Genome Evolution Research Articles

ZW sex chromosome differentiation in paleognathous birds is associated with mitochondrial effective population size but not mitochondrial genome size or mutation rate.

Eukaryotic genome size varies considerably, even among closely related species. The causes of this variation are unclear, but weak selection against supposedly costly "extra" genomic sequences has been central to the debate for over 50 years. The mutational hazard hypothesis, which focuses on the increased mutation rate to null alleles in superfluous sequences, is particularly influential, though challenging to test. This study examines the sex chromosomes and mitochondrial genomes of 15 flightless or semi-flighted paleognathous bird species. In this clade, the non-recombining portion of the W chromosome has independently expanded stepwise in multiple lineages. Given the shared maternal inheritance of the W chromosome and mitochondria, theory predicts that mitochondrial effective population size (Ne) should decrease due to increased Hill-Robertson Interference in lineages with expanded non-recombining W regions. Our findings support the extent of the non-recombining W region with three indicators of reduced selective efficiency: (1) the ratio of non-synonymous to synonymous nucleotide changes in the mitochondrion, (2) the probability of radical amino acid changes, and (3) the number of ancient, W-linked genes lost through evolution. Next, we tested whether reduced Ne affects mitochondrial genome size, as predicted by weak selection against genome expansion. We find no support for a relationship between mitochondrial genome size and expanded non-recombining W regions, nor with increased mitochondrial mutation rates (predicted to modulate selective costs). These results highlight the utility of non-recombining regions and mitochondrial genomes for studying genome evolution and challenge the general idea of a negative relation between the efficacy of selection and genome size.

Multilevel gene expression changes in lineages containing adaptive copy number variants.

Copy-number variants (CNVs) are an important class of genetic variation that can mediate rapid adaptive evolution. Whereas CNVs can increase the relative fitness of the organism, they can also incur a cost due to the associated increased gene expression and repetitive DNA. We previously evolved populations of Saccharomyces cerevisiae over hundreds of generations in glutamine-limited (Gln-) chemostats and observed the recurrent evolution of CNVs at the GAP1 locus. To understand the role that gene expression plays in adaptation, both in relation to the adaptation of the organism to the selective condition and as a consequence of the CNV, we measured the transcriptome, translatome, and proteome of 4 strains of evolved yeast, each with a unique CNV, and their ancestor in Gln- conditions. We find CNV-amplified genes correlate with higher mRNA abundance; however, this effect is reduced at the level of the proteome, consistent with post-transcriptional dosage compensation. By normalizing each level of gene expression by the abundance of the preceding step we were able to identify widespread differences in the efficiency of each level of gene expression. Genes with significantly different translational efficiency were enriched for potential regulatory mechanisms including either upstream open reading frames (uORFs), RNA binding sites for Ssd1, or both. Genes with lower protein expression efficiency were enriched for genes encoding proteins in protein complexes. Taken together, our study reveals widespread changes in gene expression at multiple regulatory levels in lineages containing adaptive CNVs highlighting the diverse ways in which genome evolution shapes gene expression.

Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes

Intrinsically disordered regions are flexible regions that complement the typical structured regions of proteins. Little is known however about their evolution. Here we leverage a comparative and evolutionary genomics approach to analyze intrinsic disorder in the structural domains of thousands of proteomes. Our analysis revealed that viral and cellular proteomes employ similar strategies to increase disorder but achieve different goals. Viral proteomes evolve disorder for economy of genomic material and multifunctionality. On the other hand, cellular proteomes evolve disorder to advance functionality with increasing genomic complexity. Remarkably, phylogenomic analysis of intrinsic disorder showed that ancient domains were ordered and that disorder evolved as a benefit acquired later in evolution. Evolutionary chronologies of domains indexed with disorder levels and distributions across Archaea, Bacteria, Eukarya and viruses revealed six evolutionary phases, the oldest two harboring only ordered and moderate disorder domains. A biphasic spectrum of disorder versus proteome makeup captured the dichotomy in the evolutionary trajectories of viral and cellular ancestors, one following reductive evolution driven by viral spread of molecular wealth and the other following expansive evolutionary trends to advance functionality through massive domain-forming co-option of disordered loop regions.

Multi-gene precision editing tool using CRISPR-Cas12a/Cpf1 system in Ogataea polymorpha

BackgroundOgataea polymorpha, a non-conventional methylotrophic yeast, has demonstrated significant potential for heterologous protein expression and the production of high-value chemicals and biopharmaceuticals. However, the lack of precise and efficient genome editing tools severely hinders the construction of cell factories. Although the CARISP-Cas9 system has been established in Ogataea polymorpha, the gene editing efficiency, especially for multiple genes edition, needs to be further improved.ResultsIn this study, we developed an efficient CRISPR-Cpf1-mediated genome editing system in O. polymorpha that exhibited high editing efficiency for single gene (98.1 ± 1.7%), duplex genes (93.9 ± 2.4%), and triplex genes (94.0 ± 6.0%). Additionally, by knocking out non-homologous end joining (NHEJ) related genes, homologous recombination (HR) efficiency was increased from less than 30% to 90 ~ 100%, significantly enhancing precise genome editing capabilities. The increased HR rates enabled over 90% integration efficiency of triplex genes, as well as over 90% deletion rates of large DNA fragments up to 20 kb. Furthermore, using this developed CRISPR-Cpf1 system, triple genes were precisely integrated into the genome by one-step, enabling lycopene production in O. polymorpha.ConclusionsThis novel multiplexed genome-editing tool mediated by CRISPR-Cpf1 can realize the deletion and integration of multiple genes, which holds great promise for accelerating engineering efforts on this non-conventional methylotrophic yeast for metabolic engineering and genomic evolution towards its application as an industrial cell factory.

Population genomics of premature termination codons in cavefish with substantial trait loss.

Loss-of-function alleles are a pertinent source of genetic variation with the potential to contribute to adaptation. Cave-adapted organisms exhibit striking loss of ancestral traits such as eyes and pigment, suggesting that loss-of-function alleles may play an outsized role in these systems. Here, we leverage 141 whole genome sequences to evaluate the evolutionary history and adaptive potential of single nucleotide premature termination codons (PTCs) in Mexican tetra. We find that cave populations contain significantly more PTCs at high frequency than surface populations. We also find that PTCs occur more frequently in genes with inherent relaxed evolutionary constraint relative to the rest of the genome. Using SLiM to simulate PTC evolution in a cavefish population, we show that the smaller population size and increased genetic drift is sufficient to account for the observed increase in PTC frequency in cave populations without positive selection. Using CRISPR-Cas9, we show that mutation of one of these genes, pde6c, produces phenotypes in surface Mexican tetra that mimic cave-derived traits. Finally, we identify a small subset of candidate genes that contain high frequency PTCs in cave populations, occur within selective sweeps, and may contribute to beneficial traits such as reduced energy expenditure, suggesting that a handful of PTCs may be adaptive. Overall, our work provides a rare characterization of PTCs across wild populations and finds that they may have an important role in loss-of-function phenotypes, contributing to a growing body of literature showing genome evolution through relaxed constraint in subterranean organisms.

Cotton2035: From Genomics Research to Optimized Breeding.

Cotton is the world's most important natural fiber crop and serves as an ideal model for studying plant genome evolution, cell differentiation, elongation, and cell wall biosynthesis. The first draft of the cotton genome for Gossypium raimondii, completed in 2012, marked the beginning of global efforts in cotton genomics. Over the past decade, the cotton research community has continued to assemble and refine genomes for both wild and cultivated Gossypium species. With the accumulation of de novo genome assemblies and resequencing data across cotton populations, significant progress has been made in uncovering the genetic basis of key agronomic traits. Achieving the goal of cotton genomics-to-breeding (G2B) will require a deeper understanding of the spatiotemporal regulatory mechanisms involved in genome information storage and expression. We advocate for a cotton ENCODE project to systematically decode the functional elements and regulatory networks within the cotton genome. Technological advances, particularly in single-cell sequencing and high-resolution spatiotemporal omics, will be essential in elucidating these regulatory mechanisms. By integrating multi-omics data, genome editing tools, and artificial intelligence, these efforts will empower the genomics-driven strategies needed for future cotton G2B breeding.

Deciphering Plant NLR Genomic Evolution: Synteny-Informed Classification Unveils Insights into TNL Gene Loss.

Nucleotide-binding leucine-rich repeat receptor (NLR) genes encode a pivotal class of plant immune receptors. However, their rampant duplication and loss have made inferring their genomic evolutionary trajectory difficult, exemplified by the loss of TNL family genes in monocots. In this study, we introduce a novel classification system for angiosperm NLR genes, grounded in network analysis of micro-synteny information. This refined classification categorizes these genes into five classes: CNL_A, CNL_B, CNL_C, TNL, and RNL. Compared to the previous classification, we further subdivided CNLs into three subclasses. The credibility of this classification is supported by phylogenetic analysis and examination of protein domain structures. Importantly, this classification enabled a model to explain the extinction of TNL genes in monocots. Compelling micro-synteny evidence underscores this revelation, indicating a clear synteny correspondence between the non-TNLs in monocots and the extinct TNL subclass. Our study provides crucial insights into the genomic origin and divergence of plant NLR subfamilies, unveiling the malleability-driven journey that has shaped the functionality and diversity of plant NLR genes.

De novo genome assembly and annotations of Bombus lapidarius and Bombus niveatus provide insights into the environmental adaptability

Bumblebees are ubiquitous, cold-adapted, primitively eusocial bees and important pollinators for crops and vegetation. However, many species are declining worldwide due to multiple factors, including human-induced habitat loss, agricultural chemicals, global warming, and climate change. In particular, future climate scenarios predict a shift in the spatial distribution of bumblebees under global warming, with some species declining and others potentially expanding. Here, we report a de novo genome assembly and annotation for Bombus lapidarius and Bombus niveatus to decipher species-specific potential genomic capacity against such environmental stressors. With harboring more than 23,000 protein-coding genes, the assembled genomes of B. lapidarius and B. niveatus are 244.44 Mb (scaffold N50 of 9.45 Mb) and 259.84 Mb (scaffold N50 of 10.94 Mb), respectively, which exhibit similar trends in terms of genome size and composition with other bumblebees. Gene family analysis reveals differences in species-specific expanded gene families. B. lapidarius exhibits expanded genes related to pre/postsynaptic organization, while B. niveatus shows a distinct expansion in gene families regulating cellular growth, aging, and responses to abiotic and biotic stressors, such as those containing SCAN domains, WD-repeats, and Ras-related proteins. Our genome-wide screens revealed positive selection on environmental stress-responsive genes such as dip2, yme1l, and spg7 in B. lapidarius, whereas positive selection signatures were found in genes such as myd88, mybbp1A, and rhau, which are involved in environmental stress resistance for B. niveatus. These high-quality genome assemblies and comparative genome analysis unveil potential drivers that underlie genome evolution in bumblebees, offering valuable insights into environmental adaptation and conservation efforts.

Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution

BackgroundPleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species.ResultsOur analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices.ConclusionsThis study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations.

FadA antigen of Fusobacterium nucleatum: implications for ceRNA network in colorectal cancer and adenomatous polyps progression

IntroductionColorectal cancer (CRC) is the second most common cause of cancer-related deaths globally. The gut microbiota, along with adenomatous polyps (AP), has emerged as a plausible contributor to CRC progression. This study aimed to scrutinize the impact of the FadA antigen derived from Fusobacterium nucleatum on the expression levels of the ANXA2 ceRNA network and assess its relevance to CRC advancement.Material and methodsThe functions of ANXA2 and LINC00460 in CRC have been partially clarified. According to our previous study to identify shared MicroRNA-Interaction-Targets (MITs) between ANXA2 and LINC00460, TargetScanHuman (V7.2) and miRDB databases have been used respectively. The Bioinformatics and Evolutionary Genomics web tool was employed to intersect the sets of shared microRNAs and their common targets. Then, the ANXA2 ceRNA network was constructed. Subsequently, the mRNA, miRNA, and lncRNA expression levels were examined in intestinal biopsy specimens from 30 healthy controls, 30 Adenoma patients, and 30 cases of CRC stage I using qRT-PCR.ResultsElevated expression levels of FadA, ANXA2, hsa-let-7a-2, and LINC00460 were observed in CRC specimens, followed by AP cases, in comparison to samples from normal individuals. Application of the Spearman test revealed a strong and significant correlation between FadA and LINC00460 (rS = 0.9311, p < 0.0001). Also, the functional analysis of ANXA2 revealed its impact on CRC progression through JAK-STAT and Hippo signaling pathways.ConclusionFadA appears to potentiate CRC progression by inducing the upregulation of LINC00460, consequently leading to the hyperexpression of ANXA2 through the ceRNA network.

Shallow-water mussels (Mytilus galloprovincialis) adapt to deep-sea environment through transcriptomic and metagenomic insights

Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.

Comparative insights into genomic variability and adaptation in the chloroplast genomes of Salvia japonica and Salvia rosmarinus

Chloroplast genomes provide important information about phylogenetics, plant evolution, and adaptive processes. This study examines the chloroplast genomes of Salvia japonica and Salvia rosmarinus. We conducted structural and functional annotations to identify significant variations in gene content and organization. We found that S. rosmarinus has fewer photosystem II (psb) genes and a greater abundance of hypothetical genes (ycf). This may help maintain genomic stability while facilitating species evolution. There are big differences in insertion-deletion events (indels) and single nucleotide polymorphisms (SNPs) in important gene families, like NADH dehydrogenase and ribosomal proteins. We determined this organizational difference by applying Principal Component Analysis (PCA) to the genomes of the two species, which belong to different and distinct gene categories. Sequence alignment revealed gaps and inconsistencies in genes related to RNA polymerase and photosynthesis. The fact that S. japonica and S. rosmarinus have a lot of different genes and may have adapted to live in different environments suggests that they have had different evolutionary paths. These results give us important information about how Salvia species have evolved and give us a way to think about how chloroplast genomes change in different ecological settings. This study provides a basis for understanding the evolution of the chloroplast genome in the genus Salvia. This study has been significant in clarifying the role of photosynthetic and hypothetical genes in controlling environmental responses. Future study must use transcriptome and ecological data to enhance our understanding of the impact of genetic variants on functionality.

Identification of novel genes responsible for a pollen killer present in local natural populations of Arabidopsis thaliana.

Gamete killers are genetic loci that distort segregation in the progeny of hybrids because the killer allele promotes the elimination of the gametes that carry the sensitive allele. They are widely distributed in eukaryotes and are important for understanding genome evolution and speciation. We had previously identified a pollen killer in hybrids between two distant natural accessions of Arabidopsis thaliana. This pollen killer involves three genetically linked genes, and we previously reported the identification of the gene encoding the antidote that protects pollen grains from the killer activity. In this study, we identified the two other genes of the pollen killer by using CRISPR-Cas9 induced mutants. These two genes are necessary for the killer activity that we demonstrated to be specific to pollen. The cellular localization of the pollen killer encoded proteins suggests that the pollen killer activity involves the mitochondria. Sequence analyses reveal predicted domains from the same families in the killer proteins. In addition, the C-terminal half of one of the killer proteins is identical to the antidote, and one amino acid, crucial for the antidote activity, is also essential for the killer function. Investigating more than 700 worldwide accessions of A. thaliana, we confirmed that the locus is subject to important structural rearrangements and copy number variation. By exploiting available de novo genomic sequences, we propose a scenario for the emergence of this pollen killer in A. thaliana. Furthermore, we report the co-occurrence and behavior of killer and sensitive genotypes in several local populations, a prerequisite for studying gamete killer evolution in the wild. This highlights the potential of the Arabidopsis model not only for functional studies of gamete killers but also for investigating their evolutionary trajectories at complementary geographical scales.

Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium.

Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. Here we construct and analyse chromosome-scale de novo assembled genomes of 17 representative accessions spanning 12 sections in Dendrobium, one of the largest orchid genera. These accessions represent a broad spectrum of phenotypes, lineages and geographical distributions. We first construct haplotype-resolved genomes for a Dendrobium hybrid and uncover haplotypic variations and allelic imbalance in the heterozygous genome, demonstrating the significance of diverse ancestry. At Dendrobium genus-wide scale, we further elucidate phylogenetic relationships, evolutionary dynamics, entire gene repertoire, and the mechanisms of preserving ancient genetic variants and rapid recent genome evolution for habitat adaption. We also showcase distinctive evolutionary trajectories in MADS-box and PEBP families over 28 Ma. These results considerably contribute to unearthing the mystery of orchid origin, evolution and diversification, laying the foundation for efficient use of genetic diversity in breeding.

Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.

Transposable elements (TEs) are significant drivers of genome evolution, yet their recent dynamics and impacts within and among species, as well as the roles of host genes and non-coding RNAs in the transposition process, remain elusive. With advancements in large-scale pan-genome sequencing and the development of open data sharing, large-scale comparative genomics studies have become feasible. Here, we performed complete de novo TE annotations and identified active TEs in 310 plant genome assemblies across 119 species and seven crop populations. Using 811 high-quality genomes, we detected 13 844 553 TE-induced structural variants (TE-SVs), providing unprecedented resolution in delineating recent TE activities. Our integrative analysis revealed a mutual evolutionary relationship between TEs and host genomes. On one hand, host genes and ncRNAs are involved in the transposition process, as evidenced by their colocalization and coactivation with TEs, and may play a role in chromatin regulation. On the other hand, TEs drive genetic innovation by promoting the duplication of host genes and inserting into regulatory regions. Moreover, genes influenced by active TEs are linked to plant growth, nutrient absorption, storage metabolism and environmental adaptation, aiding in crop domestication and adaptation. This TE dynamics atlas not only reveals evolutionary and functional features linked to transposition activity but also highlights the role of TEs in crop domestication and adaptation, paving the way for future exploration of TE-mediated genome evolution and crop improvement strategies.

Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.

Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B.subtilis, shedding light on bacterial genome evolution and phage-host dynamics.

Comparative genomic analysis of Fusarium oxysporum f. sp. lycopersici reveals telomeric duplications of a lineage-specific region carrying SIX8 and PSL1 and genome-wide expansion of Foxy transposable elements.

Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of tomato wilt disease, is a soil-borne, vascular-colonizing fungal pathogen that severely impacts tomato production in most growing regions worldwide. Despite the availability of over thirty Fol genome sequences in public databases, only one chromosome-scale assembly exists, comprising the low sequence-coverage Fol4287 reference genome generated using Sanger sequencing. Thus, genome structural variation and comparative genomics analyses of Fol remain largely unexplored. Here, using third generation Nanopore long-read sequencing in combination with high-throughput chromosome conformation capture (Hi-C) data, we have independently constructed a high-quality assembly and annotation of the Fol007 race 2 genome that consists of 15 pseudochromosomes with 25 telomeres, including 10 telomere-to-telomere chromosomes. The Fol007 genome is predicted to contain 29,148 protein-encoding genes, including all known SIX genes except for SIX4, which is absent in Fol race 2. Compared to the genome of Fusarium verticillioides, the Fol007 genome contains four complete lineage-specific (LS) chromosomes, including chromosome 5 (Chr5), chromosome 13 (Chr13), and two small chromosomes, Chr14 and Chr15. Comparative genomic analysis between the newly assembled Fol007 genome and Fol4287_2010 deposited in the GenBank database reveals that the completely assembled Chr13 of Fol007 carrying all known SIX genes (except SIX4 and SIX8) and three novel candidate effector genes is relatively stable and corresponds to pathogenicity chromosome Chr14 in Fol4287_2010. It also reveals a telomeric duplication of an LS region carrying SIX8 and PSL1 on core chromosomes Chr6, Chr7 and Chr11, and LS chromosome Chr15, as well as the absence of segmental duplications on LS chromosomes of the Fol007 genome. Furthermore, compared to the genomes of Fol race 1 and non-pathogenic Fo strains, an active and specific Foxy transposable element, responsible for the inactivation of a second copy of SIX13, was identified and found to have expanded in the genomes of Fol race 2 and 3 strains. This element may contribute to Fusarium oxysporum genome evolution and has potential as a genetic marker for studying phylogenetic relationships among formae speciales of Fusarium oxysporum. These findings provide a basis for further genetic and genomic understanding of Fol evolution and virulence mechanisms employed by Fol and contribute another reference genome for Fusarium study more broadly.

Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years

Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. Here, we show that two retrotransposons, Shellder and Spoink, invaded the genomes of multiple species of the melanogaster subgroup within the last 50 years. Through horizontal transfer, Spoink spread in D. melanogaster during the 1980s, while both Shellder and Spoink invaded D. simulans in the 1990s. Possibly following hybridization, D. simulans infected the island endemic species D. mauritiana (Mauritius) and D. sechellia (Seychelles) with both TEs after 1995. In the same approximate time-frame, Shellder also invaded D. teissieri, a species confined to sub-Saharan Africa. We find that the donors of Shellder and Spoink are likely American Drosophila species from the willistoni, cardini, and repleta groups. Thus, the described cascade of TE invasions could only become feasible after D. melanogaster and D. simulans extended their distributions into the Americas 200 years ago, likely aided by human activity. Our work reveals that cascades of TE invasions, likely initiated by human-mediated range expansions, could have an impact on the genomic and phenotypic evolution of geographically dispersed species. Within a few decades, TEs could invade many species, including island endemics, with distributions very distant from the donor of the TE.

Mutational Selection: Fragile Sites, Replicative Stress, and Genome Evolution

Mutational Selection: Fragile Sites, Replicative Stress, and Genome Evolution

Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution.

Given the presence of highly repetitive genomic regions such as subtelomeric regions, understanding human genomic evolution remains challenging. Recently, long-read sequencing technology has facilitated the identification of complex genetic variants, including structural variants (SVs), at the single-nucleotide level. Here, we resolved SVs and their underlying DNA damage-repair mechanisms in subtelomeric regions, which are among the most uncharted genomic regions. We generated ∼20×high-fidelity long-read sequencing data from three Korean individuals and their partially phased high-quality de novo genome assemblies (contig N50: 6.3-58.2 Mb). We identified 131138 deletion and 121461 insertion SVs, 41.6% of which were prevalent in the East Asian population. The commonality of the SVs identified among the Korean population was examined by short-read sequencing data from 103 Korean individuals, providing the first comprehensive SV set representing the population based on the long-read assemblies. Manual investigation of 19 large subtelomeric SVs (≥5 kb) and their associated repair signatures revealed the potential repair mechanisms leading to the formation of these SVs. Our study provides mechanistic insight into human telomere evolution and can facilitate our understanding of human SV formation.