High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

Identification and characterization of a laterally transferred alternative oxidase (AOX) in a terrestrial insect, the dipteran Pseudolycoriella hygida

Alternative oxidase (AOX) (EC 1.10.3.11) is a terminal oxidase in the mitochondrial inner membrane that branches the canonical electron transport system (ETS). AOX is ubiquitous in plants, frequently found in fungi and protists and presents a more sporadic distribution in metazoans. More recently, AOX has gained attention due to its potential application in gene therapy for treatment of mitochondrial diseases. Here we characterized the AOX in the basal Dipteran, Pseudolycoriella hygida using a combination of genomic analyses, molecular, functional and in vivo survival assays. AOX is a single copy gene that encodes three developmental stage specific protein isoforms. AOX localizes to the mitochondria in adult thoracic muscles, which present cyanide-resistant respiration that is sensitive to the AOX inhibitor salicylhydroxamic acid (SHAM). Both the cyanide-resistant respiration and AOX levels gradually increase during aging, but are not influenced by thermal stress. Thoracic mitochondria respire using substrates derived from several metabolic routes, such as pyruvate, proline, acylcarnitine, NADH and glycerol-3P, and present values of oxidative phosphorylation capacity ((P-L)/E = 0.70) and coupling (P/L = 4.35; L/E = 0.21). Adult flies exhibit a high survival resistance for SHAM-sensitive complex III inhibition. Together, our results demonstrate the presence of a functional AOX in a terrestrial arthropod and provide insights regarding AOX function in animals and evolution of respiratory systems in metazoans. Psl. hygida emerges as a natural and valuable model for comprehensive AOX research at the whole-organism level which complements models expressing the heterologous enzyme.

Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences

BACKGROUND

The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.

RESULTS

We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.

CONCLUSIONS

The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.

Gene novelty and gene family expansion in the early evolution of Lepidoptera

BACKGROUND

Almost 10% of all known animal species belong to Lepidoptera: moths and butterflies. To understand how this incredible diversity evolved we assess the role of gene gain in driving early lepidopteran evolution. Here, we compared the complete genomes of 115 insect species, including 99 Lepidoptera, to search for novel genes coincident with the emergence of Lepidoptera.

RESULTS

We find 217 orthogroups or gene families which emerged on the branch leading to Lepidoptera; of these 177 likely arose by gene duplication followed by extensive sequence divergence, 2 are candidates for origin by horizontal gene transfer, and 38 have no known homology outside of Lepidoptera and possibly arose via de novo gene genesis. We focus on two new gene families that are conserved across all lepidopteran species and underwent extensive duplication, suggesting important roles in lepidopteran biology. One encodes a family of sugar and ion transporter molecules, potentially involved in the evolution of diverse feeding behaviours in early Lepidoptera. The second encodes a family of unusual propeller-shaped proteins that likely originated by horizontal gene transfer from Spiroplasma bacteria; we name these the Lepidoptera propellin genes.

CONCLUSION

We provide the first insights into the role of genetic novelty in the early evolution of Lepidoptera. This gives new insight into the rate of gene gain during the evolution of the order as well as providing context on the likely mechanisms of origin. We describe examples of new genes which were retained and duplicated further in all lepidopteran species, suggesting their importance in Lepidoptera evolution.

Canonical terpene synthases in arthropods: Intraphylum gene transfer

Insects employ terpenoids for communication both within and between species. While terpene synthases derived from isoprenyl diphosphate synthase have been shown to catalyze terpenoid biosynthesis in some insects, canonical terpene synthases (TPS) commonly found in plants, fungi, and bacteria were previously unidentified in insects. This study reveals the presence of TPS genes in insects, likely originating via horizontal gene transfer from noninsect arthropods. By examining 361 insect genomes, we identified TPS genes in five species of the Sciaridae family (fungus gnats). Additionally, TPS genes were found in Collembola (springtails) and Acariformes (mites) among diverse noninsect arthropods. Selected TPS enzymes from Sciaridae, Collembola, and Acariformes display monoterpene, sesquiterpene, and/or diterpene synthase activities. Through comprehensive protein database search and phylogenetic analysis, the TPS genes in Sciaridae were found to be most closely related to those in Acariformes, suggesting transfer of TPS genes from Acariformes to Sciaridae. In the model Sciaridae Bradysia coprophila, all five TPS genes are most highly expressed in adult males, suggesting a sex- and developmental stage-specific role of their terpenoid products. The finding of TPS genes in insects and their possible evolutionary origin through intraphylum gene transfer within arthropods sheds light on metabolic innovation in insects.

Bradysia (Sciara) coprophila larvae up-regulate DNA repair pathways and down-regulate developmental regulators in response to ionizing radiation

The level of resistance to radiation and the developmental and molecular responses can vary between species, and even between developmental stages of one species. For flies (order: Diptera), prior studies concluded that the fungus gnat Bradysia (Sciara) coprophila (sub-order: Nematocera) is more resistant to irradiation-induced mutations that cause visible phenotypes than the fruit fly Drosophila melanogaster (sub-order: Brachycera). Therefore, we characterized the effects of and level of resistance to ionizing radiation on B. coprophila throughout its life cycle. Our data show that B. coprophila embryos are highly sensitive to even low doses of gamma-irradiation, whereas late-stage larvae can tolerate up to 80 Gy (compared to 40 Gy for D. melanogaster) and still retain their ability to develop to adulthood, though with a developmental delay. To survey the genes involved in the early transcriptional response to irradiation of B. coprophila larvae, we compared larval RNA-seq profiles with and without radiation treatment. The up-regulated genes were enriched for DNA damage response genes, including those involved in DNA repair, cell cycle arrest, and apoptosis, whereas the down-regulated genes were enriched for developmental regulators, consistent with the developmental delay of irradiated larvae. Interestingly, members of the PARP and AGO families were highly up-regulated in the B. coprophila radiation response. We compared the transcriptome responses in B. coprophila to the transcriptome responses in D. melanogaster from 3 previous studies: whereas pathway responses are highly conserved, specific gene responses are less so. Our study lays the groundwork for future work on the radiation responses in Diptera.

Paternal genome elimination: patterns and mechanisms of drive and silencing

In thousands of arthropod species, males inherit, but subsequently eliminate the entire haploid genome of their father. However, why this peculiar reproductive strategy evolved repeatedly across diverse species and what mechanisms are involved in paternal genome elimination (PGE) remains largely unknown. In this review, we summarize what we know about the patterns of paternal chromosome elimination during various stages of development in the diverse taxa that have been studied. We also discuss some other unusual features often associated with PGE, such as the transcriptional silencing of paternally derived chromosomes in males and sex determination through the early embryonic elimination of X chromosomes. Little is known about the molecular mechanisms underlying the parent-of-origin-dependent chromosome elimination and silencing under PGE, but we discuss the insight of several studies that are pioneering this work and highlight directions for future research.

Aliens in the CYPome of the black fungus gnat, Bradysia coprophila

The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.

Why put all your eggs in one basket? Evolutionary perspectives on the origins of monogenic reproduction

Sexual reproduction is ubiquitous in eukaryotes, but the mechanisms by which sex is determined are diverse and undergo rapid turnovers in short evolutionary timescales. Usually, an embryo's sex is fated at the moment of fertilisation, but in rare instances it is the maternal genotype that determines the offspring's sex. These systems are often characterised by mothers producing single-sex broods, a phenomenon known as monogeny. Monogenic reproduction is well documented in Hymenoptera (ants, bees and wasps), where it is associated with a eusocial lifestyle. However, it is also known to occur in three families in Diptera (true flies): Sciaridae, Cecidomyiidae and Calliphoridae. Here we review current knowledge of monogenic reproduction in these dipteran clades. We discuss how this strange reproductive strategy might evolve, and we consider the potential contributions of inbreeding, sex ratio distorters, and polygenic control of the sex ratio. Finally, we provide suggestions on future work to elucidate the origins of this unusual reproductive strategy. We propose that studying these systems will contribute to our understanding of the evolution and turnover of sex determination systems.

Biocatalytic potential of Pseudolycoriella CAZymes (Sciaroidea, Diptera) in degrading plant and fungal cell wall polysaccharides

Soil biota has a crucial impact on soil ecology, global climate changes, and effective crop management and studying the diverse ecological roles of dipteran larvae deepens the understanding of soil food webs. A multi-omics study of Pseudolycoriella hygida comb. nov. (Diptera: Sciaroidea: Sciaridae) aimed to characterize carbohydrate-active enzymes (CAZymes) for litter degradation in this species. Manual curation of 17,881 predicted proteins in the Psl. hygida genome identified 137 secreted CAZymes, of which 33 are present in the saliva proteome, and broadly confirmed by saliva CAZyme catalytic profiling against plant cell wall polysaccharides and pNP-glycosyl substrates. Comparisons with two other sciarid species and the outgroup Lucilia cuprina (Diptera: Calliphoridae) identified 42 CAZyme families defining a sciarid CAZyme profile. The litter-degrading potential of sciarids corroborates their significant role as decomposers, yields insights to the evolution of insect feeding habits, and highlights the importance of insects as a source of biotechnologically relevant enzymes.

Non-random chromosome segregation and chromosome eliminations in the fly Bradysia (Sciara)

Mendelian inheritance is based upon random segregation of homologous chromosomes during meiosis and perfect duplication and division of chromosomes in mitosis so that the entire genomic content is passed down to the daughter cells. The unusual chromosome mechanics of the fly Bradysia (previously called Sciara) presents many exceptions to the canonical processes. In male meiosis I, there is a monopolar spindle and non-random segregation such that all the paternal homologs move away from the single pole and are eliminated. In male meiosis II, there is a bipolar spindle and segregation of the sister chromatids except for the X dyad that undergoes non-disjunction. The daughter cell that is nullo-X degenerates, whereas the sperm has two copies of the X. Fertilization restores the diploid state, but there are three copies of the X chromosome, of which one or two of the paternally derived X chromosomes will be eliminated in an early cleavage division. Bradysia (Sciara) coprophila also has germ line limited L chromosomes that are eliminated from the soma. Current information and the molecular mechanisms for chromosome imprinting and eliminations, which are just beginning to be studied, will be reviewed here.

De novo genome assembly of Bradysia cellarum (Diptera: Sciaridae), a notorious pest in traditional special vegetables in China

Bradysia cellarum (Diptera: Sciaridae) is a destructive vegetable insect pest infesting more than 30 species of host plants from seven families in Asia and Europe. B. cellarum causes grave problems in Chinese chive, which originated in China and is cultivated widely in East Asia. The B. cellarum infestation results in economic losses and subsequent severe food safety problems in farm productions, insecticide resistance and environmental pollution. The genomic and molecular information of B. cellarum to delineate the biological features, insecticide resistance, evolution remains poorly understood. Herein, we decode the whole genome of B. cellarum to delineate the underlying molecular mechanisms causing insecticide resistance. We constructed a highly reliable genome for B. cellarum using PacBio, Illumina and 10X Genomics sequencing platforms. The genome size of B. cellarum was 375.91 Mb with a contig N50 of 1.57 Mb. A total of 16,231 genes were identified, among which 93.8% were functionally annotated, and 42.06% were repeat sequences. According to phylogenetic analysis, B. cellarum diverged from the common ancestor of Drosophila melanogaster and Musca domestica ~139.3-191.0 million years ago. Moreover, some important genes responsible for significant insecticide resistance, such as cytochrome P450s, ABC transporters and those involved in glutathione metabolism, were expanded in B. cellarum. We assembled a high-quality B. cellarum genome to provide valuable insights into their life history strategies, insecticide resistance and biological behaviours. It also lays the foundation for exploring gene structure and functional evolution, as well as comparative genomics of B. cellarum and other model insect species.

De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

The black carpenter ant (Camponotus pennsylvanicus) is a pest species found widely throughout North America. From a single individual I used long-read nanopore sequencing to assemble a phased diploid genome of 306 Mb and 60X coverage, with quality assessed by a 97.0% BUSCO score, improving upon other ant assemblies. The mitochondrial genome reveals minor rearrangements from other ants. The reads also allowed assembly of parasitic and symbiont genomes. I include a complete Wolbachia bacterial assembly with a size of 1.2 Mb, as well as a commensal symbiont Blochmannia pennsylvanicus, at 791 kb. DNA methylation and hydroxymethylation were measured at base-pair resolution level from the same reads and confirmed extremely low levels seen in the Formicidae family. There was moderate heterozygosity, with 0.16% of bases being biallelic from the parental haplotypes. Protein prediction yielded 14 415 amino acid sequences with 95.8% BUSCO score and 86% matching to previously known proteins. All assemblies were derived from a single MinION flow cell generating 20 Gb of sequence for a cost of $1047 including consumable reagents. Adding fixed costs for equipment brings the total for an ant-sized genome to less than $5000. All analyses were performed in 1 week on a single desktop computer.

Development of Transformation for Genome Editing of an Emerging Model Organism

With the advances in genomic sequencing, many organisms with novel biological properties are ripe for use as emerging model organisms. However, to make full use of them, transformation methods need to be developed to permit genome editing. Here, we present the development of transformation for the fungus fly Bradysia (Sciara) coprophila; this may serve as a paradigm for the development of transformation for other emerging systems, especially insects. Bradysia (Sciara) has a variety of unique biological features, including locus-specific developmentally regulated DNA amplification, chromosome imprinting, a monopolar spindle in male meiosis I, non-disjunction of the X chromosome in male meiosis II, X chromosome elimination in early embryogenesis, germ-line-limited (L) chromosomes and high resistance to radiation. Mining the unique biology of Bradysia (Sciara) requires a transformation system to test mutations of DNA sequences that may play roles for these features. We describe a Bradysia (Sciara) transformation system using a modified piggyBac transformation vector and detailed protocols we have developed to accommodate Bradysia (Sciara) specific requirements. This advance will provide a platform for us and others in the growing Bradysia (Sciara) community to take advantage of this unique biological system. In addition, the versatile piggyBac vectors described here and transformation methods will be useful for other emerging model systems.

Gene-rich germline-restricted chromosomes in black-winged fungus gnats evolved through hybridization

Germline-restricted DNA has evolved in diverse animal taxa and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline-restricted DNA has evolved, especially in flies, in which 3 diverse families, Chironomidae, Cecidomyiidae, and Sciaridae, carry germline-restricted chromosomes (GRCs). We conducted a genomic analysis of GRCs in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which has 2 large germline-restricted "L" chromosomes. We sequenced and assembled the genome of B. coprophila and used differences in sequence coverage and k-mer frequency between somatic and germline tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene rich, and have many genes with divergent homologs on other chromosomes in the genome. We also found that 2 divergent GRCs exist in the population we sequenced. GRC genes are more similar in sequence to genes from another Dipteran family (Cecidomyiidae) than to homologous genes from Sciaridae. This unexpected finding suggests that these chromosomes likely arose in Sciaridae through hybridization with a related lineage. These results provide a foundation from which to answer many questions about the evolution of GRCs in Sciaridae, such as how this hybridization event resulted in GRCs and what features on these chromosomes cause them to be restricted to the germline.

DNA Damage Responses during the Cell Cycle: Insights from Model Organisms and Beyond

Genome damage is a threat to all organisms. To respond to such damage, DNA damage responses (DDRs) lead to cell cycle arrest, DNA repair, and cell death. Many DDR components are highly conserved, whereas others have adapted to specific organismal needs. Immense progress in this field has been driven by model genetic organism research. This review has two main purposes. First, we provide a survey of model organism-based efforts to study DDRs. Second, we highlight how model organism study has contributed to understanding how specific DDRs are influenced by cell cycle stage. We also look forward, with a discussion of how future study can be expanded beyond typical model genetic organisms to further illuminate how the genome is protected.