulos CS, Manousaki T. (2023) Near-chromosome level genome assembly of devil firefish, Pterois miles. BioRxiv, ver. 6 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.01.10.523469
2. Kiriake A, Shiomi K. (2011) Some properties and cDNA cloning of proteinaceous toxins from two species of lionfish (Pterois antennata and Pterois volitans). Toxicon, 58(6-7):494–501. https://doi.org/10.1016/j.toxicon.2011.08.010
3. Katsanevakis S, et al. (2020) Un- published Mediterranean records of marine alien and cryptogenic species. BioInvasions Records, 9:165–182. https://doi.org/10.3391/bir.2020.9.2.01
4. Lyons TJ, Tuckett QM, Hill JE. (2019) Data quality and quantity for invasive species: A case study of the lionfishes. Fish and Fisheries, 20:748–759. https://doi.org/10.1111/faf.12374
|Near-chromosome level genome assembly of devil firefish, *Pterois miles*||Christos V. Kitsoulis, Vasileios Papadogiannis, Jon B. Kristoffersen, Elisavet Kaitetzidou, Aspasia Sterioti, Costas S. Tsigenopoulos, Tereza Manousaki||<p style="text-align: justify;">Devil firefish (<em>Pterois miles</em>), a member of Scorpaenidae family, is one of the most successful marine non-native species, dominating around the world, that was rapidly spread into the Mediterranean Sea, thr...||Evolutionary genomics||Iker Irisarri||2023-01-17 12:37:20||View|
07 Sep 2023
The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological nichesNikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin https://doi.org/10.1101/2023.06.01.543285
Natural variation and adaptation in Brachypodium distachyonRecommended by Josep Casacuberta based on reviews by Thibault Leroy and 1 anonymous reviewer
Identifying the genetic factors that allow plant adaptation is a major scientific question that is particularly relevant in the face of the climate change that we are already experiencing. To address this, it is essential to have genetic information on a high number of accessions (i.e., plants registered with unique accession numbers) growing under contrasting environmental conditions. There is already an important number of studies addressing these issues in the plant Arabidopsis thaliana, but there is a need to expand these analyses to species that play key roles in wild ecosystems and are close to very relevant crops, as is the case of grasses.
The work of Minadakis, Roulin and co-workers (1) presents a Brachypodium distachyon panel of 332 fully sequences accessions that covers the whole species distribution across a wide range of bioclimatic conditions, which will be an invaluable tool to fill this gap. In addition, the authors use this data to start analyzing the population structure and demographic history of this plant, suggesting that the species experienced a shift of its distribution following the Last Glacial Maximum, which may have forced the species into new habitats. The authors also present a modeling of the niches occupied by B. distachyon together with an analysis of the genetic clades found in each of them, and start analyzing the different adaptive loci that may have allowed the species’ expansion into different bioclimatic areas.
In addition to the importance of the resources made available by the authors for the scientific community, the analyses presented are well done and carefully discussed, and they highlight the potential of these new resources to investigate the genetic bases of plant adaptation.
1. Nikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin. The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches. bioRxiv, 2023.06.01.543285, ver. 5 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2023.06.01.543285
|The demographic history of the wild crop relative *Brachypodium distachyon* is shaped by distinct past and present ecological niches||Nikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin||<p style="text-align: justify;">Closely related to economically important crops, the grass <em>Brachypodium distachyon</em> has been originally established as a pivotal species for grass genomics but more recently flourished as a model for develop...||Evolutionary genomics, Functional genomics, Plants, Population genomics||Josep Casacuberta||2023-06-14 15:28:30||View|
23 Aug 2022
A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomicsKevin G. Daly, Benjamin S. Arbuckle, Conor Rossi, Valeria Mattiangeli, Phoebe A. Lawlor, Marjan Mashkour, Eberhard Sauer, Joséphine Lesur, Levent Atici, Cevdet Merih Erek, Daniel G. Bradley https://doi.org/10.1101/2022.04.08.487619
Goat ancient DNA analysis unveils a new lineage that may have hybridized with domestic goatsRecommended by Laura Botigué based on reviews by Torsten Günther and 1 anonymous reviewer
The genomic analysis of ancient remains has revolutionized the study of the past over the last decade. On top of the discoveries related to human evolution, plant and animal archaeogenomics has been used to gain new insights into the domestication process and the dispersal of domestic forms.
In this study, Daly and colleagues analyse the genomic data from seven goat specimens from the Epipalaeolithic recovered from the Direkli Cave in the Taurus Mountains in southern Turkey. They also generate new genomic data from Capra lineages across the phylogeny, contributing to the availability of genomic resources for this genus. Analysis of the ancient remains is compared to modern genomic variability and sheds light on the complexity of the Tur wild Capra lineages and their relationship with domestic goats and their wild ancestors.
Authors find that during the Late Pleistocene in the Taurus Mountains wild goats from the Tur lineage, today restricted to the Caucasus region, were not rare and cohabited with Bezoar, the wild goats that are the ancestors of domestic goats. They identify the Direkli Cave specimens as a lineage separate from the
A modified D statistic, Dex, is developed to examine the contribution of the ancient Tur lineage in domestic goats through time and space. Dex measures the relative degree of allele sharing, derived specifically in a selected genome or group of genomes, and may have some utility in genera with complex admixture histories or admixture from ghost lineages. Results confirm that Neolithic European goat had an excess of allele sharing with this ancient Tur lineage, something that is absent in contemporary goats eastwards or in modern goats.
Interspecific gene flow is not uncommon among mammals, but the case of Capra has the additional motivation of understanding the origins of the domestic species. This work uncovers an ancient Tur lineage that is different from the modern ones and is additionally found in another geographic area. Furthermore, evidence shows that this ancient lineage exhibits substantial amounts of allele sharing with the wild ancestor of the domestic goat, but also with the Neolithic Eurasian domestic goats, highlighting the complexity of the domestication process.
This work has also important implications in understanding the effect of over-hunting and habitat disruption during the Anthropocene on the evolution of the Capra genus. The availability of more ancient specimens and better coverage of the modern genomic variability can help quantifying the lineages that went lost and identify the causes of their extinction.
This work is limited by the current availability of whole genomes from modern Capra specimens, but pieces of evidence as well that an effort is needed to obtain more genomic data from ancient goats from different geographic ranges to determine to what extent these lineages contributed to goat domestication.
Daly KG, Arbuckle BS, Rossi C, Mattiangeli V, Lawlor PA, Mashkour M, Sauer E, Lesur J, Atici L, Cevdet CM and Bradley DG (2022) A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics. bioRxiv, 2022.04.08.487619, ver. 5 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.04.08.487619
|A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics||Kevin G. Daly, Benjamin S. Arbuckle, Conor Rossi, Valeria Mattiangeli, Phoebe A. Lawlor, Marjan Mashkour, Eberhard Sauer, Joséphine Lesur, Levent Atici, Cevdet Merih Erek, Daniel G. Bradley||<p>Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and p...||Evolutionary genomics, Population genomics, Vertebrates||Laura Botigué||2022-04-15 12:05:47||View|