Editorial Material
Biochemistry & Molecular Biology
Heather N. Chamberlain-Irwin, Matthew B. Hufford
Summary: A recent study reveals that during the domestication of maize and rice, the orthologs encoding WD40 protein undergo convergent selection. Knocking out these genes can increase yield in both crops without affecting other agronomic traits.
Article
Multidisciplinary Sciences
Joana Damas, Marco Corbo, Jaebum Kim, Jason Turner-Maier, Marta Farre, Denis M. Larkin, Oliver A. Ryder, Cynthia Steiner, Marlys L. Houck, Shaune Hall, Lily Shiue, Stephen Thomas, Thomas Swale, Mark Daly, Jonas Korlach, Marcela Uliano-Silva, Camila J. Mazzoni, Bruce W. Birren, Diane P. Genereux, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Martin T. Nweeia, Rebecca N. Johnson, Harris A. Tewin
Summary: Decrypting the rearrangements that drive mammalian chromosome evolution is crucial for understanding speciation, adaptation, and disease susceptibility. By computationally reconstructing ancestral karyotypes and syntenic relationships, the study reveals the chromosome structure and evolutionary history of the mammalian ancestors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Entomology
Zhixiang Pan, Yinhuan Ding, Shusheng Zhang, Luxian Li, Fangzhou Ma
Summary: This study presents the chromosome-level genome assembly of the butterfly species Papilio elwesi, which is endemic to China. The assembly of this genome enriches the available butterfly genome resources and provides a foundation for future research.
Article
Microbiology
Lajos Acs-Szabo, Laszlo Attila Papp, Matthias Sipiczki, Ida Miklos
Summary: Fission yeasts exhibit stable genome structures despite relatively fast evolution, with ancestral locally collinear blocks (aLCBs) proving to be the most conserved regions and potentially maintained by natural selection. Gene order within aLCBs is fission-yeast-specific, suggesting filamentous ancestors and not necessarily related to biological functions or co-expression rates.
Article
Evolutionary Biology
Timothy B. Yates, Kai Feng, Jin Zhang, Vasanth Singan, Sara S. Jawdy, Priya Ranjan, Paul E. Abraham, Kerrie Barry, Anna Lipzen, Chongle Pan, Jeremy Schmutz, Jin-Gui Chen, Gerald A. Tuskan, Wellington Muchero
Summary: Orphan genes, unique to Populus trichocarpa, were identified, and evidence of de novo gene evolution was provided through comparison across different species and genomes. By associating orphan genes with expression quantitative trait loci, common biological themes such as stress response and defense were identified. Additionally, a putative cis-element for a de novo gene and the evolution of a putative transcription factor binding site were described using conserved synteny.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Masato Mikami, Toshinao Ineno, Andrew W. Thompson, Ingo Braasch, Mikio Ishiyama, Kazuhiko Kawasaki
Summary: The study revealed that Polypteriformes and Lepisosteiformes have more SCPP genes, which may be involved in the formation of ganoid scales, while many genes have been lost in Acipenseriformes and Amiiformes. The common ancestors of extant actinopterygians likely had a large repertoire of SCPP genes, with many genes independently lost in evolution.
Article
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Evolutionary Biology
Bin Yan, Houding Ou, Lan Wei, Xiuqin Wang, Xiaofei Yu, Jianfeng Liu, Maofa Yang
Summary: This study generated a chromosome-level genome assembly of the storage pest Ephestia elutella using Nanopore long reads and Hi-C data, revealing expanded gene families related to digestion, detoxification, and chemosensation. The findings provide a valuable genomic basis for better understanding the biology of E. elutella.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Melquizedec Luiz Silva Pinheiro, Cleusa Yoshiko Nagamachi, Talita Fernanda Augusto Ribas, Cristovam Guerreiro Diniz, Patricia Caroline Mary O'Brien, Malcolm Andrew Ferguson-Smith, Fengtang Yang, Julio Cesar Pieczarka
Summary: The order Charadriiformes is one of the largest and diverse orders of birds, making it an excellent model for studying evolution. This study used chromosome painting to analyze two species of Charadriidae, revealing chromosome conservation as a common characteristic. Comparative analysis between Charadriiformes suborders and the order Gruiformes provided insights into phylogenetic relationships and karyotypic evolution. However, no shared rearrangements were found among Charadriiformes suborders, indicating independent evolutionary paths.
Article
Biochemistry & Molecular Biology
Petr Fajkus, Vratislav Peska, Jiri Fajkus, Eva Sykorova
Summary: This study examined the presence and functional status of TERT variants in allotetraploid Nicotiana species of diverse evolutionary ages, as well as in other diploid and polyploid plant species. Results showed various patterns of retention or loss of parental TERT variants and divergence in their functions, with all identified TERT variants confirmed to be expressed. Synteny analyses revealed the conservation and translocation of TERT genes in representative plant genomes, with translocation becoming fixed in target loci in various diploid and polyploid species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Yuki Kimura, Masato Nikaido
Summary: Type I and type II keratins are subgroups of intermediate filament proteins that provide toughness to the epidermis and protect it from water loss. Ancient fish lineages share keratin gene clusters, with a novel subcluster found in reedfish. Molecular evolutionary analyses suggest that amphibians' epidermal keratin gene subclusters originated from non-terrestrial ancestors.
Article
Biotechnology & Applied Microbiology
Qian Xiong, Yuxin Hu, Wenqi Lv, Qinghua Wang, Guoxiang Liu, Zhengyu Hu
Summary: The study identified five chloroplast genomes of Oedogonium species, revealing their structural conservation but variation in genome sizes, AT contents, introns, and repeats. Phylogenetic analyses suggested that both Oedocladium and Oedogonium are polyphyletic groups. The identification of a positively selected gene in certain species indicates adaptive evolution in terrestrial Oedogoniales taxa.
Article
Genetics & Heredity
Theodoros Danis, Vasileios Papadogiannis, Alexandros Tsakogiannis, Jon B. Kristoffersen, Daniel Golani, Dimitris Tsaparis, Aspasia Sterioti, Panagiotis Kasapidis, Georgios Kotoulas, Antonios Magoulas, Costas S. Tsigenopoulos, Tereza Manousaki
Summary: This study presents the first near-chromosome level genome assembly of L. sceleratus and explores its evolutionary landscape, positioning it closer to T. nigroviridis through phylogenomic analysis. Gene family evolution analysis reveals rapid expansion of genes associated with immune response, providing insights into the genetic basis of successful colonization by L. sceleratus. Additionally, mutations in voltage-gated sodium channel (NaV 1.4) linked to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, indicating a complex evolution of this trait.
FRONTIERS IN GENETICS
(2021)
Article
Ecology
Aya Kuretani, Takayoshi Yamamoto, Masanori Taira, Tatsuo Michiue
Summary: In this study, by phylogenetic and synteny analyses, the orthologous and paralogous relationships of hes genes in various species including humans, mice, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark, and three species of frogs were elucidated. It was found that hes5 clusters were not duplicated in mammals, however, they were conserved in teleost with fewer genes compared to frogs. The hes5 cluster-like structure was also identified in the elephant shark genome, but not in cyclostomes.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Yuanning Li, Hongyue Liu, Jacob L. Steenwyk, Abigail L. LaBella, Marie-Claire Harrison, Marizeth Groenewald, Xiaofan Zhou, Xing-Xing Shen, Tao Zhao, Chris Todd Hittinger, Antonis Rokas
Summary: Examining the changes in order and arrangement of homologous genes is crucial for understanding genome evolution in eukaryotes. This study analyzed 120 high quality genomes of budding yeast species to investigate the evolution of genome organization and compared it with animals and plants. The decay of macrosynteny and microsynteny was strongly associated with evolutionary divergence in the budding yeast major clades. However, the microsynteny of many genes, especially in metabolic clusters, was deeply conserved within major clades and across subphylum. Comparing genomes with similar divergence times, budding yeasts showed lower conservation in macrosynteny compared to animals and filamentous fungi, but higher conservation than angiosperms. In contrast, they exhibited similar levels of microsynteny conservation with mammals, while angiosperms had very low conservation.
Review
Behavioral Sciences
Jose Luis Ferran, Manuel Irimia, Luis Puelles
Summary: This essay re-examines the unique rostrally elongated notochord described in amphioxus and proposes an alternative interpretation that it represents a variant form of the prechordal plate. The author compares the observed patterns and gene expression patterns with those of other vertebrates and concludes that the hypothesis of a prechordal nature of the elongated amphioxus notochord is consistent with the evidence presented.
BRAIN BEHAVIOR AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Luna Tammer, Ofir Hameiri, Ifat Keydar, Vanessa Rachel Roy, Asaf Ashkenazy-Titelman, Noelia Custodio, Itay Sason, Ronna Shayevitch, Victoria Rodriguez-Vaello, Jose Rino, Galit Lev Maor, Yodfat Leader, Doha Khair, Erez Lieberman Aiden, Ran Elkon, Manuel Irimia, Roded Sharan, Yaron Shav-Tal, Maria Carmo-Fonseca, Gil Ast
Summary: This study reveals that the peripheral and central regions of the nucleus harbor genes with different exon-intron architectures and that they lead to different splicing outcomes. Genes in the periphery have low GC content exons and undergo exon definition splicing, while genes in the nuclear center have high GC content exons and undergo intron definition splicing. This highlights the importance of 3D genome organization in splicing regulation.
Article
Multidisciplinary Sciences
Antonio Torres-Mendez, Sinziana Pop, Sophie Bonnal, Isabel Almudi, Alida Avola, Ruairi J. Roberts, Chiara Paolantoni, Ana Alcaina-Caro, Ane Martin-Anduaga, Irmgard U. Haussmann, Violeta Morin, Fernando Casares, Matthias Soller, Sebastian Kadener, Jean-Yves Roignant, Lucia Prieto-Godino, Manuel Irimia
Summary: Alternative splicing increases transcriptomic complexity of neurons throughout animal evolution. The neuronal microexon program in Drosophila and mammals exhibit differences, but both are involved in neuronal activity and ion channels.
Article
Biochemistry & Molecular Biology
Ester Anton-Galindo, Elisa Dalla Vecchia, Javier G. Orlandi, Gustavo Castro, Emilio J. Gualda, Andrew M. J. Young, Marc Guasch-Piqueras, Concepcio Arenas, Carlos Herrera-Ubeda, Jordi Garcia-Fernandez, Fernando Aguado, Pablo Loza-Alvarez, Bru Cormand, William H. J. Norton, Noelia Fernandez-Castillo
Summary: Genetic variants in YWHAZ contribute to neurodevelopmental disorders such as autism spectrum disorder and schizophrenia. Using zebrafish as a model, researchers found that YWHAZ is expressed widely in neurons during development and limited to Purkinje cells in the adult cerebellum. Knocking out YWHAZ resulted in altered neuronal activity and connectivity in the hindbrain, decreased monoamine levels, and freeze behavior in adult fish, which could be reversed with drugs targeting monoamine neurotransmission.
MOLECULAR PSYCHIATRY
(2022)
Article
Biochemical Research Methods
Anne F. Nielsen, Albrecht Bindereif, Irene Bozzoni, Mor Hanan, Thomas B. Hansen, Manuel Irimia, Sebastian Kadener, Lasse S. Kristensen, Ivano Legnini, Mariangela Morlando, Morten T. Jarlstad Olesen, R. Jeroen Pasterkamp, Stephan Preibisch, Nikolaus Rajewsky, Christin Suenkel, Jorgen Kjems
Summary: There is a growing number of circular RNA (circRNA) papers in recent years, highlighting the urgent need for common experimental standards and best practice principles to advance the field and enhance understanding of this group of RNA molecules.
Article
Biochemistry & Molecular Biology
Thomas Spruce, Mireya Plass, Andre Gohr, Debashish Ray, Maria Martinez de Lagran, Gregor Rot, Ana Novoa, Demian Burguera, Jon Permanyer, Marta Miret, Hong Zheng, Maurice S. Swanson, Quaid Morris, Moises Mallo, Mara Dierssen, Timothy R. Hughes, Barbara Pernaute, Manuel Irimia
Summary: Understanding the regulatory interactions that control gene expression during the development of novel tissues is a key goal of evolutionary developmental biology. Here, we show that Mbnl3 has evolved a novel placental function in eutherian mammals as a result of evolutionary specialization. Mbnl3 loss leads to increased placental growth and fetal resource allocation under limiting conditions.
Article
Multidisciplinary Sciences
Christopher D. R. Wyatt, Barbara Pernaute, Andre Gohr, Marta Miret-Cuesta, Lucia Goyeneche, Quirze Rovira, Marion C. Salzer, Elvan Boke, Ozren Bogdanovic, Sophie Bonnal, Manuel Irimia
Summary: Alternative splicing regulation during embryonic development leads to the production of disruptive noncanonical isoforms, especially in genes enriched for DNA damage response. Two core spliceosomal components, Snrpb and Snrpd2, regulate this process.
Article
Biochemistry & Molecular Biology
Hong Han, Andrew J. Best, Ulrich Braunschweig, Nicholas Mikolajewicz, Jack Daiyang Li, Jonathan Roth, Fuad Chowdhury, Federica Mantica, Syed Nabeel-Shah, Guillermo Parada, Kevin R. Brown, Dave O'Hanlon, Jiarun Wei, Yuxi Yao, Abdelrahman Abou Zid, Lim Caden Comsa, Mark Jen, Jenny Wang, Alessandro Datti, Thomas Gonatopoulos-Pournatzis, Robert J. Weatheritt, Jack F. Greenblatt, Jeffrey L. Wrana, Manuel Irimia, Anne-Claude Gingras, Jason Moffat, Benjamin J. Blencowe
Summary: This study identifies factors controlling dynamic splicing events during mammalian neurogenesis. Rbm38 is found to negatively control neural splicing, while Puf60 promotes neural splicing patterns. A neural-differential exon plays a crucial role in this regulation, and its removal rewires splicing networks at different stages of neurogenesis. Single-cell transcriptome analysis reveals distinct roles for Rbm38 and Puf60 isoforms in neuronal differentiation.
Article
Biochemistry & Molecular Biology
Toby Doyle, Eva Jimenez-Guri, Will L. S. Hawkes, Richard Massy, Federica Mantica, Jon Permanyer, Luca Cozzuto, Toni Hermoso Pulido, Tobias Baril, Alex Hayward, Manuel Irimia, Jason W. Chapman, Chris Bass, Karl R. Wotton
Summary: In this study, the researchers assembled a high-quality draft genome of the marmalade hoverfly and compared the transcriptomes of actively migrating and non-migratory hoverflies. The results revealed a set of genes with strong differential expression in metabolism, muscle structure and function, hormonal regulation, immunity, and other aspects related to migration. These features of the migrant phenotype have evolved through the integration and modification of various genetic pathways.
Article
Multidisciplinary Sciences
Ludovica Ciampi, Federica Mantica, Laura Lopez-Blanch, Jon Permanyer, Cristina Rodriguez-Marin, Jingjing Zang, Damiano Cianferoni, Senda Jimenez-Delgado, Sophie Bonnal, Samuel Miravet-Verde, Verena Ruprecht, Stephan C. F. Neuhauss, Sandro Banfi, Sabrina Carrella, Luis Serrano, Sarah A. Head, Manuel Irimia
Summary: Retinal photoreceptors have a unique transcriptomic profile, including distinct microexons and a microexon program regulated by Srrm3. Deletion of Srrm3 may lead to retinal diseases, highlighting the transcriptomic specialization and functionality of photoreceptors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Genetics & Heredity
Federica Mantica, Manuel Irimia
Summary: Animal species exhibit high gene conservation but also display diverse cell types and tissue phenotypes. The diversity of phenotypes is mainly regulated through differential gene usage, which involves mechanisms such as regulated gene transcription and regulated alternative splicing. This review proposes a novel framework, the 3D-evo space, for the comprehensive comparison between regulated gene transcription and regulated alternative splicing, highlighting their molecular basis, tissue-specific contributions, and evolutionary determinants. By discussing general trends and specific examples of tissue program evolution, the review provides insights into the common regulatory principles and unique properties of these two molecular mechanisms.
ANNUAL REVIEW OF GENETICS
(2022)
Article
Multidisciplinary Sciences
Ksenia Skvortsova, Stephanie Bertrand, Danila Voronov, Paul E. Duckett, Samuel E. Ross, Marta Silvia Magri, Ignacio Maeso, Robert J. Weatheritt, Jose Luis Gomez Skarmeta, Maria Ina Arnone, Hector Escriva, Ozren Bogdanovic
Summary: The study shows that invertebrate deuterostomes use TET enzymes for targeted demethylation of regulatory regions associated with developmental genes, indicating a conservation of this major gene-regulatory module in vertebrates.
Article
Endocrinology & Metabolism
Jonas Juan-Mateu, Simon Bajew, Marta Miret-Cuesta, Luis P. iniguez, Amaya Lopez-Pascual, Sophie Bonnal, Goutham Atla, Silvia Bonas-Guarch, Jorge Ferrer, Juan Valcarcel, Manuel Irimia
Summary: The presence of microexons in pancreatic islet cells is regulated by the RNA binding protein SRRM3 and is sensitive to glucose levels. Manipulation of SRRM3 or specific microexons leads to abnormal insulin secretion and is associated with diabetes or hypoglycaemia.
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
Biotechnology & Applied Microbiology
Goutham Atla, Silvia Bonas-Guarch, Mirabai Cuenca-Ardura, Anthony Beucher, Daniel J. M. Crouch, Javier Garcia-Hurtado, Ignasi Moran, Manuel Irimia, Rashmi B. Prasad, Anna L. Gloyn, Lorella Marselli, Mara Suleiman, Thierry Berney, Eelco J. P. de Koning, Julie Kerr-Conte, Francois Pattou, John A. Todd, Lorenzo Piemonti, Jorge Ferrer
Summary: This study reveals the widespread effects of common genetic variations on RNA splicing in pancreatic islets. It identifies the association between splicing variations and susceptibility to T2D and T1D, providing biologically plausible explanations for diabetes susceptibility and potential therapeutic targets.
