Genome Biology and Evolution最新文献

In this Perspective article, we follow the journey of a gene that breaks free from its stringent chromosomal transmission dynamics to become an independently multiplying agent on so-called extrachromosomal circular DNA (ecDNA/eccDNA). We discuss how the release of a gene from its chromosomal anchor can affect its dosage, regulatory context, and potential evolutionary trajectory before examining the phenotypic implications for unicellular and multicellular eukaryotes that transmit genes on circular DNA. We also briefly explore the fundamental difference between circularized genes in flowering plants (angiosperms) and mammals (primarily cancer) concerning somatic and germline inheritance.

Vocal learning, the ability to imitate sounds, is a complex convergent trait crucial for spoken language and observed in a few independent lineages of mammals and birds. While convergences in gene expression have been found in vocal learning brain regions, amino acid convergences remain unclear. Here, we investigated whether avian vocal learning clades have amino acid convergences linked to their specialized trait. We developed a tool, Convergent Variant Finder, and applied it to an alignment of 48 species representing nearly all bird orders to identify convergent single amino acid variants among vocal learners and over 8,000 other polyphyletic species combinations. We discovered that the number of convergent variants was associated with the product of branch lengths of the most recent common ancestors of each species combination. The number of convergent variants in vocal learning clades did not exceed that of control species combinations. However, a subset of genes with vocal learner-specific convergent amino acid variants was enriched in the "learning" process, under positive selection, and significantly overlapped with gene sets for FOXP2 targets, singing-induced regulation in vocal learning nuclei, and differentially expressed in vocal learning nuclei. Moreover, we confirmed that the majority of convergent patterns in vocal learners were in the genomes of 363 species densely sampled across the avian tree. We propose that amino acid and nucleotide convergence accumulates at a steady state, with the rate proportional to divergence time. Selection associated with convergent traits, such as vocal learning, then likely acts on a subset of these changes.

Chromosomal structural changes happen when genomic stability is compromised, such as in disease or in species hybrids. In these contexts, diminished control of repetitive elements has been reported, but the reasons for this are not yet well understood. There are causal associations between repetitive elements and phenotypes such as disease progression, leading us to the hypothesis that chromosomal structure may be affected by transposable elements (TEs). In an intraspecific hybrid Drosophila melanogaster cell line (PnM), the degree of pairing among trans homologous chromosomes was affected by the presence of nearby TEs, in particular, LINE and LTR elements, such as Baggins1 or Gypsy. Chromosomal pairing was significantly lower in windows containing TEs than in windows without any TEs. Pairing was also affected by TEs in mouse, which suggests a possible general association between TEs and pairing that is highly conserved.

The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6 to 9, 2023, represented the first-ever opportunity for scientists studying the evolution and biology of de novo genes to gather through a dedicated meeting and discuss about groundbreaking discoveries in this emerging and exciting field of gene evolution. In this perspective, we discuss recent advances and major open questions in de novo gene emergence and evolution that were presented at the SMBE satellite meeting, as well as some of the key recent findings published before or since the conference. These key themes include de novo gene identification, function, and evolution, what we are learning about de novo genes from experimental analyses of random peptides, de novo gene birth and microproteins, and the role of de novo genes in human disease.

Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding the trajectory of such a genome has largely been done through the study of animal-associated bacteria, especially insect endosymbionts. Yet, endofungal bacteria provide another natural experimental model for investigating how microbial genomes change when living inside of a host cell. Mycetohabitans spp. are culturable bacterial endosymbionts of the Mucoromycota fungus Rhizopus microsporus. To investigate the genome dynamics resulting from the endohyphal nature of this emerging model genus, we long-read sequenced and assembled new complete genomes to combine with previous assemblies, creating a global dataset of 28 complete Mycetohabitans genomes. All genomes were between 3.3 and 3.9 Mbp in size and were multipartite, structured into two conserved replicons with some strains having an additional plasmid. Based on evolutionary rate and gene content analysis of the different replicons, we termed the two major ones a chromosome and chromid. The differential presence of a third, mobilome-rich plasmid in some strains and the proliferation of transposable elements provide putative mechanisms for recombination or gene loss. The conservation of intact prophage and putative toxin-antitoxin systems and extensive enrichment of secondary metabolite clusters in the Mycetohabitans genomes highlight the dynamic nature of this reducing genome. With fungal-bacterial symbioses becoming increasingly apparent phenomena, lessons learned from this symbiosis will inform our understanding of bacterial adaptation to novel hosts and the process of microbe-microbe coevolution.

The Mexican cavefish, Astyanax mexicanus, is a captivating model for probing cave adaptations, showcasing pronounced divergence in traits like vision, brain morphology, behavior, pigmentation, metabolism, and hypoxia tolerance compared to its surface-dwelling counterpart. However, only a small number of protein-coding variants have been found in cave-morphs, leaving the vast phenotypic gap between the two morphs largely unexplained. We aligned the genomes of five closely related teleosts and identified 46,914 conserved noncoding elements, of which 473 were specifically lost in cave-morphs. These conserved noncoding elements, confirmed in Zebrafish, displayed activating histone modifications, possessed binding sites of neuronal transcription factors, and interacted with cognate genes through chromatin loops. Genes crucial for eye and nervous system development were located adjacent to conserved noncoding elements lost in cave morphs. Notably, the flanking genes were gradually downregulated during embryonic development of cave-morphs, contrasting with surface morphs. These insights underscore how dampened developmental pathways, stemming from the loss of distal regulatory elements, may have contributed to the evolutionary regression of phenotypes in cave morphs.

Unisexual species of whiptail lizards in the genus Aspidoscelis arose by interspecific hybridization. They reproduce clonally through parthenogenesis and are thought to maintain the fixed heterozygosity that resulted from their hybrid origin by avoiding recombination between homeologous chromosomes. In the absence of chromosome-level assemblies for the sexual progenitor species, questions relating to the long-term consequences of clonal reproduction have remained largely unanswered. Here, we present chromosome-level genome assemblies for A. marmoratus and A. arizonae, the parental species of the unisexual A. neomexicanus. Using these references, we have analyzed whole-genome sequencing data from both wild and laboratory-reared A. neomexicanus individuals as well as newly generated F1 hybrids. Our analysis identified population-specific losses of heterozygosity affecting multiple syntenic chromosome pairs, demonstrating that homeologous chromosome pairing and recombination must occur at a low frequency and contribute to genome erosion in these unisexual lineages. The loss of heterozygosity patterns we observed further suggest that the genomes of unisexual lineages diverge over time more quickly than anticipated based on mutation accumulation alone. Our results establish genomic resources for Aspidoscelis and provide new insights into how genome structure can evolve in the absence of sexual reproduction.

The glucose kinase superfamily, which includes enzymes such as hexokinases and glucokinases, plays a central role in energy metabolism across all domains of life. This study explores their evolutionary origins, functional diversity, and adaptation to ecological niches, tracing their journey from early life forms to modern organisms. Recent advances reveal how these enzymes have diversified, with some retaining broad specificity, while others evolved high substrate specificity, reflecting the metabolic demands of their environments. By integrating phylogenetic, structural, and functional analyses, this work sheds light on the evolutionary pressures that shaped these enzymes and their role in metabolic innovation, not only deepening our understanding of life's biochemical evolution but also connecting ancient metabolic pathways to contemporary cellular processes.

Mounting discoveries of avian neo-sex chromosomes are providing opportunities to understand the extent of variation in fundamental aspects of avian neo-sex chromosome evolution. We integrated cytogenetic data, long-read assemblies, and whole-genome resequencing to test phylogenetic hypotheses of recombination suppression and to elucidate the phylogenetic distribution of neo-sex chromosomes in honeyeaters (Aves: Meliphagidae). We find that neo-sex chromosomes in honeyeaters evolved through a fusion of the long arm of chromosome 5 and the pseudoautosomal region (PAR) of both ancestral Z and W sex chromosomes. Resequencing data from 11 species of honeyeaters and outgroups supports our cytogenetic evidence that these neo-sex chromosomes are derived within honeyeaters. Phylogenetic analyzes confirm that all tested honeyeaters share the same breakpoint for a new 17.4 Mb PAR at the end of the neo-sex chromosomes and suggest a single, large expansion of recombination suppression, encompassing 44.6 Mb, is most supported in the newly fused region of the neo-W. We also discovered phylogenetic discordance between the mapping of neo-sex chromosomes on the established nuclear and mitochondrial (mtDNA) phylogenies. We conclude that neo-sex chromosomes arose once in honeyeaters because they form a monophyletic clade on the mtDNA tree, which shares the phylogenetic history of the neo-W through matrilineal coinheritance. Overall, our findings provide new insights on recombination suppression dynamics of avian neo-sex chromosomes and demonstrate the value of comparing nuclear and mtDNA trees to determine the phylogenetic distribution of neo-sex chromosomes, especially in the presence of mitonuclear discordance, which is common across the avian tree of life.

The evolutionary history of eukaryotic supergroups has been investigated primarily by large-scale phylogenomics, but one major hindrance to continued progress is that some major eukaryotic groups have extremely sparse sampling. The phylum Telonemia is one such group. Environmental sampling shows two major subgroups of Telonemia, but there are only multigene phylogenomic data from three closely related species belonging to one of the subgroups, TEL1. Here, a single cell was isolated from the pelagic Pacific Ocean, which SSU phylogenetic analysis reveals to be a telonemid of the TEL2 subgroup and distantly related to telonemids with multigene sequence data. Through single-cell transcriptome sequencing and phylogenomic analysis, we investigate the impact of this new telonemid on the relation of Telonemia to the Stramenopila-Alveolata-Rhizaria supergroup (SAR) and other sparsely sampled or historically unstable supergroups, namely, Hemimastigophora, Provora, and Haptista. Our maximum-likelihood (ML) analysis supports Telonemia as sister to Hemimastigophora, together as sister to SAR, with Haptista and Provora forming a clade and sister to all three. However, our Bayesian analysis failed to converge on a topology. Throughout different Telonemia sampling, gene sampling, alignment trimming, and site removal schemes, the sisterhood of Telonemia and Hemimastigophora remained largely supported in ML trees, even when their sisterhood to SAR dissolved, as was the sisterhood of Haptista and Provora. Inclusion of our TEL2 telonemid largely did not influence these relationships. However, our results also highlight the unstable placements of aforementioned groups throughout variations of our data, of which subsets give results consistent with other previously published analyses of this scale.