Entangled and non-modular enhancer sequences producing independent spatial activities.

The modularity of transcriptional enhancers is central to our understanding of morphological evolution, allowing specific changes to a gene expression pattern component, without affecting others. Enhancer modularity refers to physically separated stretches of regulatory sequence producing discrete spatiotemporal transcriptional activity. This concept stems from assays that test the sufficiency of a DNA segment to drive spatial reporter expression resembling that of the corresponding gene.

Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab.

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab.

A single-cell atlas of the sexually dimorphic Drosophila foreleg and its sensory organs during development.

To respond to the world around them, animals rely on the input of a network of sensory organs distributed throughout the body. Distinct classes of sensory organs are specialized for the detection of specific stimuli such as strain, pressure, or taste. The features that underlie this specialization relate both to the neurons that innervate sensory organs and the accessory cells they comprise.

Evolution and development of male-specific leg brushes in Drosophilidae.

The origin, diversification, and secondary loss of sexually dimorphic characters are common in animal evolution. In some cases, structurally and functionally similar traits have evolved independently in multiple lineages. Prominent examples of such traits include the male-specific grasping structures that develop on the front legs of many dipteran insects.

Secondary reversion to sexual monomorphism associated with tissue-specific loss of doublesex expression.

Animal evolution is characterized by frequent turnover of sexually dimorphic traits-new sex-specific characters are gained, and some ancestral sex-specific characters are lost, in many lineages. In insects, sexual differentiation is predominantly cell autonomous and depends on the expression of the doublesex (dsx) transcription factor. In most cases, cells that transcribe dsx have the potential to undergo sex-specific differentiation, while those that lack dsx expression do not.

Interspecific variation in sex-specific gustatory organs in Drosophila.

Drosophila males use leg gustatory bristles to discriminate between male and female cuticular pheromones as an important part of courtship behavior. In Drosophila melanogaster, several male-specific gustatory bristles are present on the anterior surface of the first tarsal segment of the prothoracic leg, in addition to a larger set of gustatory bristles found in both sexes. These bristles are thought to be specialized for pheromone detection.

Highly contiguous assemblies of 101 drosophilid genomes.

Over 100 years of studies in and related species in the genus have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated.

Modular tissue-specific regulation of underpins sexually dimorphic development in .

The ability of a single genome to produce distinct and often dramatically different male and female forms is one of the wonders of animal development. In , most sexually dimorphic traits are controlled by sex-specific isoforms of the () transcription factor, and expression is mostly limited to cells that give rise to sexually dimorphic traits. However, it is unknown how this mosaic of sexually dimorphic and monomorphic organs arises.

A Distalless-responsive enhancer of the Hox gene Sex combs reduced is required for segment- and sex-specific sensory organ development in Drosophila.

Hox genes are involved in the patterning of animal body parts at multiple levels of regulatory hierarchies. Early expression of Hox genes in different domains along the embryonic anterior-posterior (A/P) axis in insects, vertebrates, and other animals establishes segmental or regional identity. However, Hox gene function is also required later in development for the patterning and morphogenesis of limbs and other organs.

Evolving doublesex expression correlates with the origin and diversification of male sexual ornaments in the Drosophila immigrans species group.

Male ornaments and other sex-specific traits present some of the most dramatic examples of evolutionary innovations. Comparative studies of similar but independently evolved traits are particularly important for identifying repeated patterns in the evolution of these traits. Male-specific modifications of the front legs have evolved repeatedly in Drosophilidae and other Diptera.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data.

Genetic basis of a violation of Dollo's Law: re-evolution of rotating sex combs in Drosophila bipectinata.

Phylogenetic analyses suggest that violations of "Dollo's law"--that is, re-evolution of lost complex structures--do occur, albeit infrequently. However, the genetic basis of such reversals has not been examined. Here, we address this question using the Drosophila sex comb, a recently evolved, male-specific morphological structure composed of modified bristles.

Intrathecally synthesized IgG in multiple sclerosis cerebrospinal fluid recognizes identical epitopes over time.

Intrathecal antibody production manifest as oligoclonal bands (OCBs) is a hallmark of multiple sclerosis (MS). Once present, OCBs can be detected in CSF throughout the lifetime of MS patients. To determine the specificity of the OCBs, we applied CSF IgG obtained from 2 consecutive lumbar punctures of 5 MS patients to screen phage-displayed random peptide libraries, and selected identical and related peptides that reacted with the paired CSF IgGs from each patient.

Evolution of sex-specific traits through changes in HOX-dependent doublesex expression.

Almost every animal lineage is characterized by unique sex-specific traits, implying that such traits are gained and lost frequently in evolution. However, the genetic mechanisms responsible for these changes are not understood. In Drosophila, the activity of the sex determination pathway is restricted to sexually dimorphic tissues, suggesting that spatial regulation of this pathway may contribute to the evolution of sex-specific traits.

Peptide reactivity between multiple sclerosis (MS) CSF IgG and recombinant antibodies generated from clonally expanded plasma cells in MS CSF.

We employed 19 recombinant antibodies (rAbs) generated from clonally expanded plasma cells, and native IgG from cerebrospinal fluid (CSF) of three multiple sclerosis (MS) patients for panning with phage displayed random peptide libraries. Specific peptide epitopes/mimotopes were identified and characterized. Importantly, peptide-antibody interactions were shared by rAbs and native IgG from the same patient.

Distinct developmental mechanisms underlie the evolutionary diversification of Drosophila sex combs.

Similar selective pressures can lead to independent origin of similar morphological structures in multiple evolutionary lineages. Developmental mechanisms underlying convergent evolution remain poorly understood. In this report, we show that similar sex comb morphology in closely related Drosophila species is produced by different cellular mechanisms.

Identification of measles virus epitopes using an ultra-fast method of panning phage-displayed random peptide libraries.

Phage-displayed random peptide libraries, in which high affinity phage peptides are enriched by repetitive selection (panning) on target antibody, provide a unique tool for identifying antigen specificity. This paper describes a new panning method that enables selection of peptides in 1 day as compared to about 6 days required in traditional panning to identify virus-specific epitopes. The method, termed ultra-fast selection of peptide (UFSP), utilizes phage produced by bacterial infection (phage amplification) directly for subsequent panning.

Genetic basis of sex-specific color pattern variation in Drosophila malerkotliana.

Pigmentation is a rapidly evolving trait that can play important roles in mimicry, sexual selection, thermoregulation, and other adaptive processes in many groups of animals. In Drosophila, pigmentation can differ dramatically among closely related taxa, presenting a good opportunity to dissect the genetic changes underlying species divergence. In this report, we investigate the genetic basis of color pattern variation between two allopatric subspecies of Drosophila malerkotliana, a widespread member of the ananassae species subgroup.

Evolution of gene expression in the Drosophila olfactory system.

Host plant shifts by phytophagous insects play a key role in insect evolution and plant ecology. Such shifts often involve major behavioral changes as the insects must acquire an attraction and/or lose the repulsion to the new host plant's odor and taste. The evolution of chemotactic behavior may be due, in part, to gene expression changes in the peripheral sensory system.

Sex-specific expression of a HOX gene associated with rapid morphological evolution.

Animal diversity is shaped by the origin and diversification of new morphological structures. Many examples of evolutionary innovations are provided by male-specific traits involved in mating and sexual selection. The origin of new sex-specific characters requires the evolution of new regulatory interactions between sex-determining genes and genes that control spatial patterning and cell differentiation.

New candidate genes for sex-comb divergence between Drosophila mauritiana and Drosophila simulans.

A large-effect QTL for divergence in sex-comb tooth number between Drosophila simulans and D. mauritiana was previously mapped to 73A-84AB. Here we identify genes that are likely contributors to this divergence.

Interspecific divergence, intrachromosomal recombination, and phylogenetic utility of Y-chromosomal genes in Drosophila.

Reconstruction of phylogenetic relationships among recently diverged species is complicated by three general problems: segregation of polymorphisms that pre-date species divergence, gene flow during and after speciation, and intra-locus recombination. In light of these difficulties, the Y chromosome offers several important advantages over other genomic regions as a source of phylogenetic information. These advantages include the absence of recombination, rapid coalescence, and reduced opportunity for interspecific introgression due to hybrid male sterility.

Sex- and segment-specific modulation of gene expression profiles in Drosophila.

Homeotic and sex-determining genes control a wide range of morphological traits by regulating the expression of different target genes in different tissues. The identity of most of these target genes remains unknown, and it is not even clear what fraction of the genome is regulated in a segment- and sex-specific manner. In this report, we examine segment- and sex-specific gene expression in Drosophila pupal legs.