-
Chromosome-level assembly and annotation of the pearly heath Coenonympha arcania butterfly genome Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-15 Fabrice Legeai, Sandra Romain, Thibaut Capblancq, Paul Doniol-Valcroze, Mathieu Joron, Claire Lemaitre, Laurence Després
We present the first chromosome-level genome assembly and annotation of the pearly heath Coenonympha arcania, generated with a PacBio HiFi sequencing approach, and complemented with Hi-C data. We additionally compare synteny, gene and repeat content between C. arcania and other Lepidopteran genomes. This reference genome will enable future population genomics studies with Coenonympha butterflies, a
-
Calling structural variants with confidence from short-read data in wild bird populations Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-15 Gabriel David, Alicia Bertolotti, Ryan Layer, Douglas Scofield, Alexander Hayward, Tobias Baril, Hamish A Burnett, Erik Gudmunds, Henrik Jensen, Arild Husby
Comprehensive characterisation of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation (SV), reproducible and high-confidence SV callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus)
-
Evidence of Nonrandom Patterns of Functional Chromosome Organization in Danaus plexippus Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-15 Ashlyn Kimura, Alwyn C Go, Therese Markow, José M Ranz
Our understanding on the interplay between gene functionality and gene arrangement at different chromosome scales relies on a few Diptera and the honeybee, species with quality-reference genome assemblies, accurate gene annotations, and abundant transcriptome data. Using recently generated ‘omics resources in the monarch butterfly D. plexippus, a species with many more and smaller chromosomes relative
-
The complex landscape of structural divergence between the Drosophila pseudoobscura and D. persimilis genomes Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-14 Javier Carpinteyro-Ponce, Carlos A Machado
Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we
-
Background selection from unlinked sites causes non-independent evolution of deleterious mutations Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-13 Joseph Matheson, Joanna Masel
Background selection describes the reduction in neutral diversity caused by selection against deleterious alleles at other loci. It is typically assumed that the purging of deleterious alleles affects linked neutral variants, and indeed simulations typically only treat a genomic window. However, background selection at unlinked loci also depresses neutral diversity. In agreement with previous analytical
-
Where are the formerly Y-linked genes in the Ryukyu spiny rat that has lost its Y chromosome? Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-13 Jiachen Li, Siliang Song, Jianzhi Zhang
It has been predicted that the highly degenerate mammalian Y chromosome will be lost eventually. Indeed, Y was lost in the Ryukyu spiny rat Tokudaia osimensis, but the fate of the formerly Y-linked genes is not completely known. We looked for all 12 ancestrally Y-linked genes in a draft T. osimensis genome sequence. Zfy1, Zfy2, Kdm5d, Eif2s3y, Usp9y, Uty, and Ddx3y are putatively functional and are
-
Highly resolved genomes of two closely related lineages of the rodent louse Polyplax serrata with different host specificities Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-13 Jana Martinů, Hassan Tarabai, Jan Štefka, Václav Hypša
Sucking lice of the parvorder Anoplura are permanent ectoparasites with specific lifestyle and highly derived features. Currently, genomic data are only available for a single species, the human louse Pediculus humanus. Here, we present genomes of two distinct lineages, with different host spectra, of a rodent louse Polyplax serrata. Genomes of these ecologically different lineages are closely similar
-
Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Marie Morel, Anna Zhukova, Frédéric Lemoine, Olivier Gascuel
Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent
-
Ancient loss of catalytic selenocysteine spurred convergent adaptation in a mammalian oxidoreductase Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Jasmin Rees, Gaurab Sarangi, Qing Cheng, Martin Floor, Aida M Andrés, Baldomero Oliva Miguel, Jordi Villà-Freixa, Elias SJ Arnér, Sergi Castellano
Selenocysteine (Sec), the 21st amino acid specified by the genetic code, is a rare selenium-containing residue found in the catalytic site of selenoprotein oxidoreductases. Sec is analogous to the common cysteine (Cys) amino acid but its selenium atom offers physical-chemical properties not provided by the corresponding sulfur atom in Cys. Catalytic sites with Sec in selenoproteins of vertebrates are
-
Chromosome-scale genome assembly for clubrush (Bolboschoenus planiculmis) indicates a karyotype with high chromosome number and heterogeneous centromere distribution Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Yu Ning, Yang Li, Hai Yan Lin, En Ze Kang, Yu Xin Zhao, Shu Bin Dong, Yong Li, Xiao Fei Xia, Yi Fei Wang, Chun Yi Li
Bolboschoenus planiculmis (F.Schmidt) T.V.Egorova is a typical wetland plant in the species-rich Cyperaceae family. This species contributes prominently to carbon dynamics and trophic integration in wetland ecosystems.Previous studies have reported that the chromosomes of B. planiculmis are holocentric, i.e. they have kinetic activity along their entire length and carry multiple centromeres. This feature
-
Distribution and functional analysis of isocitrate dehydrogenases across kinetoplastids Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Ľubomíra Chmelová, Kristína Záhonová, Amanda T S Albanaz, Liudmyla Hrebenyk, Anton Horváth, Vyacheslav Yurchenko, Ingrid Škodová-Sveráková
Isocitrate dehydrogenase (IDH) is an enzyme converting isocitrate to α-ketoglutarate in the canonical tricarboxylic acid (TCA) cycle. There are three different types of IDH documented in eukaryotes. Our study points out the complex evolutionary history of IDHs across kinetoplastids, where the common ancestor of Trypanosomatidae and Bodonidae was equipped with two isoforms of the IDH enzyme: the NADP+-dependent
-
Genomic resources and annotations for a colonial ascidian, the light-bulb sea squirt Clavelina lepadiformis Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-05 Vladimir Daric, Maxence Lanoizelet, Hélène Mayeur, Cécile Leblond, Sébastien Darras
Ascidian embryos have been studied since the birth of experimental embryology at the end of the 19th century. They represent textbook examples of mosaic development characterized by a fast development with very few cells and invariant cleavage patterns and lineages. Ascidians belong to tunicates, the vertebrate sister group, and their study is essential to shed light on the emergence of vertebrates
-
Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-27 Bennet J McComish, Michael A Charleston, Matthew Parks, Carlo Baroni, Maria Cristina Salvatore, Ruiqiang Li, Guojie Zhang, Craig D Millar, Barbara R Holland, David M Lambert
Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using
-
Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-27 Sofia Moura, Ingrid Hartl, Veronika Brumovska, Peter P Calabrese, Atena Yasari, Yasmin Striedner, Marina Bishara, Theresa Mair, Thomas Ebner, Gerhard J Schütz, Eva Sevcsik, Irene Tiemann-Boege
Delayed fatherhood results in a higher risk of inheriting a new germline mutation that might result in a congenital disorder in the offspring. In particular, some FGFR3 mutations increase in frequency with age, but there are still a large number of uncharacterized FGFR3 mutations that could be expanding in the male germline with potentially early- or late-onset effects in the offspring. Here, we used
-
Turnovers of sex-determining mutation in the golden pompano and related species provide insights into microevolution of undifferentiated sex chromosome Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-25 Liang Guo, Danilo Malara, Pietro Battaglia, Khor Waiho, D Allen Davis, Yu Deng, Zhongyuan Shen, Ke Rao
The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within
-
Mutational signatures in wild type Escherichia coli strains reveal predominance of DNA polymerase errors Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-23 Sofya K Garushyants, Mrudula Sane, Maria V Selifanova, Deepa Agashe, Georgii A Bazykin, Mikhail S Gelfand
While mutational processes operating in the Escherichia coli genome have been revealed by multiple laboratory experiments, the contribution of these processes to accumulation of bacterial polymorphism and evolution in natural environments is unknown. To address this question, we reconstruct signatures of distinct mutational processes from experimental data on E. coli hypermutators, and ask how these
-
Impact of homologous recombination on core genome evolution and host adaptation of Pectobacterium parmentieri Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-22 Dario Arizala, Mohammad Arif
Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution
-
High-quality genome assemblies of four members of the Podospora anserina species complex Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-22 S Lorena Ament-Velásquez, Aaron A Vogan, Ola Wallerman, Fanny Hartmann, Valérie Gautier, Philippe Silar, Tatiana Giraud, Hanna Johannesson
The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of seven, closely related species. In addition to P. anserina, high-quality genomic resources are available
-
The genome of Plasmodium gonderi: Insights into the evolution of human malaria parasites Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-19 Axl S Cepeda, Beatriz Mello, M Andreína Pacheco, Zunping Luo, Steven A Sullivan, Jane M Carlton, Ananias A Escalante
Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that is not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other
-
The Biofilm Lifestyle Shapes the Evolution of β-Lactamases Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-17 Øyvind M Lorentzen, Anne Sofie B Haukefer, Pål J Johnsen, Christopher Frøhlich
The evolutionary relationship between the biofilm lifestyle and antibiotic resistance enzymes remains a subject of limited understanding. Here, we investigate how β-lactamases affect biofilm formation in Vibrio cholerae and how selection for a biofilm lifestyle impacts the evolution of these enzymes. Genetically diverse β-lactamases expressed in V. cholerae displayed a strong inhibitory effect on biofilm
-
Nucleosomes at the dawn of eukaryotes Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-16 Antoine Hocher, Tobias Warnecke
Genome regulation in eukaryotes revolves around the nucleosome, the fundamental building block of eukaryotic chromatin. Its constituent parts, the four core histones (H3, H4, H2A, H2B), are universal to eukaryotes. Yet despite its exceptional conservation and central role in orchestrating transcription, repair, and other DNA-templated processes, the origins and early evolution of the nucleosome remain
-
A chromosome-level genome assembly and annotation for the clouded apollo butterfly (Parnassius mnemosyne), a species of global conservation concern Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-15 J Höglund, G Dias, R -A Olsen, A Soares, I Bunikis, V Talla, N Backström
The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. Development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity
-
Cytogenetic analysis of the fish genus Carassius indicates divergence, fission and segmental duplication as drivers of tandem repeat and microchromosome evolution Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-08 Nicola R Fornaini, Halina Černohorská, Lívia do Vale Martins, Martin Knytl
Fishes of the genus Carassius are useful experimental vertebrate models for study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Carassius polyploids with ≥ 150 chromosomes have microchromosomes, but their origin, especially in European populations, is unknown
-
Cryogenian origins of multicellularity in Archaeplastida Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-08 Alexander M C Bowles, Christopher J Williamson, Tom A Williams, Philip C J Donoghue
Earth was impacted by global glaciations during the Cryogenian (720-635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the
-
Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment across Cells, Organisms, and Populations Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-07 Samuel N Bogan, Soojin V Yi
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and, subsequently impact phenotypes. We first discuss origins
-
Lack of dosage balance and incomplete dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-06 Timothy H Webster, Annika Vannan, Brendan J Pinto, Grant Denbrock, Matheo Morales, Greer A Dolby, Ian T Fiddes, Dale F DeNardo, Melissa A Wilson
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and
-
Divergent evolutionary rates of primate brain regions as revealed by genomics and transcriptomics Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-05 Xiao-Lin Zhuang, Yong Shao, Chun-Yan Chen, Long Zhou, Yong-Gang Yao, David N Cooper, Guo-Jie Zhang, Wen Wang, Dong-Dong Wu
Although the primate brain contains numerous functionally distinct structures that have experienced diverse genetic changes during the course of evolution and development, these changes remain to be explored in detail. Here we utilize two classic metrics from evolutionary biology, the evolutionary rate index (ERI) and the transcriptome age index (TAI), to investigate the evolutionary alterations that
-
The Addis Ababa Lions: whole-genome sequencing of a rare and precious population Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-01 Marjan Barazandeh, Divya Kriti, Jörns Fickel, Corey Nislow
Lions are widely known as charismatic predators that once roamed across the globe, but their populations have been greatly affected by environmental factors and human activities over the last 150 years. Of particular interest is the Addis Ababa lion population, which has been maintained in captivity at around 20 individuals for over 75 years, while many wild African lion populations have become extinct
-
Patterns of genomic diversity in a fig-associated close relative of C. elegans Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-01 Gavin C Woodruff, John H Willis, Patrick C Phillips
The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics
-
Phylogenomics of the ecdysteroid kinase-like (EcKL) gene family in insects highlights roles in both steroid hormone metabolism and detoxification Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-31 Jack L Scanlan, Charles Robin
The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid moulting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown and there is little information on their evolution across all insects
-
The mutational road not taken: using Ancestral Sequence Resurrection to evaluate the evolution of plant enzyme substrate preferences Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-30 Emily M Catania, Nicole M Dubs, Shejal Soumen, Todd J Barkman
We investigated the flowering plant Salicylic Acid Methyl Transferase (SAMT) enzyme lineage to understand the evolution of substrate preference change. Previous studies indicated that a single amino acid replacement to the SAMT active site (H150 M) was sufficient to change ancestral enzyme substrate preference from benzoic acid to the structurally similar substrate, salicylic acid. Yet, subsequent
-
Epigenetic and genetic differentiation between Coregonus species pairs Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-25 Clare J Venney, Claire Mérot, Eric Normandeau, Clément Rougeux, Martin Laporte, Louis Bernatchez
Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental
-
The Site/Group Extended Data format and tools Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-22 Julien Y Dutheil, Diyar Hamidi, Basile Pajot
Comparative sequence analysis permits unravelling the molecular processes underlying gene evolution. Many statistical methods generate candidate positions within genes, such as fast or slowly-evolving sites, coevolving groups of residues, sites undergoing positive selection or changes in evolutionary rates. Understanding the functional causes of these evolutionary patterns requires combining the results
-
Transposon removal Reveals Their Adaptive Fitness Contribution Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-21 Susanne Cranz-Mileva, Eve Reilly, Noor Chalhoub, Rohan Patel, Tania Atanassova, Weihuan Cao, Christopher Ellison, Mikel Zaratiegui
Transposable Elements (TE) are molecular parasites that persist in their host genome by generating new copies to outpace natural selection. TE exert a large influence on host genome evolution, in some cases providing adaptive changes. Here we measure the fitness effect of the TE insertions in the fission yeast Schizosaccharomyces pombe type strain by removing all insertions of its only native TE family
-
Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-21 Vincent Kiplangat Bett, Ariana Macon, Beatriz Vicoso, Marwan Elkrewi
Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources
-
The Promise of Inferring the Past using the Ancestral Recombination Graph (ARG) Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-20 Débora Y C Brandt, Christian D Huber, Charleston W K Chiang, Diego Ortega-Del Vecchyo
The Ancestral Recombination Graph (ARG) is a structure that represents the history of coalescent and recombination events connecting a set of sequences (Hudson 1991). The full ARG can be represented as a set of genealogical trees at every locus in the genome, annotated with recombination events that change the topology of the trees between adjacent loci and the mutations that occurred along the branches
-
Genomic architecture predicts tree topology, population structuring, and demographic history in Amazonian birds Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-18 Gregory Thom, Lucas Rocha Moreira, Romina Batista, Marcelo Gehara, Alexandre Aleixo, Brian Tilston Smith
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the
-
Flatworm Transcriptomes Reveal Widespread Parasitism by Histophagous Ciliates Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-17 M Ryan Woodcock, Kaleigh Powers, Kirsten Snead, Jason Pellettieri
Unicellular ciliates like Tetrahymena are best known as free-living bacteriovores, but many species are facultative or obligate parasites. These ‘histophages’ feed on the tissues of hosts ranging from planarian flatworms to commercially important fish and the larvae of imperiled freshwater mussels. Here, we developed a novel bioinformatics pipeline incorporating the nonstandard ciliate genetic code
-
Signatures of co-evolution and co-regulation in the CYP3A and CYP4F genes in humans Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-10 Alex Richard-St-Hilaire, Isabel Gamache, Justin Pelletier, Jean-Christophe Grenier, Raphael Poujol, Julie G Hussin
Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated
-
The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-10 Vivak Soni, Susanne P Pfeifer, Jeffrey D Jensen
Disentangling the effects of demography and selection has remained a focal point of population genetic analysis. Knowledge about mutation and recombination is essential in this endeavour; however, despite clear evidence that both mutation and recombination rates vary across genomes, it is common practice to model both rates as fixed. In this study, we quantify how this unaccounted for rate heterogeneity
-
Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-10 Karen Bascón-Cardozo, Andrea Bours, Georg Manthey, Gillian Durieux, Julien Y Dutheil, Peter Pruisscher, Linda Odenthal-Hesse, Miriam Liedvogel
Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales
-
Chromosome Level Genome Assembly and Annotation of a Periodical Cicada Species: Magicicada septendecula Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-05 Jonas Bush, Cynthia Webster, Jill Wegrzyn, Chris Simon, Edward Wilcox, Ruqayya Khan, David Weisz, Olga Dudchenko, Erez Lieberman Aiden, Paul Frandsen
We present a high-quality assembly and annotation of the periodical cicada species, Magicicada septendecula (Hemiptera: Auchenorrhyncha: Cicadidae). Periodical cicadas have a significant ecological impact, serving as a food source for many mammals, reptiles, and birds. Magicicada are well known for their massive emergences of one to three species that appear in different locations in the eastern United
-
High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the Drosophila virilis sub-group Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-30 Jullien M Flynn, Yasir H Ahmed-Braimah, Manyuan Long, Rod A Wing, Andrew G Clark
High-quality genome assemblies across a range of non-traditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in the Drosophila genus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model
-
Novel plastid genome characteristics in Fugacium kawagutii and the trend of accelerated evolution of plastid proteins in dinoflagellates Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-29 Jiamin He, Yulin Huang, Ling Li, Sitong Lin, Minglei Ma, Yujie Wang, Senjie Lin
Typical (peridinin-containing) dinoflagellates possess plastid genomes composed of small plasmids named ‘minicircles’. Despite the ecological importance of dinoflagellate photosynthesis in corals and marine ecosystems, the structural characteristics, replication dynamics, and evolutionary forcing of dinoflagellate plastid genomes remain poorly understood. Here we sequenced the plastid genome of the
-
Astrocytes drive divergent metabolic gene expression in humans and chimpanzees Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-29 Trisha M Zintel, Jason Pizzollo, Christopher G Claypool, Courtney C Babbitt
The human brain utilizes ∼ 20% of all of the body’s metabolic resources, while chimpanzee brains use less than 10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell-type specific interspecies differences in brain gene expression, we conducted
-
Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-29 Aivars Cīrulis, Anna K Nordén, Allison M Churcher, Steven A Ramm, Kira S Zadesenets, Jessica K Abbott
The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical
-
No evidence that selection on synonymous codon usage affects patterns of protein evolution in bacteria Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-27 Ana Filipa Moutinho, Adam Eyre-Walker
Bias in synonymous codon usage has been reported across all kingdoms of life. Evidence suggests that codon usage bias is often driven by selective pressures, typically for translational efficiency. These selective pressures have been shown to depress the rate at which synonymous sites evolve. We hypothesise that selection on synonymous codon use could also slow the rate of protein evolution if a non-synonymous
-
Genomic tools in biological invasions: current state and future frontiers Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-19 Angela McGaughran, Manpreet K Dhami, Elahe Parvizi, Amy L Vaughan, Dianne M Gleeson, Kathryn A Hodgins, Lee A Rollins, Carolyn K Tepolt, Kathryn G Turner, Kamolphat Atsawawaranunt, Paul Battlay, Carlos Congrains, Angelica Crottini, Tristan P W Dennis, Claudia Lange, Xiaoyue P Liu, Paige Matheson, Henry L North, Iva Popovic, Marc Rius, Anna W Santure, Katarina C Stuart, Hui Zhen Tan, Cui Wang, Jonathan
Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here
-
Negative selection on a SOD1 mutation limits canine degenerative myelopathy while avoiding inbreeding Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-19 Hisashi Ukawa, Noriyoshi Akiyama, Fumiko Yamamoto, Ken Ohashi, Genki Ishihara, Yuki Matsumoto
Several hundred disease-causing mutations are currently known in domestic dogs. Breeding management is therefore required to minimize their spread. Recently, genetic methods such as direct-to-consumer testing have gained popularity; however, their effects on dog populations are unclear. Here, we aimed to evaluate the influence of genetic testing on the frequency of mutations responsible for canine
-
Archaic Introgression Shaped Human Circadian Traits Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-14 Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, John A Capra
When the ancestors of modern Eurasians migrated out of Africa and interbred with Eurasian archaic hominins, namely, Neanderthals and Denisovans, DNA of archaic ancestry integrated into the genomes of anatomically modern humans. This process potentially accelerated adaptation to Eurasian environmental factors, including reduced ultraviolet radiation and increased variation in seasonal dynamics. However
-
Opportunistic bacteria of grapevine crown galls are equipped with the genomic repertoire for opine utilization Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-12 Hanna Faist, Markus J Ankenbrand, Wiebke Sickel, Ute Hentschel, Alexander Keller, Rosalia Deeken
Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall (CG) disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbour a tumor-inducing (Ti) plasmid and induce formation of crown galls (CGs) due to the oncogenes encoded on the transfer-DNA (T-DNA). Expression of oncogenes in transformed host cells induce unregulated cell
-
Patchwork: alignment-based retrieval and concatenation of phylogenetic markers from genomic data Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-12 Felix Thalén, Clara G Köhne, Christoph Bleidorn
Low-coverage whole-genome sequencing (LC-WGS; also known as “genome skimming”) is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic
-
Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-12 Matthew J Penn, Neil Scheidwasser, Joseph Penn, Christl A Donnelly, David A Duchêne, Samir Bhatt
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible
-
Widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements, and duplication Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-12 Xavier Dallaire, Raphael Bouchard, Philippe Hénault, Gabriela Ulmo-Diaz, Eric Normandeau, Claire Mérot, Louis Bernatchez, Jean-Sébastien Moore
Most population genomic tools rely on accurate SNP calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate
-
Genetic affinities and adaptation of the South-west coast populations of India Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-12 Lomous Kumar, Anuhya Chowdhari, Jaison J Sequeira, Mohammed S Mustak, Moinak Banerjee, Kumarasamy Thangaraj
Evolutionary event has not only altered the genetic structure of human populations but also associated with social and cultural transformation. South Asian populations were the result of migration and admixture of genetically and culturally diverse groups. Most of the genetic studies pointed to large-scale admixture event between Ancestral North Indian (ANI) and Ancestral South Indian (ASI) groups
-
Chromosome-Level Genome Assembly of the Blacktail Brush Lizard, Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-07 Elizabeth Davalos-Dehullu, Sarah M Baty, Robert N Fisher, Peter A Scott, Greer A Dolby, Adrian Munguia-Vega, Diego Cortez
Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is
-
Novel insights into the landscape of crossover and non-crossover events in rhesus macaques (Macaca mulatta) Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-05 Cyril J Versoza, Sarah Weiss, Ravneet Johal, Bruno La Rosa, Jeffrey D Jensen, Susanne P Pfeifer
Meiotic recombination landscapes differ greatly between distantly and closely related taxa, populations, individuals, sexes, and even within genomes; however, the factors driving this variation are yet to be well elucidated. Here, we directly estimate contemporary crossover rates and, for the first-time, non-crossover rates in rhesus macaques (Macaca mulatta) from four three-generation pedigrees comprising
-
Pharmacogenetic variation in Neanderthals and Denisovans and implications for human health and response to medications Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-03 Tadeusz H Wroblewski, Kelsey E Witt, Seung-been Lee, Ripan S Malhi, David Peede, Emilia Huerta-Sánchez, Fernando A Villanea, Katrina G Claw
Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes – genes responsible for the processing of exogenous substances such as food, pollutants, and medications – as these can relate to changing environmental effects,
-
Functional divergence in solute permeability between ray-finned fish-specific paralogs of aqp10 Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-01 Genki Imaizumi, Kazutaka Ushio, Hidenori Nishihara, Ingo Braasch, Erika Watanabe, Shiori Kumagai, Tadaomi Furuta, Koji Matsuzaki, Michael F Romero, Akira Kato, Ayumi Nagashima
Aquaporin (Aqp) 10 is a member of the aquaglyceroporin subfamily of water channels, and human Aqp10 is permeable to solutes such as glycerol, urea, and boric acid. Tetrapods have a single aqp10 gene, whereas ray-finned fishes have paralogs of this gene through tandem duplication, whole-genome duplication, and subsequent deletion. A previous study on Aqps in the Japanese pufferfish Takifugu rubripes
-
Phylogenetic and protein structure analyses provide insight into the evolution and diversification of the CD36 domain ‘apex’ among scavenger receptor class B proteins across Eukarya Genome Biol. Evol. (IF 3.3) Pub Date : 2023-12-01 Reed T Boohar, Lauren E Vandepas, Nikki Traylor-Knowles, William E Browne
The cluster of differentiation 36 (CD36) domain defines the characteristic ectodomain associated with scavenger receptor class B (SR-B) proteins. In bilaterians, SR-Bs play critical roles in diverse biological processes including innate immunity functions such as pathogen recognition and apoptotic cell clearance, as well as metabolic sensing associated with fatty acid uptake and cholesterol transport