Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera

Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes and show that the chromosomes of extant lepidopterans are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact through 250 million years of evolution and diversification. Against this stable background, eight lineages have undergone extensive reorganization either through numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions often involve small, repeat-rich Merian elements and the sex-linked element. Our results reveal the constraints on genome architecture in Lepidoptera and provide a deeper understanding of chromosomal rearrangements in eukaryotic genome evolution.

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes

Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. The majority of nematode species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX/X0). Some filarial nematode species, including important parasites of humans, have heteromorphic XX/XY karyotypes. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused homologue of an autosome involved in an X-autosome fusion event. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis, a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). By mapping the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements, we infer that the ancestral filarial X chromosome was the product of a fusion between NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal). In the two filarial lineages with XY systems, there have been two independent X-autosome chromosome fusion events involving different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from the unfused homologue of the autosome. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a Y-linked sex-determining locus.

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.

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV)

We report a new visualization tool for analysis of whole genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by NCBI using assembly alignment algorithms developed by us and others. Researchers can examine the alignments between the two assemblies using two alternate views: a chromosome ideogram-based view or a 2D genome dotplot. Whole genome alignment views expose large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed in the ideogram view where available. CGV currently provides approximately 700 alignments from over 300 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

Mode and Tempo of 3D Genome Evolution in Drosophila

Topologically associating domains (TADs) are thought to play an important role in preventing gene misexpression by spatially constraining enhancer-promoter contacts. The deleterious nature of gene misexpression implies that TADs should, therefore, be conserved among related species. Several early studies comparing chromosome conformation between species reported high levels of TAD conservation; however, more recent studies have questioned these results. Furthermore, recent work suggests that TAD reorganization is not associated with extensive changes in gene expression. Here, we investigate the evolutionary conservation of TADs among 11 species of Drosophila. We use Hi-C data to identify TADs in each species and employ a comparative phylogenetic approach to derive empirical estimates of the rate of TAD evolution. Surprisingly, we find that TADs evolve rapidly. However, we also find that the rate of evolution depends on the chromatin state of the TAD, with TADs enriched for developmentally regulated chromatin evolving significantly slower than TADs enriched for broadly expressed, active chromatin. We also find that, after controlling for differences in chromatin state, highly conserved TADs do not exhibit higher levels of gene expression constraint. These results suggest that, in general, most TADs evolve rapidly and their divergence is not associated with widespread changes in gene expression. However, higher levels of evolutionary conservation and gene expression constraints in TADs enriched for developmentally regulated chromatin suggest that these TAD subtypes may be more important for regulating gene expression, likely due to the larger number of long-distance enhancer-promoter contacts associated with developmental genes.

Cytological heterogeneity of heterochromatin among 10 sequenced Drosophila species

In Drosophila chromosomal rearrangements can be maintained and are associated with karyotypic variability among populations from different geographic localities. The abundance of variability in gene arrangements among chromosomal arms is even greater when comparing more distantly related species and the study of these chromosomal changes has provided insights into the evolutionary history of species in the genus. In addition, the sequencing of genomes of several Drosophila species has offered the opportunity to establish the global pattern of genomic evolution, at both genetic and chromosomal level. The combined approaches of comparative analysis of syntenic blocks and direct physical maps on polytene chromosomes have elucidated changes in the orientation of genomic sequences and the difference between heterochromatic and euchromatic regions. Unfortunately, the centromeric heterochromatic regions cannot be studied using the cytological maps of polytene chromosomes because they are underreplicated and therefore reside in the chromocenter. In Drosophila melanogaster, a cytological map of the heterochromatin has been elaborated using mitotic chromosomes from larval neuroblasts. In the current work, we have expanded on that mapping by producing cytological maps of the mitotic heterochromatin in an additional 10 sequenced Drosophila species. These maps highlight 2 apparently different paths, for the evolution of the pericentric heterochromatin between the subgenera Sophophora and Drosophila. One path leads toward a progressive complexity of the pericentric heterochromatin (Sophophora) and the other toward a progressive simplification (Drosophila). These maps are also useful for a better understanding how karyotypes have been altered by chromosome arm reshuffling during evolution.

Ecology and the evolution of sex chromosomes

Sex chromosomes are common features of animal genomes, often carrying a sex determination gene responsible for initiating the development of sexually dimorphic traits. The specific chromosome that serves as the sex chromosome differs across taxa as a result of fusions between sex chromosomes and autosomes, along with sex chromosome turnover-autosomes becoming sex chromosomes and sex chromosomes 'reverting' back to autosomes. In addition, the types of genes on sex chromosomes frequently differ from the autosomes, and genes on sex chromosomes often evolve faster than autosomal genes. Sex-specific selection pressures, such as sexual antagonism and sexual selection, are hypothesized to be responsible for sex chromosome turnovers, the unique gene content of sex chromosomes and the accelerated evolutionary rates of genes on sex chromosomes. Sex-specific selection has pronounced effects on sex chromosomes because their sex-biased inheritance can tilt the balance of selection in favour of one sex. Despite the general consensus that sex-specific selection affects sex chromosome evolution, most population genetic models are agnostic as to the specific sources of these sex-specific selection pressures, and many of the details about the effects of sex-specific selection remain unresolved. Here, I review the evidence that ecological factors, including variable selection across heterogeneous environments and conflicts between sexual and natural selection, can be important determinants of sex-specific selection pressures that shape sex chromosome evolution. I also explain how studying the ecology of sex chromosome evolution can help us understand important and unresolved aspects of both sex chromosome evolution and sex-specific selection.

Evolution of the odorant-binding protein gene family in Drosophila

Odorant-binding proteins (OBPs) are encoded by a gene family involved in the perception of olfactory signals in insects. This chemosensory gene family has been advocated as a candidate to mediate host preference and host shifts in insects, although it also participates in other physiological processes. Remarkable differences in the OBP gene repertoire have been described across insect groups, suggesting an accelerated gene turnover rate. The genus Drosophila, is a valuable resource for ecological genomics studies since it comprises groups of ecologically diverse species and there are genome data for many of them. Here, we investigate the molecular evolution of this chemosensory gene family across 19 Drosophila genomes, including the melanogaster and repleta species groups, which are mostly associated with rotting fruit and cacti, respectively. We also compared the OBP repertoire among the closely related species of the repleta group, associated with different subfamilies of Cactaceae that represent disparate chemical challenges for the flies. We found that the gene family size varies widely between species, ranging from 39 to 54 candidate OBPs. Indeed, more than 54% of these genes are organized in clusters and located on chromosomes X, 2, and 5, with a distribution conserved throughout the genus. The family sizes in the repleta group and D. virilis (virilis-repleta radiation) were smaller than in the melanogaster group. We tested alternative evolutionary models for OBP family size and turnover rates based on different ecological scenarios. We found heterogeneous gene turnover rates (GR) in comparisons involving columnar cactus specialists, prickly pear specialists, and fruit dwellers lineages, and signals of rapid molecular evolution compatible with positive selection in specific OBP genes. Taking ours and previous results together, we propose that this chemosensory gene family is involved in host adaptation and hypothesize that the adoption of the cactophilic lifestyle in the repleta group accelerated the evolution of members of the family.

The relevance of chromatin architecture to genome rearrangements in Drosophila

DNA within chromosomes in the nucleus is non-randomly organized into chromosome territories, compartments and topologically associated domains (TADs). Chromosomal rearrangements have the potential to alter chromatin organization and modify gene expression leading to selection against these structural variants. Drosophila pseudoobscura has a wealth of naturally occurring gene arrangements that were generated by overlapping inversion mutations caused by two chromosomal breaks that rejoin the central region in reverse order. Unlike humans, Drosophila inversion heterozygotes do not have negative effects associated with crossing over during meiosis because males use achiasmate mechanisms for proper segregation, and aberrant recombinant meiotic products generated in females are lost in polar bodies. As a result, Drosophila populations are found to harbour extensive inversion polymorphisms. It is not clear, however, whether chromatin architecture constrains which inversions breakpoints persist in populations. We mapped the breakpoints of seven inversions in D. pseudoobscura to the TAD map to determine if persisting inversion breakpoints are more likely to occur at boundaries between TADs. Our results show that breakpoints occur at TAD boundaries more than expected by chance. Some breakpoints may alter gene expression within TADs supporting the hypothesis that position effects contribute to inversion establishment. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.

Interpopulation variation of transposable elements of the hAT superfamily in Drosophila willistoni (Diptera: Drosophilidae): in-situ approach

Transposable elements are abundant and dynamic part of the genome, influencing organisms in different ways through their presence or mobilization, or by acting directly on pre- and post-transcriptional regulatory regions. We compared and evaluated the presence, structure, and copy number of three hAT superfamily transposons (hobo, BuT2, and mar) in five strains of Drosophila willistoni species. These D. willistoni strains are of different geographical origins, sampled across the north-south occurrence of this species. We used sequenced clones of the hAT elements in fluorescence in-situ hybridizations in the polytene chromosomes of three strains of D. willistoni. We also analyzed the structural characteristics and number of copies of these hAT elements in the 10 currently available sequenced genomes of the willistoni group. We found that hobo, BuT2, and mar were widely distributed in D. willistoni polytene chromosomes and sequenced genomes of the willistoni group, except for mar, which is restricted to the subgroup willistoni. Furthermore, the elements hobo, BuT2, and mar have different evolutionary histories. The transposon differences among D. willistoni strains, such as variation in the number, structure, and chromosomal distribution of hAT transposons, could reflect the genomic and chromosomal plasticity of D. willistoni species in adapting to highly variable environments.

Deeply conserved synteny and the evolution of metazoan chromosomes

Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.

Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera

How chromosome gene organization and gene content evolve among distantly related and structurally malleable genomes remains unresolved. This is particularly the case when considering different insect orders. We have compared the highly contiguous genome assemblies of the lepidopteran Danaus plexippus and the dipteran Drosophila melanogaster, which shared a common ancestor around 290 Ma. The gene content of 23 out of 30 D. plexippus chromosomes was significantly associated with one or two of the six chromosomal elements of the Drosophila genome, denoting common ancestry. Despite the phylogenetic distance, 9.6% of the 1-to-1 orthologues still reside within the same ancestral genome neighbourhood. Furthermore, the comparison D. plexippus-Bombyx mori indicated that the rates of chromosome repatterning are lower in Lepidoptera than in Diptera, although still within the same order of magnitude. Concordantly, 14 developmental gene clusters showed a higher tendency to retain full or partial clustering in D. plexippus, further supporting that the physical association between the SuperHox and NK clusters existed in the ancestral bilaterian. Our results illuminate the scope and limits of the evolution of the gene organization and content of the ancestral chromosomes to the Lepidoptera and Diptera while helping reconstruct portions of the genome in their most recent common ancestor.

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes

Eukaryotic chromosomes have phylogenetic persistence. In many taxa, each chromosome has a single functional centromere with essential roles in spindle attachment and segregation. Fusion and fission can generate chromosomes with no or multiple centromeres, leading to genome instability. Groups with holocentric chromosomes (where centromeric function is distributed along each chromosome) might be expected to show karyotypic instability. This is generally not the case, and in Caenorhabditis elegans, it has been proposed that the role of maintenance of a stable karyotype has been transferred to the meiotic pairing centers, which are found at one end of each chromosome. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60-Mb O. tipulae genome is resolved into six chromosomal molecules. We find the evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes, we identify seven ancestral chromosomal elements (Nigon elements) and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex chromosome-associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.

Evolution of genome structure in the Drosophila simulans species complex

The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.

Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species

Pericentromeric heterochromatin in Drosophila generally consists of repetitive DNA, forming the environment associated with gene silencing. Despite the expanding knowledge of the impact of transposable elements (TEs) on the host genome, little is known about the evolution of pericentromeric heterochromatin, its structural composition, and age. During the evolution of the Drosophilidae, hundreds of genes have become embedded within pericentromeric regions yet retained activity. We investigated a pericentromeric heterochromatin fragment found in D. virilis and related species, describing the evolution of genes in this region and the age of TE invasion. Regardless of the heterochromatic environment, the amino acid composition of the genes is under purifying selection. However, the selective pressure affects parts of genes in varying degrees, resulting in expansion of gene introns due to TEs invasion. According to the divergence of TEs, the pericentromeric heterochromatin of the species of virilis group began to form more than 20 million years ago by invasions of retroelements, miniature inverted repeat transposable elements (MITEs), and Helitrons. Importantly, invasions into the heterochromatin continue to occur by TEs that fall under the scope of piRNA silencing. Thus, the pericentromeric heterochromatin, in spite of its ability to induce silencing, has the means for being dynamic, incorporating the regions of active transcription.

Population Genomics on the Fly: Recent Advances in Drosophila

Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.

3D genome evolution and reorganization in the Drosophila melanogaster species group

Topologically associating domains, or TADs, are functional units that organize chromosomes into 3D structures of interacting chromatin. TADs play an important role in regulating gene expression by constraining enhancer-promoter contacts and there is evidence that deletion of TAD boundaries leads to aberrant expression of neighboring genes. While the mechanisms of TAD formation have been well-studied, current knowledge on the patterns of TAD evolution across species is limited. Due to the integral role TADs play in gene regulation, their structure and organization is expected to be conserved during evolution. However, more recent research suggests that TAD structures diverge relatively rapidly. We use Hi-C chromosome conformation capture to measure evolutionary conservation of whole TADs and TAD boundary elements between D. melanogaster and D. triauraria, two early-branching species from the melanogaster species group which diverged ∼15 million years ago. We find that the majority of TADs have been reorganized since the common ancestor of D. melanogaster and D. triauraria, via a combination of chromosomal rearrangements and gain/loss of TAD boundaries. TAD reorganization between these two species is associated with a localized effect on gene expression, near the site of disruption. By separating TADs into subtypes based on their chromatin state, we find that different subtypes are evolving under different evolutionary forces. TADs enriched for broadly expressed, transcriptionally active genes are evolving rapidly, potentially due to positive selection, whereas TADs enriched for developmentally-regulated genes remain conserved, presumably due to their importance in restricting gene-regulatory element interactions. These results provide novel insight into the evolutionary dynamics of TADs and help to reconcile contradictory reports related to the evolutionary conservation of TADs and whether changes in TAD structure affect gene expression.

A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly

BACKGROUND

The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics.

RESULTS

Most of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS).

CONCLUSIONS

Steganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.

Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins

Pericentromeric heterochromatin is generally composed of repetitive DNA forming a transcriptionally repressive environment. Dozens of genes were embedded into pericentromeric heterochromatin during evolution of Drosophilidae lineage while retaining activity. However, factors that contribute to insusceptibility of gene loci to transcriptional silencing remain unknown. Here, we find that the promoter region of genes that can be embedded in both euchromatin and heterochromatin exhibits a conserved structure throughout the Drosophila phylogeny and carries motifs for binding of certain chromatin remodeling factors, including insulator proteins. Using ChIP-seq data, we demonstrate that evolutionary gene relocation between euchromatin and pericentric heterochromatin occurred with preservation of sites of insulation of BEAF-32 in evolutionarily distant species, i.e. D. melanogaster and D. virilis. Moreover, promoters of virtually all protein-coding genes located in heterochromatin in D. melanogaster are enriched with insulator proteins BEAF-32, GAF and dCTCF. Applying RNA-seq of a BEAF-32 mutant, we show that the impairment of BEAF-32 function has a complex effect on gene expression in D. melanogaster, affecting even those genes that lack BEAF-32 association in their promoters. We propose that conserved intrinsic properties of genes, such as sites of insulation near the promoter regions, may contribute to adaptation of genes to the heterochromatic environment and, hence, facilitate the evolutionary relocation of genes loci between euchromatin and heterochromatin.

Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower

Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here, we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package syntR. The syntR algorithm performs as well as previous ad hoc methods while being systematic, repeatable, and applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax Using syntR, we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years, a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between one and three translocations involving only 8 of the 17 chromosomes. This nonrandom exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.

Comparative Cytology of Female Meiosis I Among Drosophila Species

The physical connections established by recombination are normally sufficient to ensure proper chromosome segregation during female Meiosis I. However, nonexchange chromosomes (such as the Muller F element or "dot" chromosome in D. melanogaster) can still segregate accurately because they remain connected by heterochromatic tethers. A recent study examined female meiosis in the closely related species D. melanogaster and D. simulans, and found a nearly twofold difference in the mean distance the obligately nonexchange dot chromosomes were separated during Prometaphase. That study proposed two speculative hypotheses for this difference, the first being the amount of heterochromatin in each species, and the second being the species' differing tolerance for common inversions in natural populations. We tested these hypotheses by examining female meiosis in 12 additional Drosophila species. While neither hypothesis had significant support, we did see 10-fold variation in dot chromosome sizes, and fivefold variation in the frequency of chromosomes out on the spindle, which were both significantly correlated with chromosome separation distances. In addition to demonstrating that heterochromatin abundance changes chromosome behavior, this implies that the duration of Prometaphase chromosome movements must be proportional to the size of the F element in these species. Additionally, we examined D. willistoni, a species that lacks a free dot chromosome. We observed that chromosomes still moved out on the meiotic spindle, and the F element was always positioned closest to the spindle poles. This result is consistent with models where one role of the dot chromosomes is to help organize the meiotic spindle.

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

In this study, Renschler et al. set out to analyze the impact of genomic rearrangements on genome topology using the Drosophila genus and X chromosome dosage compensation as a model. The authors developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. Their data provides unique insights into genome topology evolution. RA

Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs), and spatial contacts between high-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservation at various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarily flexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential processes such as dosage compensation of the X chromosome.

Dynamic turnover of centromeres drives karyotype evolution in Drosophila

Centromeres are the basic unit for chromosome inheritance, but their evolutionary dynamics is poorly understood. We generate high-quality reference genomes for multiple Drosophila obscura group species to reconstruct karyotype evolution. All chromosomes in this lineage were ancestrally telocentric and the creation of metacentric chromosomes in some species was driven by de novo seeding of new centromeres at ancestrally gene-rich regions, independently of chromosomal rearrangements. The emergence of centromeres resulted in a drastic size increase due to repeat accumulation, and dozens of genes previously located in euchromatin are now embedded in pericentromeric heterochromatin. Metacentric chromosomes secondarily became telocentric in the pseudoobscura subgroup through centromere repositioning and a pericentric inversion. The former (peri)centric sequences left behind shrunk dramatically in size after their inactivation, yet contain remnants of their evolutionary past, including increased repeat-content and heterochromatic environment. Centromere movements are accompanied by rapid turnover of the major satellite DNA detected in (peri)centromeric regions.

Local adaptation and the evolution of inversions on sex chromosomes and autosomes

Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic divergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.

The chromosomes of Drosophila suzukii (Diptera: Drosophilidae): detailed photographic polytene chromosomal maps and in situ hybridization data

The spotted wing drosophila, D. suzukii, is a serious agricultural pest attacking a variety of soft fruits and vegetables. Although originating from East Asia it has recently invaded America and Europe raising major concern about its expansion potential and the consequent economic losses. Since cytogenetic information on the species is scarce, we report here the mitotic karyotype and detailed photographic maps of the salivary gland polytene chromosomes of D. suzukii. The mitotic metaphase complement contains three pairs of autosomes, one of which is dot-like, and one pair of heteromorphic (XX/XY) sex chromosomes. The salivary gland polytene complement consists of five long polytene arms, representing the two metacentric autosomes and the acrocentric X chromosome, and one very short polytene element, which corresponds to the dot-like autosome. Banding pattern as well as the most characteristic features and prominent landmarks of each polytene chromosome arm are presented and discussed. Furthermore, twelve gene markers have been mapped on the polytene chromosomes of D. suzukii by in situ hybridization. Their distribution pattern was found quite similar to that of D. melanogaster revealing conservation of synteny although the relative position within each chromosome arm for most of the genes differed significantly between D. suzukii and D. melanogaster. The chromosome information presented here is suitable for comparative cytogenetic studies and phylogenetic exploration, while it could also facilitate the assembly of the genome sequence and support the development of genetic tools for species-specific and environment-friendly biological control applications such as the sterile insect technique.

Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects

BACKGROUND

Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup.

RESULTS

We generated a highly-contiguous ~ 129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic-island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes.

CONCLUSIONS

We present the first high-quality, long-read sequencing of a D. subobscura genome. Our findings generally support genome structure evolution in this species being driven indirectly, through the inversions' recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow. The resources developed will serve to further establish the subobscura subgroup as model for comparative genomics and evolutionary indicator of global change.

How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis

The gene arrangements of Drosophila have played a prominent role in the history of evolutionary biology from the original quantification of genetic diversity to current studies of the mechanisms for the origin and establishment of new inversion mutations within populations and their subsequent fixation between species supporting reproductive barriers. This review examines the genetic causes and consequences of inversions as recombination suppressors and the role that recombination suppression plays in establishing inversions in populations as they are involved in adaptation within heterogeneous environments. This often results in the formation of clines of gene arrangement frequencies among populations. Recombination suppression leads to the differentiation of the gene arrangements which may accelerate the accumulation of fixed genetic differences among populations. If these fixed mutations cause incompatibilities, then inversions pose important reproductive barriers between species. This review uses the evolution of inversions in Drosophila pseudoobscura and D. persimilis as a case study for how inversions originate, establish and contribute to the evolution of reproductive isolation.

The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats

The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the "dot chromosome" because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb "long arm." The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g, low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5' ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.

The molecular characterization of fixed inversions breakpoints unveils the ancestral character of the Drosophila guanche chromosomal arrangements

Cytological studies revealed that the number of chromosomes and their organization varies across species. The increasing availability of whole genome sequences of multiple species across specific phylogenies has confirmed and greatly extended these cytological observations. In the Drosophila genus, the ancestral karyotype consists of five rod-like acrocentric chromosomes (Muller elements A to E) and one dot-like chromosome (element F), each exhibiting a generally conserved gene content. Chromosomal fusions and paracentric inversions are thus the major contributors, respectively, to chromosome number variation among species and to gene order variation within chromosomal element. The subobscura cluster of Drosophila consists in three species that retain the genus ancestral karyotype and differ by a reduced number of fixed inversions. Here, we have used cytological information and the D. guanche genome sequence to identify and molecularly characterize the breakpoints of inversions that became fixed since the D. guanche-D. subobscura split. Our results have led us to propose a modified version of the D. guanche cytological map of its X chromosome, and to establish that (i) most inversions became fixed in the D. subobscura lineage and (ii) the order in which the four X chromosome overlapping inversions occurred and became fixed.

Origin and Consequences of Chromosomal Inversions in the virilis Group of Drosophila

In Drosophila, large variations in rearrangement rate have been reported among different lineages and among Muller’s elements. Nevertheless, the mechanisms that are involved in the generation of inversions, their increase in frequency, as well as their impact on the genome are not completely understood. This is in part due to the lack of comparative studies on species distantly related to Drosophila melanogaster. Therefore, we sequenced and assembled the genomes of two species of the virilis phylad (Drosophila novamexicana [15010-1031.00] and Drosophila americana [SF12]), which are diverging from D. melanogaster for more than 40 Myr. Based on these data, we identified the precise location of six novel inversion breakpoints. A molecular characterization provided clear evidence that DAIBAM (a miniature inverted–repeat transposable element) was involved in the generation of eight out of the nine inversions identified. In contrast to what has been previously reported for D. melanogaster and close relatives, ectopic recombination is thus the prevalent mechanism of generating inversions in species of the virilis phylad. Using pool-sequencing data for three populations of D. americana, we also show that common polymorphic inversions create a high degree of genetic differentiation between populations for chromosomes X, 4, and 5 over large physical distances. We did not find statistically significant differences in expression levels between D. americana (SF12) and D. novamexicana (15010-1031.00) strains for the three genes surveyed (CG9588, Fig 4, and fab1) flanking three inversion breakpoints.

A phylogenetic examination of host use evolution in the quinaria and testacea groups of Drosophila

Adaptive radiations provide an opportunity to examine complex evolutionary processes such as ecological specialization and speciation. While a well-resolved phylogenetic hypothesis is critical to completing such studies, the rapid rates of evolution in these groups can impede phylogenetic studies. Here we study the quinaria and testacea species groups of the immigrans-tripunctata radiation of Drosophila, which represent a recent adaptive radiation and are a developing model system for ecological genetics. We were especially interested in understanding host use evolution in these species. In order to infer a phylogenetic hypothesis for this group we sampled loci from both the nuclear genome and the mitochondrial DNA to develop a dataset of 43 protein-coding loci for these two groups along with their close relatives in the immigrans-tripunctata radiation. We used this dataset to examine their evolutionary relationships along with the evolution of feeding behavior. Our analysis recovers strong support for the monophyly of the testacea but not the quinaria group. Results from our ancestral state reconstruction analysis suggests that the ancestor of the testacea and quinaria groups exhibited mushroom-feeding. Within the quinaria group, we infer that transition to vegetative feeding occurred twice, and that this transition did not coincide with a genome-wide change in the rate of protein evolution.

Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics

The concept of synteny, or conservation of genes on the same chromosome, traces its origins to the early days of Drosophila genetics. This discovery emerged from comparisons of linkage maps from different species of Drosophila with the goal of understanding the process of speciation. H. J. Muller published a landmark article entitled Bearings of the "Drosophila" work on systematics, where he synthesized genetic and physical map data and proposed a model of speciation and chromosomal gene content conservation. These models have withstood the test of time with the advent of molecular genetic analysis from protein to genome level variation. Muller's ideas provide a framework to begin to answer questions about the evolutionary forces that shape the structure of the genome.

Inversions are bigger on the X chromosome

In many insects, X-linked inversions fix at a higher rate and are much less polymorphic than autosomal inversions. Here, we report that in Drosophila, X-linked inversions also capture 67% more genes. We estimated the number of genes captured through an approximate Bayesian computational analysis of gene orders in nine species of Drosophila. X-linked inversions fixed with a significantly larger gene content. Further, X-linked inversions of intermediate size enjoy highest fixation rate, while the fixation rate of autosomal inversions decreases with size. A less detailed analysis in Anopheles suggests a similar pattern holds in mosquitoes. We develop a population genetic model that assumes the fitness effects of inversions scale with the number of genes captured. We show that the same conditions that lead to a higher fixation rate also produce a larger size for inversions on the X.

Comparative genomics and the nature of placozoan species

Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites.

Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome

Background

Malaria mosquitoes have had a remarkable stability in the number of chromosomes in their karyotype (2n = 6) during 100 million years of evolution. Moreover, autosomal arms were assumed to maintain their integrity even if their associations with each other changed via whole-arm translocations. Here we use high-coverage comparative physical genome mapping of three Anopheles species to test the extent of evolutionary conservation of chromosomal arms in malaria mosquitoes.

Results

In this study, we developed a physical genome map for Anopheles atroparvus, one of the dominant malaria vectors in Europe. Using fluorescence in situ hybridization (FISH) of DNA probes with the ovarian nurse cell polytene chromosomes and synteny comparison, we anchored 56 genomic scaffolds to the An. atroparvus chromosomes. The obtained physical map represents 89.6% of the An. atroparvus genome. This genome has the second highest mapping coverage among Anophelinae assemblies after An. albimanus, which has 98.2% of the genome assigned to its chromosomes. A comparison of the An. atroparvus, An. albimanus, and An. gambiae genomes identified partial-arm translocations between the autosomal arms that break down the integrity of chromosome elements in evolution affecting the structure of the genetic material in the pericentromeric regions. Unlike An. atroparvus and An. albimanus, all chromosome elements of An. gambiae are fully syntenic with chromosome elements of the putative ancestral Anopheles karyotype. We also detected nonrandom distribution of large conserved synteny blocks and confirmed a higher rate of inversion fixation in the X chromosome compared with autosomes.

Conclusions

Our study demonstrates the power of physical mapping for understanding the genome evolution in malaria mosquitoes. The results indicate that syntenic relationships among chromosome elements of Anopheles species have not been fully preserved because of multiple partial-arm translocations.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4663-4) contains supplementary material, which is available to authorized users.

Genomes of Diptera

Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, and limited types of evolutionary events. Here, we provide an alternative way to resolve phylogenetic problems based on analyses of real genome data. We use phylogenetic signals from all types of genome level evolutionary events, and overcome the conflicting issues existing in traditional phylogenetic approaches. Further, we build an automated computational pipeline to reconstruct phylogenies and ancestral genomes for two high-resolution real yeast genome datasets. Comparison results with recent studies and publications show that we reconstruct very accurate and robust phylogenies and ancestors. Finally, we identify and analyze the conserved syntenic blocks among reconstructed ancestral genomes and present yeast species.

Comparative Gene Mapping as a Tool to Understand the Evolution of Pest Crop Insect Chromosomes

The extent of the conservation of synteny and gene order in aphids has been previously investigated only by comparing a small subset of linkage groups between the pea aphid Acyrthosiphon pisum and a few other aphid species. Here we compared the localization of eight A. pisum scaffolds (covering more than 5 Mb and 83 genes) in respect to the Drosophila melanogaster Muller elements identifying orthologous loci spanning all the four A. pisum chromosomes. Comparison of the genetic maps revealed a conserved synteny across different loci suggesting that the study of the fruit fly Muller elements could favour the identification of chromosomal markers useful for the study of chromosomal rearrangements in aphids. A. pisum is the first aphid species to have its genome sequenced and the finding that there are several chromosomal regions in synteny between Diptera and Hemiptera indicates that the genomic tools developed in A. pisum will be broadly useful not only for the study of other aphids but also for other insect species.

Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.

The chromosomes and the mitogenome of Ceratitis fasciventris (Diptera: Tephritidae): two genetic approaches towards the Ceratitis FAR species complex resolution

Ceratitis fasciventris is a serious agricultural pest of the Tephritidae family that belongs to the African Ceratitis FAR species complex. Species limits within the FAR complex are obscure and multidisciplinary approaches have attempted to resolve phylogenetic relationships among its members. These studies support the existence of at least three additional species in the complex, C. anonnae, C. rosa and C. quilicii, while they indicate the presence of two structured populations (F1 and F2) within the C. fasciventris species. In the present study we present the mitotic karyotype, polytene chromosome maps, in situ hybridization data and the complete mitochondrial genome sequence of an F2 population of C. fasciventris. This is the first polytene chromosome map and complete mitogenome of a member of the FAR complex and only the second reported for the Ceratitis genus. Both polytene chromosomes and mitochondrial sequence could provide valuable information and be used as reference for comparative analysis among the members of the complex towards the clarification of their phylogenetic relationships.

Evolutionary origin and function of NOX4-art, an arthropod specific NADPH oxidase

BACKGROUND

NADPH oxidases (NOX) are ROS producing enzymes that perform essential roles in cell physiology, including cell signaling and antimicrobial defense. This gene family is present in most eukaryotes, suggesting a common ancestor. To date, only a limited number of phylogenetic studies of metazoan NOXes have been performed, with few arthropod genes. In arthropods, only NOX5 and DUOX genes have been found and a gene called NOXm was found in mosquitoes but its origin and function has not been examined. In this study, we analyzed the evolution of this gene family in arthropods. A thorough search of genomes and transcriptomes was performed enabling us to browse most branches of arthropod phylogeny.

RESULTS

We have found that the subfamilies NOX5 and DUOX are present in all arthropod groups. We also show that a NOX gene, closely related to NOX4 and previously found only in mosquitoes (NOXm), can also be found in other taxonomic groups, leading us to rename it as NOX4-art. Although the accessory protein p22-phox, essential for NOX1-4 activation, was not found in any of the arthropods studied, NOX4-art of Aedes aegypti encodes an active protein that produces H₂O₂. Although NOX4-art has been lost in a number of arthropod lineages, it has all the domains and many signature residues and motifs necessary for ROS production and, when silenced, H₂O₂ production is considerably diminished in A. aegypti cells.

CONCLUSIONS

Combining all bioinformatic analyses and laboratory work we have reached interesting conclusions regarding arthropod NOX gene family evolution. NOX5 and DUOX are present in all arthropod lineages but it seems that a NOX2-like gene was lost in the ancestral lineage leading to Ecdysozoa. The NOX4-art gene originated from a NOX4-like ancestor and is functional. Although no p22-phox was observed in arthropods, there was no evidence of neo-functionalization and this gene probably produces H₂O₂ as in other metazoan NOX4 genes. Although functional and present in the genomes of many species, NOX4-art was lost in a number of arthropod lineages.

Chromosome inversions and ecological plasticity in the main African malaria mosquitoes

Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.

Dense gene physical maps of the non-model species Drosophila subobscura

The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism. These maps are based on 462 markers: 115, 236, and 111 markers for elements A, C, and E, respectively. The availability of these dense maps will facilitate genome assembly and will thus greatly contribute to obtaining a good reference genome, which is a required step for D. subobscura to attain the model species status. The comparative analysis of these physical maps and those obtained from the D. pseudoobscura and D. melanogaster genomes allowed us to infer the number of fixed inversions and chromosomal evolutionary rates for each pairwise comparison. For all three elements, rates inferred from the more closely related species were higher than those inferred from the more distantly related species, which together with results of relative-rate tests point to an acceleration in the D. subobscura lineage at least for elements A and E.