Article
Biochemistry & Molecular Biology
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sovi, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio Mello, Samantha R. Friedrich, Peter Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O'Brien, Jonas Korlach, Harris A. Lewin, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, Erich D. Jarvis
Summary: The Vertebrate Genome Project and the international Genome 10K consortium have collaborated to generate high-quality genome assemblies for 16 species representing six major vertebrate lineages, leading to new biological discoveries. Long-read sequencing technologies are essential for maximizing genome quality, and addressing complex repeats and haplotype heterozygosity are crucial for reducing assembly errors and improving completeness of reference genomes. The lessons learned from this project have paved the way for the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all known vertebrate species.
Article
Biochemistry & Molecular Biology
Sarah Farhat, Maria Vittoria Modica, Nicolas Puillandre
Summary: The diversity of venomous organisms and the toxins they produce have been increasingly investigated, but taxonomic bias remains important. Neogastropods, a group of marine predators representing almost 22% of the known gastropod diversity, evolved a wide range of feeding strategies, including the production of toxins to subdue their preys. However, whether the diversity of these compounds is at the origin of the hyperdiversification of the group and how genome evolution may correlate with both the compounds and species diversities remain understudied.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Madeleine E. Aase-Remedios, Clara Coll-Llado, David E. K. Ferrier
Summary: Research on muscle responses to feeding-fasting-refeeding experiments reveals the genetic mechanisms involved in muscle degradation and maintenance, providing insight into the regulatory pathways of muscle nutrient response.
Article
Multidisciplinary Sciences
Javier Gutierrez, Roy Platt, Juan C. Opazo, David A. Ray, Federico Hoffmann, Michael Vandewege
Summary: PIWIs are regulatory proteins that protect germline against transposable elements and are primarily expressed in gonads in vertebrates. The duplication history of Piwi genes is complex, with some genes being retained in all members, while others being derived from duplication events in common ancestors and subsequently lost in certain lineages. Despite two rounds of whole genome duplication in vertebrate evolution, Piwi expansion seems to have occurred independently of these events.
Article
Plant Sciences
Jessie A. Pelosi, Emily H. Kim, W. Brad Barbazuk, Emily B. Sessa
Summary: In this study, we assembled the largest nuclear dataset for ferns and investigated the fern phylogeny, whole genome duplications (WGDs), and gene retention patterns following WGDs. Our results revealed high levels of gene tree-species tree conflict in the fern phylogeny and identified multiple WGDs events. We also found that functions of retained genes following WGDs were largely convergent.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Marina Braso-Vives, Ferdinand Marletaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, Jose L. Gomez-Skarmeta, Diego A. Hartasanchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia, Marc Robinson-Rechavi
Summary: The small-scale gene duplication history of amphioxus resembles that of vertebrates, despite their slower molecular and morphological evolution. Amphioxus gene duplicates show similar levels of expression and patterns of functional specialization as vertebrate duplicated genes.
Article
Multidisciplinary Sciences
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer
Summary: This study introduces a genome alignment method called AnchorWave, which shows significant improvement when applied to species with complex genomes. It can accurately identify multikilobase indels and improve the recall rate of transcription factor-binding sites.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Chi-Fa Huang, Wen-Yu Liu, Mei-Yeh Jade Lu, Yi-Hua Chen, Maurice S. B. Ku, Wen-Hsiung Li
Summary: Through studying leaf-development transcriptomes, it was found that whole-genome duplication (WGD) facilitated four aspects of C-4 photosynthesis evolution in G. gynandra, including the retention of duplicated genes related to nitrogen recycling and vein development, the evolution of C-4 enzyme genes, and upregulation of genes encoding photosystem I proteins.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biology
Lindsey Ray, Daniel Medeiros
Summary: Neural crest cells and their gene regulatory network are unique to vertebrates and are not dependent on genome duplications. However, these duplications may have facilitated the diversification of neural crest derivatives.
Article
Biology
Nissanka P. De Silva, Christopher Lee, Paul Battlay, A. Fournier-Level, Joslin L. Moore, Kathryn A. Hodgins
Summary: This study presents the genome assembly and annotation of Bothriochloa decipiens, an Australian grass species with a complex history of hybridization and polyploidy. Comparative analysis reveals a recent whole-genome duplication event and differences in repeat activity and gene retention between subgenomes. Bothriochloa decipiens has ecological importance and potential for climate change-resilient restoration of Australian grasslands. The reference genome provides a valuable resource for future population genomic research on Australian grasses.
Article
Biochemistry & Molecular Biology
Jean-Francois Gout, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G. Doak, Simran Bhullar, Arnaud Couloux, Frederic Guerin, Sophie Malinsky, Alexey Potekhin, Natalia Sawka, Linda Sperling, Karine Labadie, Eric Meyer, Sandra Duharcourt, Michael Lynch
Summary: Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages, but the maintenance of WGD-derived paralogs is still debated. The analysis of 13 Paramecium species revealed that gene retention biases and strong selective pressures against post-WGD gene loss play a major role in maintaining duplicate genes. Paramecium is an exceptional model organism in evolutionary cell biology, and this dataset of 13 species sharing an ancestral WGD will be useful for future studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Biochemistry & Molecular Biology
Donald C. Dearborn, Sophie Warren, Frank Hailer
Summary: Pathogen-mediated selection and sexual selection are important drivers of evolution. The major histocompatibility complex (MHC) genes play a crucial role in these processes. However, previous research has shown a lack of emphasis on the class II MHC gene, MHC-IIA, in infectious disease and sexual selection studies. In this study, MHC-IIA sequence data from 50 vertebrate species were analyzed, revealing high levels of polymorphism and positive selection in MHC-IIA. Fish species exhibited stronger positive selection on MHC-IIA compared to other surveyed vertebrate groups. These findings highlight the importance of MHC-IIA as a target of selection and suggest the need for further characterization of MHC-IIA at both allelic and genomic levels.
Correction
Biotechnology & Applied Microbiology
Oliver M. Selmoni, Diane Maitre, Julien Roux, Laetitia G. E. Wilkins, Lucas Marques da Cunha, Etienne L. M. Vermeirssen, Susanne Knoerr, Marc Robinson-Rechavi, Claus Wedekind
Review
Biotechnology & Applied Microbiology
Sara S. Fonseca Costa, Marc Robinson-Rechavi, Jurgen A. Ripperger
BRIEFINGS IN FUNCTIONAL GENOMICS
(2020)
Article
Genetics & Heredity
Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor
GENOMICS PROTEOMICS & BIOINFORMATICS
(2020)
Article
Biology
Jialin Liu, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson-Rechavi
Article
Evolutionary Biology
Kamil S. Jaron, Jens Bast, Reuben W. Nowell, T. Rhyker Ranallo-Benavidez, Marc Robinson-Rechavi, Tanja Schwander
Summary: Systematic characterization of genomic features in 26 parthenogenetic animals revealed no consistent patterns across transitions to asexuality, indicating lineage-specific rather than general consequences of parthenogenesis. Only parthenogens of hybrid origin showed high heterozygosity levels, while non-hybrid parthenogens appeared largely homozygous, regardless of the cellular mechanism underlying parthenogenesis.
JOURNAL OF HEREDITY
(2021)
Article
Biochemistry & Molecular Biology
Frederic B. Bastian, Julien Roux, Anne Niknejad, Aurelie Comte, Sara S. Fonseca Costa, Tarcisio Mendes de Farias, Sebastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angelique Escoriza, Walid H. Gharib, Mar Gonzales-Porta, Yohan Jarosz, Balazs Laurenczy, Philippe Moret, Emilie Person, Patrick Roelli, Komal Sanjeev, Mathieu Seppey, Marc Robinson-Rechavi
Summary: Bgee is a database that allows retrieval and comparison of gene expression patterns in multiple animal species using curated healthy wild-type data, enabling the detection of expression conditions for any single gene across different species. It integrates various data types and ensures consistent data annotation and processing for cross-species comparisons.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Patrick Tran Van, Yoann Anselmetti, Jens Bast, Zoe Dumas, Nicolas Galtier, Kamil S. Jaron, Koen Martens, Darren J. Parker, Marc Robinson-Rechavi, Tanja Schwander, Paul Simion, Isa Schon
Summary: Ostracods, as one of the oldest crustacean groups, have been lacking genome resources, hindering genomic research. However, researchers successfully assembled and annotated reference genomes for three species of nonmarine ostracods using Illumina-based sequencing technology. These genomes provide a basis for further developing ostracods as models for evolutionary and ecological research.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemical Research Methods
Victor Rossier, Alex Warwick Vesztrocy, Marc Robinson-Rechavi, Christophe Dessimoz
Summary: Assigning new sequences to known protein families and subfamilies is crucial for many functional, comparative and evolutionary genomics analyses. However, relying solely on the closest sequence in a reference database for assignment can lead to misassignments, as a query sequence may not necessarily belong to the same subfamily as its closest sequence. To overcome this issue, a novel alignment-free protein subfamily assignment method called OMAmer has been introduced, which provides better and quicker subfamily-level assignments compared to methods relying on the closest sequence.
Article
Biochemistry & Molecular Biology
Jialin Liu, Rebecca R. Viales, Pierre Khoueiry, James P. Reddington, Charles Girardot, Eileen E. M. Furlong, Marc Robinson-Rechavi
Summary: Inter-species comparisons reveal an hourglass expression pattern during embryogenesis, with a higher proportion of conserved enhancers at the phylotypic period. Positive selection is detected on developmental enhancers at early and late stages, with a depletion at the phylotypic period, suggesting positive selection as an evolutionary mechanism underlying the hourglass pattern of animal evolution.
Article
Ecology
Tina Begum, Martha Liliana Serrano-Serrano, Marc Robinson-Rechavi
Summary: The study investigates comparative methods for gene function evolution, finding that both phylogenetic independent contrasts and pairwise comparisons lose power to detect functional evolution trends when the functional trait accelerates for a long time following duplication, with better power of phylogenetic contrasts under intermediate scenarios. Improved pairwise comparisons are robust to bias, and both approaches perform equally well under rapid shifts in traits.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Giulia Zancolli, Maarten Reijnders, Robert M. Waterhouse, Marc Robinson-Rechavi
Summary: Animals have evolved specialized organs and anatomical structures to produce and release potent bioactive molecules, known as venoms, for the purpose of subduing prey or predators. A comparative analysis of venom gland transcriptomes from 20 venomous species reveals a strong convergence in gene expression profiles, indicating that different animals have independently adopted similar molecular mechanisms to perform the same function. The study also highlights the presence of stress response mechanisms in venom glands to cope with toxin production, as well as regulatory networks for epithelial development and maintenance.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Jelisaveta Djordjevic, Zoe Dumas, Marc Robinson-Rechavi, Tanja Schwander, Darren James Parker
Summary: Sexually dimorphic phenotypes are primarily caused by sex-biased gene expression during development. This study examined sex-biased gene expression during development in a hemimetabolous stick insect and compared it to a holometabolous fly. The results showed significant differences in the dynamics of sex-biased gene expression between the two insect species.
Article
Ecology
Darren J. Parker, Kamil S. Jaron, Zoe Dumas, Marc Robinson-Rechavi, Tanja Schwander
Summary: Sex chromosomes have evolved repeatedly across different species, with similar consequences such as accelerated evolution and increased accumulation of sexually antagonistic alleles. In Timema stick insects, the X chromosome has remained consistent in size and gene content over 30 million years of evolution, showing limited association with sexually biased genes.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Biochemical Research Methods
David Laloum, Marc Robinson-Rechavi
Summary: The study investigates the evolutionary origins of gene expression rhythmicity and suggests that rhythmicity of protein expression could be favored by selection to minimize costs. Furthermore, the study found that rhythmic gene expression may help reduce expression noise and genes under stronger purifying selection tend to be rhythmically expressed at the mRNA level. The adaptive role of rhythmic expression is supported by the observation that rhythmic genes are highly expressed yet tissue-specific.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tina Begum, Marc Robinson-Rechavi
Summary: Investigating how gene function evolves is crucial in evolutionary biology, and this can be done by comparing functional genomics results between species and genes. While pairwise comparisons are commonly used, they may lead to biased results due to the phylogenetic relatedness of genes. Phylogenetic comparative methods, although more accurate, rely on strong assumptions. Reanalysis of gene trees revealed biases and challenges in implementing phylogenetic methods in empirical gene studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)