Genome Biology and Evolution最新文献

Anaerobic ammonium oxidizing bacteria in the class "Candidatus Brocadiia" in the Planctomycetota are the only known group of bacteria capable of producing energy by coupling the oxidation of ammonium to the reduction of nitrite within a unique bacterial organelle called the anammoxosome. Due to the lack of homologs in other species, it is hypothesized that the key enzyme in this process, the hydrazine synthase complex, originated by de novo birth. We performed extensive searches for proteins that exhibited similarity in sequence and structure to the hydrazine synthase subunits and identified distantly related homologs in anaerobic bacteria from the phyla Planctomycetota and Desulfobacterota. However, key residues of importance for the enzymatic function were not conserved, rejecting the hypothesis that the identified genes represent previously unrecognized anammox bacteria. Phylogenetic analyses indicate that the anammox pathway has been assembled from genes acquired by horizontal gene transfer from a variety of anaerobic bacteria. The ancestral states of enzymes in the hydroxylamine oxidoreductase family were inferred, and transitions between reductive and oxidative forms of the enzymes were mapped onto the phylogenetic tree. Finally, it is shown that the signal sequences of key enzymes in the anammox pathway are able to transport a reporter gene into the periplasm of Escherichia coli cells. In conclusion, our findings suggest that the hydrazine synthase complex has evolved from already existing heme-binding periplasmic proteins and that the anammoxosome has an endogenous origin.

Metallothioneins (MTs) are central to metal metabolism and contribute to organismal adaptation to variable metal bioavailability across ecosystems. Although well studied in chordates and mollusks, MTs remain poorly investigated in many arthropod lineages, particularly within the Myriapoda subphylum. Myriapods, comprising thousands of millipede (Diplopoda) and centipede (Chilopoda) species, are especially relevant for evolutionary studies because they are the sister group to Pancrustacea (crustaceans and insects), and they are some of the earliest arthropods to colonize land. Their MTs therefore provide critical insights into the origin and evolution of arthropod MTs and into the molecular adaptations underlying the colonization of new environments. In this work, we have identified 48 putative MTs from 30 myriapod species, all classified as type 1 (MT1) and occurring in two configurations: the bidomain MT1S (S for short) or the multidomain MT1L (L for long) variants. Evolutionary analyses suggest that MT1S represents the ancestral type not only in myriapods but across Arthropoda, whereas MT1L likely arose during chilopod diversification, probably restricted to the order Glomerida. Despite shared structural features, metal-binding characterization of three myriapod MTs-GminMT1Sa, GminMT1La from Glomeridella minima, and LforMT1S from Lithobius forficatus-revealed marked functional differences. The diplopod proteins GminMT1Sa and GminMT1La displayed a Cd-thionein character, while the chilopod LforMT1S was a multipurpose protein, binding cadmium, zinc, and copper without a clear metal preference. These differences likely reflect distinct metal uptake, retention, and excretion strategies in diplopods and chilopods, associated with their ecological adaptations as peaceful decomposers and voracious predators, respectively.

Bees provide essential pollination services that contribute to ecosystem stability, as well as the sustainability of economic crop yields. Due to concerns over global and local declines, improving our understanding of these ecologically and commercially important species is crucial for determining their capacity to respond and adapt to environmental challenges. The European orchard bee (Osmia cornuta) is a solitary bee of increasing agricultural importance due to its role in the pollination of fruit crops, yet lacks genomic resources. Using cost-effective Nanopore-only long-read sequencing, we report the first genome assembly for O. cornuta, spanning 647.56 Mb across 727 contigs (N50 = 3.94 Mb) at a high level of completeness (99.88% BUSCO complete). In line with the expected number of chromosomes in this species, 16 major scaffolds were assembled to chromosome level. Also, we provisionally investigated the epigenomic architecture of O. cornuta, finding low numbers of CG dinucleotides that were either 5'-methylated or 5'-hydroxymethylated, providing additional evidence for the limited role methylation plays in gene regulation in Hymenopterans. To generate improved gene annotations, we combined transcriptomic- and orthology-based approaches, leading to the prediction of 12,144 genes and 25,964 proteins, showing exceptionally high BUSCO completeness (99.64%). Lastly, through whole-genome resequencing of a representative dataset, we provisionally find patterns of reduced nucleotide diversity and lower recombination rates within O. cornuta compared to other bee species. Collectively, our study provides a novel insight into the genome architecture of a key pollinator, providing an important resource to facilitate further genomic studies.

High-quality genomic resources are important for accurate assessments of adaptive evolution in rapidly evolving island endemic species. The golden lancehead (Bothrops insularis) is a critically endangered venomous species endemic to the Queimada Grande island located on the southeast coast of Brazil, with no reference genome available. Here, we present a high-quality near chromosome-level and well-annotated genome for the golden lancehead. A macrosyntenic analysis using genomes from other viper species revealed that microchromosomes present higher rearrangements consisting of fission and fusion events. Using our genome and genomic data from eight individuals, we conducted a survey of the genetic variation of toxin genes, which included the nucleotide diversity and copy-number variation (CNV). We also inferred a demographic history for the species in the last 100,000 years. The genetic variation analysis revealed that major components of B. insularis venom appear to be evolving largely under natural selection processes rather than genetic drift as expected for an insular species. PLA2s and CTLs are under balancing selection, whereas SVMPs and SVSPs are under positive selection. The CNV suggests recent duplication events in SVMPs and CTLs and deletion events in SVSPs and PLA2s. The demographic history indicates a stable population size over the last 10,000 years, suggesting that B. insularis is both genetically and demographically healthy. Altogether, we provide a genomic resource to better understand the differentiation of an iconic snake and evidence that selection has driven the evolution of diverse venom genes over short evolutionary timescales in an insular species.

Fungal culture collections hold a wealth of historical isolates that could be used to study fungal evolution over the past decades, an era that coincided with agricultural industrialisation. We performed population structure and temporal association analysis on three major fungal crop pathogens, Verticillium nonalfalfae, Fusarium culmorum and Botrytis cinerea, collected between 1956 and 2023. Population structure analysis indicated predominantly sexual reproduction in F. culmorum and B. cinerea, whereas V. nonalfalfae was shown to be largely asexual. Single nucleotide polymorphisms (SNPs) of the recombining species F. culmorum and B. cinerea that showed major temporal changes fell within or close to coding genes, whereas time-variant SNPs in V. nonalfalfae were located within or close to transposable elements (TEs) and a Starship element. This is consistent with the hypothesis that rare-sex fungal species often rely on TE-mediated genomic diversification rather than sexual recombination. Across all three species, rapidly evolving SNPs were associated with genes encoding Major Facilitator Superfamily (MFS) transporters, which are frequently implicated in fungicide resistance, and Zn2Cys6 fungal-type transcription factors, which play key roles in stress responses and pathogenesis. Our findings demonstrate the value of temporal association analysis as an untargeted approach for exploring fungal evolution since the advent of the green revolution. Applying this method across a broader range of fungal crop pathogens could provide deeper insights into their evolution and adaptation.

Understanding the genetic basis of adaptive responses to environmental and human mediated pressures is a central concern in evolutionary biology. Population admixture, a process wherein genetically differentiated populations interbreed, is increasingly recognized as a source of genetic material driving rapid evolutionary responses. Honey bees from Puerto Rico are a phenotypically distinct population of Africanized honey bees with demonstrably lower levels of aggression than other Africanized populations. The Puerto Rican honey bee population represents a dynamic system that has experienced both environmental and human-mediated selective pressures over a short period of time marked by a significant influx of genetic variation from mainland Africanized honey bees, which has notably influenced the genetic makeup of the local populations. In this study we detail the current population structure of the Puerto Rican honey bees, how this differs from a mainland population, and regions of the genome that have signals of ancestry-specific selection. To distinguish loci undergoing ancestry-specific selection, we use tools that co-estimate local ancestry and the strength of selection at loci across the genome. We further detail the genes and pathways highlighted through gene ontology (GO) enrichment analysis. Overall, our results suggest that the local pressures on Puerto Rico honey bee behavior may have induced significant changes favoring alleles linked to different ancestries at loci and pathways involved in neuronal development, behavior, and mating among others. Our analysis demonstrates that approaches that explicitly model selection on local ancestry may be valuable tools for understanding evolution in admixture zones.

Migration is a widespread phenomenon in animals that involves the synchronized movement of numerous individuals across habitats. While migratory traits appear to be environmentally triggered, evidence also points to a still poorly understood genetically regulated mechanism. The study of both the genomic architecture of migration and the degree of similarity across migrating taxa is a recurrent topic in evolutionary biology. Here, we investigated the genomic basis of migration in a flying mammal, the lesser long-nosed bat (Leptonycteris yerbabuenae), a nectar-feeding bat with a partially migratory behavior. Each year, the migrant group of females travels north from central Mexico to give birth in the Sonoran Desert, while the resident females remain and give birth in central Mexico. Using RAD-seq, we detected a demographic decline in this species during the Last Glacial Maximum and found that resident and migratory females form a single genetic cluster. Nevertheless, we identified 10 divergent genomic regions enriched with highly differentiated SNPs (FST values three or more orders of magnitude above the mean). Seven of such regions bear signatures of balancing selection and contain genes that have been identified in other migrating animals; such genes are qualitatively enriched for nervous system-related functions, potentially linked to circadian cycle, orientation, and navigation. Given that the migratory behavior is supposed to have originated recently in L. yerbabuenae (i.e., 10 to 20 Ka), we hypothesize that strong diversifying selection is operating in specific regions of the genome, while the rest is homogenized by the effect of males, which mate indistinctively with females from both groups.

Fungal culture collections hold a wealth of historical isolates that could be used to study fungal evolution over the past decades, an era that coincided with agricultural industrialization. We performed population structure and temporal association analysis on three major fungal crop pathogens, Verticillium nonalfalfae, Fusarium culmorum, and Botrytis cinerea, collected between 1956 and 2023. Population structure analysis indicated predominantly sexual reproduction in F. culmorum and B. cinerea, whereas V. nonalfalfae was shown to be largely asexual. Single nucleotide polymorphisms (SNPs) of the recombining species F. culmorum and B. cinerea that showed major temporal changes fell within or close to coding genes, whereas time-variant SNPs in V. nonalfalfae were located within or close to transposable elements (TEs) and a Starship element. This is consistent with the hypothesis that rare-sex fungal species often rely on TE-mediated genomic diversification rather than sexual recombination. Across all three species, rapidly evolving SNPs were associated with genes encoding Major Facilitator Superfamily transporters, which are frequently implicated in fungicide resistance, and Zn2Cys6 fungal-type transcription factors, which play key roles in stress responses and pathogenesis. Our findings demonstrate the value of temporal association analysis as an untargeted approach for exploring fungal evolution since the advent of the green revolution. Applying this method across a broader range of fungal crop pathogens could provide deeper insights into their evolution and adaptation.

Whole genome duplication (WGD) generates a new genetic material that can contribute to the evolution of developmental processes and phenotypic diversification. A WGD occurred in an ancestor of arachnopulmonates (spiders, scorpions, and their relatives), which provides an important independent comparison to WGDs in other animal lineages. After WGD, arachnopulmonates retained many duplicated copies (ohnologues) of developmental genes including clusters of homeobox genes, many of which have been inferred to have undergone subfunctionalization. However, there has been little systematic analysis of gene regulatory sequences and comparison of the expression of ohnologues versus their single-copy orthologues between arachnids. Here, we compare the regions of accessible chromatin and gene expression of ohnologues and single-copy genes during three embryonic stages between an arachnopulmonate arachnid, the spider Parasteatoda tepidariorum, and a nonarachnopulmonate arachnid, the harvestman Phalangium opilio. We found that the expression of each spider ohnologue was lower than their single-copy orthologues in the harvestman suggesting subfunctionalization. However, this was not reflected in a reduction in the number of peaks of accessible chromatin because both spider ohnologues and single-copy genes had more peaks than the orthologous harvestman genes. We also found that the number of peaks of accessible chromatin was higher in the late embryonic stage associated with activation of genes expressed later during embryogenesis in both species. Taken together, our study provides a genome-wide comparison of gene regulatory sequences and embryonic gene expression in arachnids and thus new insights into the impact of the arachnopulmonate WGD.

Mitochondrial DNA has been one of the key workhorses of evolutionary studies. Hence, understanding the dynamics of DNA sequence change in this tiny genome (15 to 20 kb) is of utmost importance. However, we are unaware of large studies examining how the functionality and chromosomal positioning of mitochondrial genes may impact their phylogenetic patterning. To examine this, we assembled a large database of animal mitochondrial genomes (>10,000 total individuals over 89 taxonomic groups) and compared their phylogenetics, functionality, and location on the mitochondrial genome (heavy and light strand in vertebrates or J and N strand in other animals and distance from the origin of replication). We found that many genes show unique evolutionary patterns, often directly tied to chromosomal location or gene function (eg NADH dehydrogenases or ribosomal RNA genes). We also found rampant phylogenetic incongruence among the linked genes of the mitochondria in most of the taxonomic groups we examined. These results suggest that mitochondrial genomes have accrued complex evolutionary patterns. The accumulated incongruence can influence phylogenetic inference in evolutionary studies, making mitochondrial gene choice for phylogenetics critical. The phenomena we show here should also be examined in other organelle and even nuclear gene studies.