Coevolution between transposable elements and recombination

How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice

Large genomic rearrangements, such as chromosomal inversions, can play a key role in evolution, but the mechanisms by which these rearrangements arise remain poorly understood. To study the origins of inversions, we generated chromosome-level de novo genome assemblies for four subspecies of the deer mouse (Peromyscus maniculatus) with known inversion polymorphisms. We identified ∼8,000 inversions, including 47 megabase-scale inversions, that together affect ∼30% of the genome. Analysis of inversion breakpoints suggests that while most small (<1 Mb) inversions arose via ectopic recombination between retrotransposons, large (>1 Mb) inversions are primarily associated with segmental duplications (SDs). Large inversion breakpoints frequently occur near centromeres, which may be explained by an accumulation of retrotransposons in pericentromeric regions driving SDs. Additionally, multiple large inversions likely arose from ectopic recombination between near-identical centromeric satellite arrays located megabases apart, suggesting that centromeric repeats may also facilitate inversions. Together, our results illuminate how repeats give rise to massive shifts in chromosome architecture.

Sex chromosome evolution in haploid plants: Microchromosomes, disappearing chromosomes, and giant chromosomes

As in many diploid organisms with genetic sex determination, haploid-dominant organisms have also evolved sex chromosomes or extensive genomic regions that lack genetic recombination. An understanding of sex chromosome evolution should explain the causes and consequences of such regions in both diploids and haploids. However, haploids have been little studied, even though differences from sex chromosomes in diploids carry implications concerning the evolution of suppressed recombination in diploid organisms, and make predictions about genome evolution in the sex-linked regions of haploids that can now be tested by approaches using genome sequences. I review these ideas, and the current empirical evidence concerning them, in more detail than recent reviews focusing on progress in understanding the mechanisms involved in sex determination. I also discuss evidence that one specific prediction, that genetic degeneration should be minor in haploids, is not upheld. I suggest that this prediction does not take account of all processes leading to gene loss from sex-linked regions and that profound degeneration may evolve if sex-linked genes become duplicated to autosomes, a process that also appears to occur in diploids. I emphasize types of data that are needed to make progress in testing several of the ideas described.

Genetic differentiation in the MAT-proximal region is not sufficient for suppressing recombination in Podospora anserina

Recombination is advantageous over the long term, as it allows efficient selection and purging deleterious mutations. Nevertheless, recombination suppression has repeatedly evolved in sex- and mating-type chromosomes. The evolutionary causes for recombination suppression and the proximal mechanisms preventing crossing overs are poorly understood. Several hypotheses have recently been suggested based on theoretical models, and in particular that divergence could accumulate neutrally around a sex-determining region and reduce recombination rates, a self-reinforcing process that could foster progressive extension of recombination suppression. We used the ascomycete fungus Podospora anserina for investigating these questions: a 0.8-Mbp region around its mating-type locus is nonrecombining, despite being collinear between the 2 mating types. This fungus is mostly selfing, resulting in highly homozygous individuals, except in the nonrecombining region around the mating-type locus that displays differentiation between mating types. Here, we test the hypothesis that sequence divergence alone is responsible for recombination cessation. We replaced the mat- idiomorph by the sequence of the mat+ idiomorph, to obtain a strain that is sexually compatible with the mat- reference strain and isogenic to this strain in the MAT-proximal region. Crosses showed that recombination was still suppressed in the MAT-proximal region in the mutant strains, indicating that other proximal mechanisms than inversions or mere sequence divergence are responsible for recombination suppression in this fungus. This finding suggests that selective mechanisms likely acted for suppressing recombination, or the spread of epigenetic marks, as the neutral model based on mere nucleotide divergence does not seem to hold in P. anserina.

Polymorphic transposable elements contribute to variation in recombination landscapes

Meiotic recombination is a prominent force shaping genome evolution, and understanding why recombination rates vary within and between species has remained a central, though challenging, question. Variation in recombination is widely thought to influence the efficacy of selection in purging transposable elements (TEs), prevalent selfish genetic elements, leading to widely observed negative correlations between TE abundance and recombination rates across taxa. However, accumulating evidence suggests that TEs could instead be the cause rather than the consequence of this relationship. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked an approach that uses PacBio long-read sequencing to efficiently, accurately, and cost-effectively identify crossovers (COs), a key recombination product, among large numbers of pooled recombinant individuals. By applying this approach to Drosophila strains with distinct TE insertion profiles, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, reduce the occurrence of COs. Such an effect leads to different CO frequencies between homologous sequences with and without TEs, contributing to varying CO maps between individuals. The suppressive effect of TEs on CO is further supported by two orthogonal approaches-analyzing the distributions of COs in panels of recombinant inbred lines in relation to TE polymorphism and applying marker-assisted estimations of CO frequencies to isogenic strains with and without transgenically inserted TEs. Our investigations reveal how the constantly changing TE landscape can actively modify recombination, shaping genome evolution within and between species.

Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko

Variation of recombination rate along the genome is of crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how and why recombination landscapes evolve in nature. Here, we reconstruct recombination maps based on linkage disequilibrium and use subsampling and simulations to derive a new measure of recombination landscape evolution: the Population Recombination Divergence Index (PRDI). Using PRDI, we show that fine-scale recombination landscapes differ substantially between two cichlid fish ecotypes of Astatotilapia calliptera that diverged only ~2,500 generations ago. Perhaps surprisingly, recombination landscape differences are not driven by divergence in terms of allele frequency (FST) and nucleotide diversity (Δ(π)): although there is some association, we observe positive PRDI in regions where FST and Δ(π) are zero. We found a stronger association between the evolution of recombination and 47 large haplotype blocks that are polymorphic in Lake Masoko, cover 21% of the genome, and appear to include multiple inversions. Among haplotype blocks, there is a strong and clear association between the degree of recombination divergence and differences between ecotypes in heterozygosity, consistent with recombination suppression in heterozygotes. Overall, our work provides a holistic view of changes in population recombination landscapes during the early stages of speciation with gene flow.

Comparative analysis using a chromosome-scale genome assembly for Funaria hygrometrica suggests greater collinearity in mosses than in seed plants

Mosses, the largest lineage of seed-free plants, have smaller and less variable genome sizes than flowering plants. Nevertheless, whether this difference results from divergent genome dynamics is poorly known. Here, we use newly generated chromosome-scale genome assemblies for Funaria hygrometrica and comparative analysis with other moss and seed plant genomes to investigate moss genome dynamics. Although some aspects of moss genome dynamics are seed plant-like, such as the mechanism of genome size change and de novo gain/loss of genes, moss genomes retain higher synteny, and collinearity over evolutionary time than seed plant genomes. Furthermore, transposable elements and genes are more evenly distributed along chromosomes in mosses than in seed plants, a feature shared with other sequenced seed-free plant genomes. Overall, our findings support the hypothesis that large-scale genome structure and dynamics of mosses and seed plants differ. In particular, our data suggest a lower rate of gene order reshuffling along chromosomes in mosses compared to seed plants. We speculate that such lower rate of structural genomic variation and unique chromosome structure in mosses may contribute to their relatively smaller and less variable genome sizes.

Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia

Some plants have massive sex-linked regions. To test hypotheses about their evolution, we sequenced the genome of Silene latifolia, in which giant heteromorphic sex chromosomes were first discovered in 1923. It has long been known that the Y chromosome consists mainly of a male-specific region that does not recombine with the X chromosome and carries the sex-determining genes and genes with other male functions. However, only with a whole Y chromosome assembly can candidate genes be validated experimentally and their locations determined and related to the suppression of recombination. We describe the genomic changes as the ancestral chromosome evolved into the current XY pair, testing ideas about the evolution of large nonrecombining regions and the mechanisms that created the present recombination pattern.

Maintenance of long-term transposable element activity through regulation by nonautonomous elements

Transposable elements are DNA sequences that can move and replicate within genomes. Broadly, there are 2 types: autonomous elements, which encode the necessary enzymes for transposition, and nonautonomous elements, which rely on the enzymes produced by autonomous elements for their transposition. Nonautonomous elements have been proposed to regulate the numbers of transposable elements, which is a possible explanation for the persistence of transposition activity over long evolutionary times. However, previous modeling studies indicate that interactions between autonomous and nonautonomous elements usually result in the extinction of one type. Here, we study a stochastic model that allows for the stable coexistence of autonomous and nonautonomous retrotransposons. We determine the conditions for this coexistence and derive an analytical expression for the stationary distribution of their copy numbers, showing that nonautonomous elements regulate stochastic fluctuations and the number of autonomous elements in stationarity. We find that the stationary variances of each element can be expressed as a function of the average copy numbers and their covariance, enabling data comparison and model validation. These results suggest that continued transposition activity of transposable elements, regulated by nonautonomous elements, is a possible evolutionary outcome that could for example explain the long coevolutionary history of autonomous LINE1 and nonautonomous Alu element transposition in the human ancestry.

Molecular fingerprints of cell size sensing and mating type differentiation in pennate diatoms

A unique cell size-sensing mechanism is at the heart of the life cycle of diatoms. During population growth, cell size decreases until a sexual size threshold (SST) is reached, below which cells become sexually competent. In most pennate diatoms, the two mating types undergo biochemical and behavioral differentiation below the SST, although the molecular pathways underlying their size-dependent maturation remain unknown. Here, we developed a method to shorten the generation time of Cylindrotheca closterium through single-cell microsurgery, enabling the transcriptomic comparison of genetically identical large and undifferentiated cells with small, sexually competent cells for six different genotypes. We identified 21 genes upregulated in small cells regardless of their mating type, revealing how cells undergo specific transcriptional reprogramming when passing the SST. Furthermore, we revealed a size-regulated gene cluster with three mating type-specific genes susceptible to sex-inducing pheromones. In addition, comparative transcriptomics confirmed the shared mating type specificity of Mating-type Related Minus 2 homologs in three pennate diatoms, suggesting them to be part of a conserved partner recognition mechanism. This study sheds light on how diatoms acquire sexual competence in a strictly size-dependent manner, revealing a complex machinery underlying size-dependent maturation, mating behavior, and heterothally in pennate diatoms.

The master male sex determinant Gdf6Y of the turquoise killifish arose through allelic neofunctionalization

Although sex determination is a fundamental process in vertebrate development, it is very plastic. Diverse genes became major sex determinants in teleost fishes. Deciphering how individual sex-determining genes orchestrate sex determination can reveal new actors in sexual development. Here, we demonstrate that the Y-chromosomal copy of the TGF-β family member gdf6 (gdf6Y) in Nothobranchius furzeri, an emerging model organism in aging research, gained the function of the male sex determinant through allelic diversification while retaining the skeletal developmental function shared with the X-chromosomal gdf6 allele (gdf6X). Concerning sex determination, gdf6Y is expressed by somatic supporting cells of the developing testes. There it induces the male sex in a germ cell-independent manner in contrast to sex determination in zebrafish and the medaka. Looking for downstream effectors of Gdf6Y, we identified besides TGF-β signaling modulators, especially the inhibitor of DNA binding genes id1/2/3, the mRNA decay activator zfp36l2 as a new GDF6 signaling target.

Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola

Plasmopara viticola, the causal agent of grapevine downy mildew, is a biotrophic oomycete engaged in a tight coevolutionary relationship with its host. Rapid adaptation of the pathogen is favored by annual sexual reproduction that generates genotypic diversity. With the aim of studying the recombination landscape across the P. viticola genome, we generated 2 half-sibling F1 progenies (N = 189 and 162). Using targeted SNP sequencing, between 1,405 and 1,894 markers were included in parental linkage maps, and a consensus map was obtained by integrating 4,509 markers. The reference genome could be assembled into 17 pseudochromosomes, anchoring 88% of its physical length. We observed a strong collinearity between parental genomes and extensive synteny with the downy mildew Peronospora effusa. In the consensus map, the median recombination rate was 13.8 cM/Mb. The local recombination rate was highly variable along chromosomes, and recombination was suppressed in putative centromeric regions. Recombination rate was found negatively correlated with repeats' coverage and positively correlated with gene coverage. However, genes encoding secreted proteins and putative effectors were underrepresented in highly recombining regions. In both progenies, about 5% of the individuals presented karyotypic anomalies. Aneuploidies and triploidies almost exclusively originated from the male-transmitted chromosomes. Triploids resulted from fertilization by diploid gametes, but also from dispermy. Obligatory sexual reproduction each year may explain the lower level of karyotypic variation in P. viticola compared to other oomycetes. The linkage maps will be useful to guide future de novo chromosome-scale assemblies of P. viticola genomes and to perform forward genetics.

The recombination landscape of the barn owl, from families to populations

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and limited data. Frequently used approaches include linkage mapping based on familial data that provides sex-specific broad-scale estimates of realized recombination and inferences based on population linkage disequilibrium that reveal a more fine-scale resolution of the recombination landscape, albeit dependent on the effective population size and the selective forces acting on the population. In this study, we use a combination of these 2 methods to elucidate the recombination landscape for the Afro-European barn owl (Tyto alba). We find subtle differences in crossover placement between sexes that lead to differential effective shuffling of alleles. Linkage disequilibrium-based estimates of recombination are concordant with family-based estimates and identify large variation in recombination rates within and among linkage groups. Larger chromosomes show variation in recombination rates, while smaller chromosomes have a universally high rate that shapes the diversity landscape. We find that recombination rates are correlated with gene content, genetic diversity, and GC content. We find no conclusive differences in the recombination landscapes between populations. Overall, this comprehensive analysis enhances our understanding of recombination dynamics, genomic architecture, and sex-specific variation in the barn owl, contributing valuable insights to the broader field of avian genomics.

Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation

Modifiers of recombination rates have been described but the selective pressures acting on them and their effect on adaptation to novel environments remain unclear. We performed experimental evolution in the nematode Caenorhabditis elegans using alternative rec-1 alleles modifying the position of meiotic crossovers along chromosomes without detectable direct fitness effects. We show that adaptation to a novel environment is impaired by the allele that decreases recombination rates in the genomic regions containing fitness variation. However, the allele that impairs adaptation is indirectly favored by selection, because it increases recombination rates and reduces the associations among beneficial and deleterious variation located in its chromosomal vicinity. These results validate theoretical expectations about the evolution of recombination but suggest that genome-wide polygenic adaptation is of little consequence to indirect selection on recombination rate modifiers.

Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories

Balanced mating type polymorphisms offer a distinct window into the forces shaping sexual reproduction strategies. Multiple hermaphroditic genera in Juglandaceae, including walnuts (Juglans) and hickories (Carya), show a 1:1 genetic dimorphism for male versus female flowering order (heterodichogamy). We map two distinct Mendelian inheritance mechanisms to ancient (>37 million years old) genus-wide structural DNA polymorphisms. The dominant haplotype for female-first flowering in Juglans contains tandem repeats of the 3' untranslated region of a gene putatively involved in trehalose-6-phosphate metabolism and is associated with increased cis gene expression in developing male flowers, possibly mediated by small RNAs. The Carya locus contains ~20 syntenic genes and shows molecular signatures of sex chromosome-like evolution. Inheritance mechanisms for heterodichogamy are deeply conserved, yet may occasionally turn over, as in sex determination.

Evolution and regulation of animal sex chromosomes

Animal sex chromosomes typically carry the upstream sex-determining gene that triggers testis or ovary development and, in some species, are regulated by global dosage compensation in response to functional decay of the Y chromosome. Despite the importance of these pathways, they exhibit striking differences across species, raising fundamental questions regarding the mechanisms underlying their evolutionary turnover. Recent studies of non-model organisms, including insects, reptiles and teleosts, have yielded a broad view of the diversity of sex chromosomes that challenges established theories. Moreover, continued studies in model organisms with recently developed technologies have characterized the dynamics of sex determination and dosage compensation in three-dimensional nuclear space and at single-cell resolution. Here, we synthesize recent insights into sex chromosomes from a variety of species to review their evolutionary dynamics with respect to the canonical model, as well as their diverse mechanisms of regulation.

Holocentric repeat landscapes: From micro-evolutionary patterns to macro-evolutionary associations with karyotype evolution

Repetitive elements can cause large-scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain chromosomal rearrangements that lead to karyotype changes such as fusions and fissions. This is because chromosome segregation during cell division should be less affected than in organisms with a localized centromere. The relationships between repetitive elements and chromosomal rearrangements and how they may translate to patterns of speciation in holocentric organisms are though poorly understood. Here, we use a reference-free approach based on low-coverage short-read sequencing data to characterize the repeat landscape of two independently evolved holocentric groups: Erebia butterflies and Carex sedges. We consider both micro- and macro-evolutionary scales to investigate the repeat landscape differentiation between Erebia populations and the association between repeats and karyotype changes in a phylogenetic framework for both Erebia and Carex. At a micro-evolutionary scale, we found population differentiation in repeat landscape that increases with overall intraspecific genetic differentiation among four Erebia species. At a macro-evolutionary scale, we found indications for an association between repetitive elements and karyotype changes along both Erebia and Carex phylogenies. Altogether, our results suggest that repetitive elements are associated with the level of population differentiation and chromosomal rearrangements in holocentric clades and therefore likely play a role in adaptation and potentially species diversification.

Chromosomal inversions and their impact on insect evolution

Insects can adapt quickly and effectively to rapid environmental change and maintain long-term adaptations, but the genetic mechanisms underlying this response are not fully understood. In this review, we summarize studies on the potential impact of chromosomal inversion polymorphisms on insect evolution at different spatial and temporal scales, ranging from long-term evolutionary stability to rapid emergence in response to emerging biotic and abiotic factors. The study of inversions has recently been advanced by comparative, population, and 3D genomics methods. The impact of inversions on insect genome evolution can be profound, including increased gene order rearrangements on sex chromosomes, accumulation of transposable elements, and facilitation of genome divergence. Understanding these processes provides critical insights into the evolutionary mechanisms shaping insect diversity.

Sex Chromosome Evolution: Hallmarks and Question Marks

Sex chromosomes are widespread in species with separate sexes. They have evolved many times independently and display a truly remarkable diversity. New sequencing technologies and methodological developments have allowed the field of molecular evolution to explore this diversity in a large number of model and nonmodel organisms, broadening our vision on the mechanisms involved in their evolution. Diverse studies have allowed us to better capture the common evolutionary routes that shape sex chromosomes; however, we still mostly fail to explain why sex chromosomes are so diverse. We review over half a century of theoretical and empirical work on sex chromosome evolution and highlight pending questions on their origins, turnovers, rearrangements, degeneration, dosage compensation, gene content, and rates of evolution. We also report recent theoretical progress on our understanding of the ultimate reasons for sex chromosomes' existence.

Recombination Rate Variation in Social Insects: An Adaptive Perspective

Social insects have the highest rates of meiotic recombination among Metazoa, but there is considerable variation within the Hymenoptera. We synthesize the literature to investigate several hypotheses for these elevated recombination rates. We reexamine the long-standing Red Queen hypothesis, considering how social aspects of immunity could lead to increases in recombination. We examine the possibility of positive feedback between gene duplication and recombination rate in the context of caste specialization. We introduce a novel hypothesis that recombination rate may be driven up by direct selection on recombination activity in response to increases in lifespan. Finally, we find that the role of population size in recombination rate evolution remains opaque, despite the long-standing popularity of this hypothesis. Moreover, our review emphasizes how the varied life histories of social insect species provide an effective framework for advancing a broader understanding of adaptively driven variation in recombination rates.

The impact of insertion bias into piRNA clusters on the invasion of transposable elements

In our current understanding of transposable element (TE) invasions TEs move freely until they accidentally insert into a piRNA cluster. They are then silenced by the production of piRNA cognate to the TE. Under this model, one would expect that TEs might evolve to avoid piRNA clusters. Yet empirical observations show that some TEs, such as the P-element, insert into piRNA clusters preferentially. We were thus wondering if such a bias could be beneficial for the TE, for example by minimizing harm to the host while still being able to selfishly spread in populations. We decided to model insertion bias to determine if there was ever a situation in which insertion bias was beneficial to the TE. We performed extensive forward simulations of TE invasions with differing insertion biases into piRNA clusters. We found that insertion bias significantly altered the invasion dynamics of TEs, primarily by changing the copy number of the TE in individuals prior to silencing. Insertion into a piRNA cluster reduced the deleterious effects of TEs to the host population, but we found that TEs avoiding piRNA clusters out-compete TEs with a bias towards cluster insertions. Insertion bias was only beneficial to the TE when there was negative selection against TEs and a lack of recombination. Different TEs show different insertion biases into piRNA clusters suggesting they are an attribute of the TE not the host, yet scenarios in which this is beneficial to the TE are quite limited. This opens up an interesting area of future research into the dynamics of insertion bias during TE invasions.

Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems

Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.

Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes

Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.

Varying recombination landscapes between individuals are driven by polymorphic transposable elements

Meiotic recombination is a prominent force shaping genome evolution, and understanding the causes for varying recombination landscapes within and between species has remained a central, though challenging, question. Recombination rates are widely observed to negatively associate with the abundance of transposable elements (TEs), selfish genetic elements that move between genomic locations. While such associations are usually interpreted as recombination influencing the efficacy of selection at removing TEs, accumulating findings suggest that TEs could instead be the cause rather than the consequence. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked a novel approach that uses PacBio long-read sequencing to efficiently, accurately, and cost-effectively identify crossovers (COs), a key recombination product, among large numbers of pooled recombinant individuals. By applying this approach to Drosophila strains with distinct TE insertion profiles, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, reduce the occurrence of COs. Such an effect leads to different CO frequencies between homologous sequences with and without TEs, contributing to varying CO maps between individuals. The suppressive effect of TEs on CO is further supported by two orthogonal approaches-analyzing the distributions of COs in panels of recombinant inbred lines in relation to TE polymorphism and applying marker-assisted estimations of CO frequencies to isogenic strains with and without transgenically inserted TEs. Our investigations reveal how the constantly changing mobilome can actively modify recombination landscapes, shaping genome evolution within and between species.

Evolutionary changes of noncoding elements associated with transition of sexual mode in Caenorhabditis nematodes

The transition of the sexual mode occurs widely in animal evolution. In Caenorhabditis nematodes, androdioecy, a sexual polymorphism composed of males and hermaphrodites having the ability to self-fertilize, has evolved independently multiple times. While the modification of noncoding regulatory elements likely contributed to the evolution of hermaphroditism, little is known about these changes. Here, we conducted a genome-wide analysis of conserved noncoding elements (CNEs) focusing on the evolution of hermaphroditism in Caenorhabditis nematodes. We found that, in androdioecious nematodes, mutations rapidly accumulated in CNEs' neighboring genes associated with sexual traits. Expression analysis indicate that the identified CNEs are involved in spermatogenesis in hermaphrodites and associated with the transition of gene expression from dioecious to androdioecious nematodes. Last, genome editing of a CNE neighboring laf-1 resulted in a change in its expression in the gonadal region undergoing spermatogenesis. Our bioinformatic and experimental analyses highlight the importance of CNEs in gene regulation associated with the development of hermaphrodites.

Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions

Recombination plays a crucial role in evolution by generating novel haplotypes and disrupting linkage between genes, thereby enhancing the efficiency of selection. Here, we analyze the genomes of 12 great reed warblers (Acrocephalus arundinaceus) in a 3-generation pedigree to identify precise crossover positions along the chromosomes. We located more than 200 crossovers and found that these were highly concentrated toward the telomeric ends of the chromosomes. Apart from this major pattern in the recombination landscape, we found significantly higher frequencies of crossovers in genic compared with intergenic regions, and in exons compared with introns. Moreover, while the number of recombination events was similar between the sexes, the crossovers were located significantly closer to the ends of paternal compared with maternal chromosomes. In conclusion, our study of the great reed warbler revealed substantial variation in crossover frequencies within chromosomes, with a distinct bias toward the sub-telomeric regions, particularly on the paternal side. These findings emphasize the importance of thoroughly screening the entire length of chromosomes to characterize the recombination landscape and uncover potential sex-biases in recombination.

Satellite DNAs and the evolution of the multiple X1X2Y sex chromosomes in the wolf fish Hoplias malabaricus (Teleostei; Characiformes)

Multiple sex chromosomes usually arise from chromosomal rearrangements which involve ancestral sex chromosomes. There is a fundamental condition to be met for their long-term fixation: the meiosis must function, leading to the stability of the emerged system, mainly concerning the segregation of the sex multivalent. Here, we sought to analyze the degree of differentiation and meiotic pairing properties in the selected fish multiple sex chromosome system present in the wolf-fish Hoplias malabaricus (HMA). This species complex encompasses seven known karyotype forms (karyomorphs) where the karyomorph C (HMA-C) exhibits a nascent XY sex chromosomes from which the multiple X1X2Y system evolved in karyomorph HMA-D via a Y-autosome fusion. We combined genomic and cytogenetic approaches to analyze the satellite DNA (satDNA) content in the genome of HMA-D karyomorph and to investigate its potential contribution to X1X2Y sex chromosome differentiation. We revealed 56 satDNA monomers of which the majority was AT-rich and with repeat units longer than 100 bp. Seven out of 18 satDNA families chosen for chromosomal mapping by fluorescence in situ hybridization (FISH) formed detectable accumulation in at least one of the three sex chromosomes (X1, X2 and neo-Y). Nine satDNA monomers showed only two hybridization signals limited to HMA-D autosomes, and the two remaining ones provided no visible FISH signals. Out of seven satDNAs located on the HMA-D sex chromosomes, five mapped also to XY chromosomes of HMA-C. We showed that after the autosome-Y fusion event, the neo-Y chromosome has not substantially accumulated or eliminated satDNA sequences except for minor changes in the centromere-proximal region. Finally, based on the obtained FISHpatterns, we speculate on the possible contribution of satDNA to sex trivalent pairing and segregation.

Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior

Eusocial Hymenoptera have the highest recombination rates among all multicellular animals studied so far, but it is unclear why this is and how this affects the biology of individual species. A high-resolution linkage map for the ant Cardiocondyla obscurior corroborates genome-wide high recombination rates reported for ants (8.1 cM/Mb). However, recombination is locally suppressed in regions that are enriched with TEs, that have strong haplotype divergence, or that show signatures of epistatic selection in C. obscurior The results do not support the hypotheses that high recombination rates are linked to phenotypic plasticity or to modulating selection efficiency. Instead, genetic diversity and the frequency of structural variants correlate positively with local recombination rates, potentially compensating for the low levels of genetic variation expected in haplodiploid social Hymenoptera with low effective population size. Ultimately, the data show that recombination contributes to within-population polymorphism and to the divergence of the lineages within C. obscurior.

Major changes in domain arrangements are associated with the evolution of termites

Domains as functional protein units and their rearrangements along the phylogeny can shed light on the functional changes of proteomes associated with the evolution of complex traits like eusociality. This complex trait is associated with sterile soldiers and workers, and long-lived, highly fecund reproductives. Unlike in Hymenoptera (ants, bees, and wasps), the evolution of eusociality within Blattodea, where termites evolved from within cockroaches, was accompanied by a reduction in proteome size, raising the question of whether functional novelty was achieved with existing rather than novel proteins. To address this, we investigated the role of domain rearrangements during the evolution of termite eusociality. Analysing domain rearrangements in the proteomes of three solitary cockroaches and five eusocial termites, we inferred more than 5,000 rearrangements over the phylogeny of Blattodea. The 90 novel domain arrangements that emerged at the origin of termites were enriched for several functions related to longevity, such as protein homeostasis, DNA repair, mitochondrial activity, and nutrient sensing. Many domain rearrangements were related to changes in developmental pathways, important for the emergence of novel castes. Along with the elaboration of social complexity, including permanently sterile workers and larger, foraging colonies, we found 110 further domain arrangements with functions related to protein glycosylation and ion transport. We found an enrichment of caste-biased expression and splicing within rearranged genes, highlighting their importance for the evolution of castes. Furthermore, we found increased levels of DNA methylation among rearranged compared to non-rearranged genes suggesting fundamental differences in their regulation. Our findings indicate the importance of domain rearrangements in the generation of functional novelty necessary for termite eusociality to evolve.

Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future

Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms of recombination are remarkably conserved across eukaryotes, yet meiotic genes and proteins show substantial variation in their sequence and function, even between closely related species. Furthermore, the rate and distribution of recombination shows a huge diversity within and between chromosomes, individuals, sexes, populations, and species. This variation has implications for many molecular and evolutionary processes, yet how and why this diversity has evolved is not well understood. A key step in understanding trait evolution is to determine its genetic basis-that is, the number, effect sizes, and distribution of loci underpinning variation. In this perspective, I discuss past and current knowledge on the genetic basis of variation in recombination rate and distribution, explore its evolutionary implications, and present open questions for future research.

A catalogue of recombination coldspots in interspecific tomato hybrids

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.

Why do sex chromosomes progressively lose recombination?

Progressive recombination loss is a common feature of sex chromosomes. Yet, the evolutionary drivers of this phenomenon remain a mystery. For decades, differences in trait optima between sexes (sexual antagonism) have been the favoured hypothesis, but convincing evidence is lacking. Recent years have seen a surge of alternative hypotheses to explain progressive extensions and maintenance of recombination suppression: neutral accumulation of sequence divergence, selection of nonrecombining fragments with fewer deleterious mutations than average, sheltering of recessive deleterious mutations by linkage to heterozygous alleles, early evolution of dosage compensation, and constraints on recombination restoration. Here, we explain these recent hypotheses and dissect their assumptions, mechanisms, and predictions. We also review empirical studies that have brought support to the various hypotheses.

Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity

Cargo-mobilizing mobile elements (CMEs) are genetic entities that faithfully transpose diverse protein coding sequences. Although common in bacteria, we know little about eukaryotic CMEs because no appropriate tools exist for their annotation. For example, Starships are giant fungal CMEs whose functions are largely unknown because they require time-intensive manual curation. To address this knowledge gap, we developed starfish, a computational workflow for high-throughput eukaryotic CME annotation. We applied starfish to 2 899 genomes of 1 649 fungal species and found that starfish recovers known Starships with 95% combined precision and recall while expanding the number of annotated elements ten-fold. Extant Starship diversity is partitioned into 11 families that differ in their enrichment patterns across fungal classes. Starship cargo changes rapidly such that elements from the same family differ substantially in their functional repertoires, which are predicted to contribute to diverse biological processes such as metabolism. Many elements have convergently evolved to insert into 5S rDNA and AT-rich sequence while others integrate into random locations, revealing both specialist and generalist strategies for persistence. Our work establishes a framework for advancing mobile element biology and provides the means to investigate an emerging dimension of eukaryotic genetic diversity, that of genomes within genomes.

Evolutionary genomics of socially polymorphic populations of Pogonomyrmex californicus

BACKGROUND

Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but also throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown.

RESULTS

We provide a first analysis of its genomic basis and evolutionary history using population genomics comparing individuals from a haplometrotic population to those from a pleometrotic population. We discovered a recently evolved (< 200 k years), 8-Mb non-recombining region segregating with the observed social niche polymorphism. This region shares several characteristics with supergenes underlying social polymorphisms in other socially polymorphic ant species. However, we also find remarkable differences from previously described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (Dnmt1).

CONCLUSIONS

Altogether, our results suggest that social morph in this species is a polygenic trait involving a potential young supergene. Further studies targeting haplo- and pleometrotic individuals from a single population are however required to conclusively resolve whether these genetic differences underlie the alternative social phenotypes or have emerged through genetic drift.

A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae

Self-incompatibility (SI) has evolved independently multiple times and prevents self-fertilization in hermaphrodite angiosperms. Several groups of Oleaceae such as jasmines exhibit distylous flowers, with two compatibility groups each associated with a specific floral morph.1 Other Oleaceae species in the olive tribe have two compatibility groups without associated morphological variation.2,3,4,5 The genetic basis of both homomorphic and dimorphic SI systems in Oleaceae is unknown. By comparing genomic sequences of three olive subspecies (Olea europaea) belonging to the two compatibility groups, we first locate the genetic determinants of SI within a 700-kb hemizygous region present only in one compatibility group. We then demonstrate that the homologous hemizygous region also controls distyly in jasmine. Phylogenetic analyses support a common origin of both systems, following a segmental genomic duplication in a common ancestor. Examination of the gene content of the hemizygous region in different jasmine and olive species suggests that the mechanisms determining compatibility groups and floral phenotypes (whether homomorphic or dimorphic) in Oleaceae rely on the presence/absence of two genes involved in gibberellin and brassinosteroid regulation.

Transposable elements cause the loss of self-incompatibility in citrus

Self-incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S-RNase-based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm-RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self-compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786-bp miniature inverted-repeat transposable element (MITE) insertion in the promoter region of the FhiS2-RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm-RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S-RNase; moreover, transgenic experiments show that deletion of this 786-bp MITE insertion recovers the expression of FhiS2-RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S-locus affecting the SI phenotype. A family-wide survey of the S-locus revealed that MITE insertions occur frequently adjacent to S-RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S-RNase system.

Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics

Transposable elements (TEs) are selfish genetic elements whose antagonistic interactions with hosts represent a common genetic conflict in eukaryotes. To resolve this conflict, hosts have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, this mechanism is imperfect and fails to fully halt TE replication. Furthermore, TE epigenetic silencing can inadvertently spread repressive marks to adjacent functional sequences, a phenomenon considered a 'curse' of this conflict resolution. Here, we used forward simulations to explore how TE epigenetic silencing and its harmful side effects shape the evolutionary dynamics of TEs and their hosts. Our findings reveal that epigenetic silencing allows TEs and their hosts to stably coexist under a wide range of conditions, because the underlying molecular mechanisms give rise to copy-number dependency of the strength of TE silencing. Interestingly, contrary to intuitive expectations that TE epigenetic silencing should evolve to be as strong as possible, we found a selective benefit for modifier alleles that weaken TE silencing under biologically feasible conditions. These results reveal that the dual nature of TE epigenetic silencing, with both positive and negative effects, complicates its evolutionary trajectory and makes it challenging to determine whether TE epigenetic silencing is a 'blessing' or a 'curse'.

Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus

Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10 MYA) and neo (<200,000 yr) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup Rumex salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed that the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 Mb) and two Y chromosomes (503 Mb) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo-sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.

Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery

Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

Universal signatures of transposable element compartmentalization across eukaryotic genomes

The evolutionary mechanisms that drive the emergence of genome architecture remain poorly understood but can now be assessed with unprecedented power due to the massive accumulation of genome assemblies spanning phylogenetic diversity1,2. Transposable elements (TEs) are a rich source of large-effect mutations since they directly and indirectly drive genomic structural variation and changes in gene expression3. Here, we demonstrate universal patterns of TE compartmentalization across eukaryotic genomes spanning ~1.7 billion years of evolution, in which TEs colocalize with gene families under strong predicted selective pressure for dynamic evolution and involved in specific functions. For non-pathogenic species these genes represent families involved in defense, sensory perception and environmental interaction, whereas for pathogenic species, TE-compartmentalized genes are highly enriched for pathogenic functions. Many TE-compartmentalized gene families display signatures of positive selection at the molecular level. Furthermore, TE-compartmentalized genes exhibit an excess of high-frequency alleles for polymorphic TE insertions in fruit fly populations. We postulate that these patterns reflect selection for adaptive TE insertions as well as TE-associated structural variants. This process may drive the emergence of a shared TE-compartmentalized genome architecture across diverse eukaryotic lineages.

rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers

Meiotic control of crossover (CO) number and position is critical for homologous chromosome segregation and organismal fertility, recombination of parental genotypes, and the generation of novel genetic combinations. We here characterize the recombination rate landscape of a rec-1 loss of function modifier of CO position in Caenorhabditis elegans, one of the first ever modifiers discovered. By averaging CO position across hermaphrodite and male meioses and by genotyping 203 single-nucleotide variants covering about 95% of the genome, we find that the characteristic chromosomal arm-center recombination rate domain structure is lost in the loss of function rec-1 mutant. The rec-1 loss of function mutant smooths the recombination rate landscape but is insufficient to eliminate the nonuniform position of CO. Lower recombination rates in the rec-1 mutant are particularly found in the autosomal arm domains containing the pairing centers. We further find that the rec-1 mutant is of little consequence for organismal fertility and egg viability and thus for rates of autosomal nondisjunction. It nonetheless increases X chromosome nondisjunction rates and thus male appearance. Our findings question the maintenance of recombination rate heritability and genetic diversity among C. elegans natural populations, and they further suggest that manipulating genetic modifiers of CO position will help find quantitative trait loci located in low-recombining genomic regions normally refractory to discovery.

The genome-wide meiotic recombination landscape in ciliates and its implications for crossover regulation and genome evolution

Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa. However, genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates: the synaptonemal complex (SC)-independent meiosis and the nuclear dimorphism. Here, we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny. We detect 1021 crossover (CO) events (35.8 per meiosis), corresponding to an overall CO rate of 9.9 cM/Mb. However, gene conversion by non-crossover is rare (1.03 per meiosis) and not biased towards G or C alleles. Consistent with the reported roles of SC in CO interference, we find no obvious sign of CO interference. CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions. Gene ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes. We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.

Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap

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 may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium-based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.

HLA Genetics for the Human Diseases

Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

Sex-limited morphs can provide profound insights into the evolution and genomic architecture of complex phenotypes. Inter-sexual mimicry is one particular type of sex-limited polymorphism in which a novel morph resembles the opposite sex. While inter-sexual mimics are known in both sexes and a diverse range of animals, their evolutionary origin is poorly understood. Here, we investigated the genomic basis of female-limited morphs and male mimicry in the common bluetail damselfly. Differential gene expression between morphs has been documented in damselflies, but no causal locus has been previously identified. We found that male mimicry originated in an ancestrally sexually dimorphic lineage in association with multiple structural changes, probably driven by transposable element activity. These changes resulted in ~900 kb of novel genomic content that is partly shared by male mimics in a close relative, indicating that male mimicry is a trans-species polymorphism. More recently, a third morph originated following the translocation of part of the male-mimicry sequence into a genomic position ~3.5 mb apart. We provide evidence of balancing selection maintaining male mimicry, in line with previous field population studies. Our results underscore how structural variants affecting a handful of potentially regulatory genes and morph-specific genes can give rise to novel and complex phenotypic polymorphisms.

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Parnassius glacialis is a typical "Out of the QTP" alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for "Out of the QTP" of P. glacialis.

How chromosomal inversions reorient the evolutionary process

Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.

Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica

Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.

Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged African Nothobranchius killifish karyotypes

Using African annual killifishes of the genus Nothobranchius from temporary savannah pools with rapid karyotype and sex chromosome evolution, we analysed the chromosomal distribution of telomeric (TTAGGG)n repeat and Nfu-SatC satellite DNA (satDNA; isolated from Nothobranchius furzeri) in 15 species across the Nothobranchius killifish phylogeny, and with Fundulosoma thierryi as an out-group. Our fluorescence in situ hybridization experiments revealed that all analysed taxa share the presence of Nfu-SatC repeat but with diverse organization and distribution on chromosomes. Nfu-SatC landscape was similar in conspecific populations of Nothobranchius guentheri and Nothobranchius melanospilus but slightly-to-moderately differed between populations of Nothobranchius pienaari, and between closely related Nothobranchius kuhntae and Nothobranchius orthonotus. Inter-individual variability in Nfu-SatC patterns was found in N. orthonotus and Nothobranchius krysanovi. We revealed mostly no sex-linked patterns of studied repetitive DNA distribution. Only in Nothobranchius brieni, possessing multiple sex chromosomes, Nfu-SatC repeat occupied a substantial portion of the neo-Y chromosome, similarly as formerly found in the XY sex chromosome system of turquoise killifish N. furzeri and its sister species Nothobranchius kadleci-representatives not closely related to N. brieni. All studied species further shared patterns of expected telomeric repeats at the ends of all chromosomes and no additional interstitial telomeric sites. In summary, we revealed (i) the presence of conserved satDNA class in Nothobranchius clades (a rare pattern among ray-finned fishes); (ii) independent trajectories of Nothobranchius sex chromosome differentiation, with recurrent and convergent accumulation of Nfu-SatC on the Y chromosome in some species; and (iii) genus-wide shared tendency to loss of telomeric repeats during interchromosomal rearrangements. Collectively, our findings advance our understanding of genome structure, mechanisms of karyotype reshuffling, and sex chromosome differentiation in Nothobranchius killifishes from the genus-wide perspective.

Transposable element evolution in plant genome ecosystems

The relationship of transposable elements (TEs) with their host genomes has usually been seen as an arms race between TEs and their host genomes. Consequently, TEs are supposed to amplify by bursts of transposition, when the TE escapes host surveillance, followed by long periods of TE quiescence and efficient host control. Recent data obtained from an increasing number of assembled plant genomes and resequencing population datasets show that TE dynamics is more complex and varies among TE families and their host genomes. This variation ranges from large genomes that accommodate large TE populations to genomes that are very active in TE elimination, and from inconspicuous elements with very low activity to elements with high transposition and elimination rates. The dynamics of each TE family results from a long history of interaction with the host in a genome populated by many other TE families, very much like an evolving ecosystem.

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation

Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.