Genome assembly of the southern pine beetle ( Dendroctonus frontalis Zimmerman) reveals the origins of gene content reduction in Dendroctonus

Dendroctonus frontalis , also known as southern pine beetle (SPB), represents the most damaging forest pest in the southeastern United States. Strategies to predict, monitor and suppress SPB outbreaks have had limited success. Genomic data are critical to inform on pest biology and to identify molecular targets to develop improved management approaches. Here, we produced a chromosome-level genome assembly of SPB using long-read sequencing data. Synteny analyses confirmed the conservation of the core coleopteran Stevens elements and validated the bona fide SPB X chromosome. Transcriptomic data were used to obtain 39,588 transcripts corresponding to 13,354 putative protein-coding loci. Comparative analyses of gene content across 14 beetle and 3 other insects revealed several losses of conserved genes in the Dendroctonus clade and gene gains in SPB and Dendroctonus that were enriched for loci encoding membrane proteins and extracellular matrix proteins. While lineage-specific gene losses contributed to the gene content reduction observed in Dendroctonus , we also showed that widespread misannotation of transposable elements represents a major cause of the apparent gene expansion in several non- Dendroctonus species. Our findings uncovered distinctive features of the SPB gene complement and disentangled the role of biological and annotation-related factors contributing to gene content variation across beetles.

A reference quality genome assembly for the Jewel scarab Chrysina gloriosa

The jewel scarab Chrysina gloriosa is one of the most charismatic beetles in the United States and is found from the mountains of West Texas to the Southeastern Arizona sky islands. This species is highly sought by professional and amateur collectors worldwide due to its gleaming metallic coloration. However, the impact of the large-scale collection of this beetle on its populations is unknown, and there is a limited amount of genetic information available to make informed decisions about its conservation. As a first step, we present the genome of C. gloriosa, which we reconstructed using a single female specimen sampled from our ongoing effort to document population connectivity and the demographic history of this beetle. Using a combination of long-read sequencing and Omni-C data, we reconstructed the C. gloriosa genome at a near-chromosome level. Our genome assembly consisted of 454 scaffolds spanning 642 MB, with the ten largest scaffolds capturing 98% of the genome. The scaffold N50 was 72 MB, and the BUSCO score was 95.5%. This genome assembly will be an essential tool to accelerate understanding C. gloriosa biology and help make informed decisions for the conservation of Chrysina and other species with similar distributions in this region. This genome assembly will further serve as a community resource for comparative genomic analysis.

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography

The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

The Genome of the Yellow Mealworm, Tenebrio molitor: It's Bigger Than You Think

BACKGROUND

Insects are a sustainable source of protein for human food and animal feed. We present a genome assembly, CRISPR gene editing, and life stage-specific transcriptomes for the yellow mealworm, Tenebrio molitor, one of the most intensively farmed insects worldwide.

METHODS

Long and short reads and long-range data were obtained from a T. molitor male pupa. Sequencing transcripts from 12 T. molitor life stages resulted in 279 million reads for gene prediction and genetic engineering. A unique plasmid delivery system containing guide RNAs targeting the eye color gene vermilion flanking the muscle actin gene promoter and EGFP marker was used in CRISPR/Cas9 transformation.

RESULTS

The assembly is approximately 53% of the genome size of 756.8 ± 9.6 Mb, measured using flow cytometry. Assembly was complicated by a satellitome of at least 11 highly conserved satDNAs occupying 28% of the genome. The injection of the plasmid into embryos resulted in knock-out of Tm vermilion and knock-in of EGFP.

CONCLUSIONS

The genome of T. molitor is longer than current assemblies (including ours) due to a substantial amount (26.5%) of only one highly abundant satellite DNA sequence. Genetic sequences and transformation tools for an insect important to the food and feed industries will promote the sustainable utilization of mealworms and other farmed insects.

A chromosome scale assembly of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), genome

OBJECTIVE

The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), is a pest damaging many cultivated crops in North America. Although partial transcriptome data are available for this pest, a genome assembly was not available for this species. This assembly of a high-quality chromosome-length genome of TPB is aimed to develop the genetic resources that can provide the foundation required for advancing research on this species.

RESULTS

The initial genome of TPB assembled with paired-end nucleotide sequences generated with Illumina technology was scaffolded with Illumina HiseqX reads generated from a proximity ligated (HiC) library to obtain a high-quality genome assembly. The final assembly contained 3963 scaffolds longer than 1 kbp to yield a genome of 599.96 Mbp. The N50 of the TPB genome assembly was 35.64 Mbp and 98.68% of the genome was assembled into 17 scaffolds larger than 1 Mbp. This megabase scaffold number is the same as the number of chromosomes observed in karyotyping of this insect. The TPB genome is known to have high repetitive DNA content, and the reduced assembled genome size compared to flowcytometric estimates of approximately 860 Mbp may be due to the collapsed assembly of highly similar regions.

Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture

Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.

Differential Gene Expression of Innate Immune Response Genes Consequent to Solenopsis invicta Virus-3 Infection

The red imported fire ant Solenopsis invicta Buren (fire ant hereafter) is a global pest that inflicts billions of dollars in damages to the United States economy and poses a major threat on a global scale. Concerns with the broad-spectrum application of insecticides have facilitated the hunt for natural enemy-mediated controls. One of these, the virus Solenopsis invicta virus-3 (SINV-3 hereafter) is exceptionally virulent in laboratory settings. However, despite high mortality rates in the laboratory and documented widespread SINV-3 prevalence in the southern United States, the fire ant remains a major pest. To explore this paradox, we document the immune response elicited by the fire ant when infected with SINV-3. We sequence the fire ant transcriptome prior to and following infection with SINV-3, and identify and discuss in detail genes in immune response pathways differentially expressed following infection with SINV-3. This information provides insights into genes and pathways involved in the SINV-3 infection response in the fire ant and offers avenues to pursue, to suppress key immune response genes and force the fire ant to succumb to SINV-3 infection in the field.

The genomic basis of evolutionary novelties in a leafhopper

Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.

Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.

High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations

The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Presently, few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high-quality, chromosome-scale genome assemblies of D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules—a reduction in assembly size of 41–45% compared with previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and annotated each assembly for repetitive elements, protein-coding genes, transfer RNAs, ribosomal RNAs, piwi-interacting RNA clusters, and endogenous viral elements. Between 19,083 and 20,357 protein-coding genes were predicted. Repetitive DNA accounts for 36.87–38.26% of each assembly. Comparative analyses and mitochondrial haplotype networks suggest that Taiwan and Uruguay D. citri are more closely related, while California D. citri are closely related to Florida D. citri. These high-quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.

The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins

Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.

Population genomics and phylogeography of the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), in the United States, northern Mexico, and Argentina

The boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), is an important pest of commercial cotton across the Americas. In the United States, eradication of this species is complicated by re-infestations of areas where eradication has been previously successful and by the existence of morphologically similar variants that can confound identification efforts. To date, no study has applied a high-throughput sequencing approach to better understand the population genetic structure of the boll weevil. Furthermore, only a single study has investigated genetic relationships between populations in North and South America. We used double digest restriction site-associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern United States, northern Mexico, and Argentina. Additionally, we assembled the first complete mitochondrial genome for this species and generated a preliminary whole genome assembly, both of which were used to improve the identification of informative loci. Downstream analyses revealed two main lineages-one consisting of populations found geographically west of the Sierra Madre Occidental mountain range and the second consisting of populations found to the east-were revealed, and both were sub-structured. Population geographic structure was consistent with the isolation by distance model, indicating that geogrpahic distance is likely a primary mechanism driving divergence in this species. Boll weevil populations from Argentina were found to be more closely related to the eastern lineage, suggesting a recent colonization of South America by the eastern lineage, but additional sampling across Mexico, Central America and South America is needed to further clarify their origin. Finally, we uncovered an instance of population turnover or replacement, highlighting the temporal instability of population structure.

Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

Sequencing, Assembly and Annotation of the Whole-Insect Genome of Lymantria dispar dispar, the European Gypsy Moth

The European gypsy moth, Lymantria dispar dispar (LDD), is an invasive insect and a threat to urban trees, forests and forest-related industries in North America. For use as a comparator with a previously published genome based on the LD652 pupal ovary-derived cell line, as well as whole-insect genome sequences obtained from the Asian gypsy moth subspecies L. dispar asiatica and L. dispar japonica, the whole-insect LDD genome was sequenced, assembled and annotated. The resulting assembly was 998 Mb in size, with a contig N50 of 662 Kb and GC content of 38.8%. Long interspersed nuclear elements (LINEs) constitute 25.4% of the whole-insect genome, and a total of 11,901 genes predicted by automated gene finding encoded proteins exhibiting homology with reference sequences in the NCBI NR and/or UniProtKB databases at the most stringent similarity cutoff level (i.e., the gold tier). These results will be especially useful in developing a better understanding of the biology and population genetics of L. dispar and the genetic features underlying Lepidoptera in general.

Whole-genome assembly of Culex tarsalis

The mosquito, Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted on Cx. tarsalis ecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. However, in-depth genetic studies have been hindered by the lack of a reference genome. In this study, we present the first whole-genome assembly of this mosquito species (CtarK1) based on PacBio HiFi reads from high-molecular-weight DNA extracted from a single male. The CtarK1 assembly is 790 Mb with an N50 of 58 kb, which is 27% larger than Culex quinquefasciatus (578 Mb). This difference appears to be mostly composed of transposable elements. To annotate CtarK1, we used a previously assembled Cx. tarsalis transcriptome and approximately 17,456 protein genes from Cx. quinquefasciatus (N = 17,456). Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. Using a Bayesian phylogeny based on mitochondrial genomes, we place Cx. tarsalis in the context of other mosquito species and estimate the divergence between Cx. tarsalis and Cx. quinquefasciatus to be between 15.8 and 22.2 million years ago (MYA). Important next steps from this work include characterizing the genetic basis of diapause and sex determination in Culex mosquitoes.

Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects

The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalizations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed these data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes, and that orders exhibit striking differences in rates of fusions, fissions and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups.

Improved reference genome of the arboviral vector Aedes albopictus

BACKGROUND

The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.

RESULTS

We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.

CONCLUSION

The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Whole genome sequence of the soybean aphid, Aphis glycines

Aphids are emerging as model organisms for both basic and applied research. Of the 5,000 estimated species, only three aphids have published whole genome sequences: the pea aphid Acyrthosiphon pisum, the Russian wheat aphid, Diuraphis noxia, and the green peach aphid, Myzus persicae. We present the whole genome sequence of a fourth aphid, the soybean aphid (Aphis glycines), which is an extreme specialist and an important invasive pest of soybean (Glycine max). The availability of genomic resources is important to establish effective and sustainable pest control, as well as to expand our understanding of aphid evolution. We generated a 302.9 Mbp draft genome assembly for Ap. glycines using a hybrid sequencing approach. This assembly shows high completeness with 19,182 predicted genes, 92% of known Ap. glycines transcripts mapping to contigs, and substantial continuity with a scaffold N50 of 174,505 bp. The assembly represents 95.5% of the predicted genome size of 317.1 Mbp based on flow cytometry. Ap. glycines contains the smallest known aphid genome to date, based on updated genome sizes for 19 aphid species. The repetitive DNA content of the Ap. glycines genome assembly (81.6 Mbp or 26.94% of the 302.9 Mbp assembly) shows a reduction in the number of classified transposable elements compared to Ac. pisum, and likely contributes to the small estimated genome size. We include comparative analyses of gene families related to host-specificity (cytochrome P450's and effectors), which may be important in Ap. glycines evolution. This Ap. glycines draft genome sequence will provide a resource for the study of aphid genome evolution, their interaction with host plants, and candidate genes for novel insect control methods.

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity

BACKGROUND

Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea, Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe.

RESULTS

By combining Illumina and PacBio sequencing of DNA derived from multiple inbred female fleas with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly for C. felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ~ 38% of protein-coding genes with two or more copies and over 4000 tRNA genes. A broad range of genome size determinations (433-551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) in C. felis. Similarly, broad genome sizes were also calculated for individuals of Xenopsylla cheopis (Oriental rat flea), indicating that this remarkable "genome-in-flux" phenomenon could be a siphonapteran-wide trait. Finally, from the C. felis sequence reads, we also generated closed genomes for two novel strains of Wolbachia, one parasitic and one symbiotic, found to co-infect individual fleas.

CONCLUSION

Rampant CNV in C. felis has dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novel Wolbachia endosymbionts-potential tools for blocking pathogen transmission-these oddities highlight a unique and underappreciated disease vector.

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

BACKGROUND

Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies.

RESULTS

Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.

CONCLUSIONS

Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

Effect of Phenotype Selection on Genome Size Variation in Two Species of Diptera

Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions.

Genome Size Evolution Differs Between Drosophila Subgenera with Striking Differences in Male and Female Genome Size in Sophophora

Genome size varies across the tree of life, with no clear correlation to organismal complexity or coding sequence, but with differences in non-coding regions. Phylogenetic methods have recently been incorporated to further disentangle this enigma, yet most of these studies have focused on widely diverged species. Few have compared patterns of genome size change in closely related species with known structural differences in the genome. As a consequence, the relationship between genome size and differences in chromosome number or inter-sexual differences attributed to XY systems are largely unstudied. We hypothesize that structural differences associated with chromosome number and X-Y chromosome differentiation, should result in differing rates and patterns of genome size change. In this study, we utilize the subgenera within the Drosophila to ask if patterns and rates of genome size change differ between closely related species with differences in chromosome numbers and states of the XY system. Genome sizes for males and females of 152 species are used to answer these questions (with 92 newly added or updated estimates). While we find no relationship between chromosome number and genome size or chromosome number and inter-sexual differences in genome size, we find evidence for differing patterns of genome size change between the subgenera, and increasing rates of change throughout time. Estimated shifts in rates of change in sex differences in genome size occur more often in Sophophora and correspond to known neo-sex events.

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

BACKGROUND

The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

RESULTS

The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.

CONCLUSIONS

With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

BACKGROUND

The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

RESULTS

The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.

CONCLUSIONS

With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Genome Size Evolution within and between the Sexes

Genome sizes are known to vary between closely related species, but the patterns behind this variation have yet to be fully understood. Although this variation has been evaluated between species and within sexes, unknown is the extent to which this variation is driven by differentiation in sex chromosomes. To address this longstanding question, we examine the mode and tempo of genome size evolution for a total of 87 species of Drosophilidae, estimating and updating male genome size values for 44 of these species. We compare the evolution of genome size within each sex to the evolution of the differences between the sexes. Utilizing comparative phylogenetic methods, we find that male and female genome size evolution is largely a neutral process, reflective of phylogenetic relatedness between species, which supports the newly proposed accordion model for genome size change. When similarly analyzed, the difference between the sexes due to heteromorphic sex chromosomes is a dynamic process; the male-female genome size difference increases with time with or without known neo-Y events or complete loss of the Y. Observed instances of rapid change match theoretical expectations and known neo-Y and Y loss events in individual species.

Genome Size Estimation and Quantitative Cytogenetics in Insects

With care, it is possible using flow cytometry to create a precise and accurate estimate of the genome size of an insect that is useful for genomics, genetics, molecular/cell biology, or systematics. Genome size estimation is a useful first step in a complete genome sequencing project. The number of sequencing reads required to produce a given level of coverage depends directly upon the 1C amount of DNA per cell, while an even more critical need is an accurate 1C genome size estimate to compare against the final assembly. Here we present a detailed protocol to estimate genome size using flow cytometry. Published genome size estimates should be submitted to genomesize.com so that they are available to all.

Improved reference genome of Aedes aegypti informs arbovirus vector control

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.

An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.

Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula

The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.

Genome Size in North American Fireflies: Substantial Variation Likely Driven by Neutral Processes

Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies). The 23 species considered represent an excellent study system because of the greater than 5-fold range of genome sizes, documented here using flow cytometry, and the 3-fold range in body size, measured using pronotum width. We also identified common genomic repetitive elements using low-coverage sequencing. We found a positive relationship between genome size and repetitive DNA, particularly retrotransposons. Both genome size and these elements were evolving as expected given phylogenetic relatedness. We also tested whether genome size varied with body size and found no relationship. Together, our results suggest that genome size is evolving neutrally in fireflies.

The mode and tempo of genome size evolution in the subgenus Sophophora

Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 Sophophora species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s C_mean and Moran’s I. In addition to testing the mode and rate of genome size evolution in Sophophora species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. Sophophora genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that Sophophora genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s C_mean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships.

SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface

BACKGROUND

Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.

RESULTS

The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.

CONCLUSIONS

Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.

Genome size correlates with reproductive fitness in seed beetles

The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the 'C-value paradox'. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4-5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution.

Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome-wide nuclear variations provide support for secondary contact from historical refugia

Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome-wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well-defined cline that bisects Iberia along a northeastern-southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human-mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir of Apis mellifera diversity.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

Endopolyploidy changes with age-related polyethism in the honey bee, Apis mellifera

Honey bees (Apis mellifera) exhibit age polyethism, whereby female workers assume increasingly complex colony tasks as they age. While changes in DNA methylation accompany age polyethism, other DNA modifications accompanying age polyethism are less known. Changes in endopolyploidy (DNA amplification in the absence of cell division) with increased larval age are typical in many insect cells and are essential in adults for creating larger cells, more copies of essential loci, or greater storage capacity in secretory cells. However, changes in endopolyploidy with increased adult worker age and polyethism are unstudied. In this study, we examined endopolyploidy in honey bee workers ranging in age from newly emerged up to 55 days old. We found a nonsignificant increase in ploidy levels with age (P < 0.1) in the most highly endopolyploid secretory cells, the Malpighian tubules. All other cell types decreased ploidy levels with age. Endopolyploidy decreased the least amount (nonsignificant) in neural (brain) cells and the stinger (P < 0.1). There was a significant reduction of endopolyploidy with age in leg (P < 0.05) and thoracic (P < 0.001) muscles. Ploidy in thoracic muscle dropped from an average of 0.5 rounds of replication in newly emerged workers to essentially no rounds of replication (0.125) in the oldest workers. Ploidy reduction in flight muscle cells is likely due to the production of G1 (2C) nuclei by amitotic division in the multinucleate striated flight muscles that are essential to foragers, the oldest workers. We suggest that ploidy is constrained by the shape, size and makeup of the multinucleate striated muscle cells. Furthermore, the presence of multiple 2C nuclei might be optimal for cell function, while higher ploidy levels might be a dead-end strategy of some aging adult tissues, likely used to increase cell size and storage capacity in secretory cells.

Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera)

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham’s F_ST, an F_ST-based outlier test, Delta, informativeness (I_n), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs.

Comparison of life history and genetic properties of cowpea bruchid strains and their response to hypoxia

The cowpea bruchid (Callosobruchus maculatus) is the most important storage pest of grain legumes and comprises geographically distinct strains. Storage under a modified atmosphere with decreased O2 content represents an alternative to chemical fumigants for pest control of stored grains. In this study, we compared reproduction, development and survival, as well as genome size of bruchid strains from South India (SI), Burkina Faso (BF), Niger (CmNnC) and the United States (OH), reared on mung bean (Vigna radiata). Fecundity and egg-to-adult duration varied significantly among these strains. Notably, strain BF had the highest fecundity, and strain SI displayed the fastest development whereas strain OH was the slowest. Differences in adult lifespan among strains were only detected in unmated but not in the mated group. Genome size of SI females was significantly larger than that of OH females, and for all four strains, the female genomes were larger than those of their corresponding males. Furthermore, we studied effects of exposure to 1% O2+99% N2 on strains SI and BF. Mortality caused by hypoxia was influenced by not only developmental stage but also by insect strain. Eggs were most sensitive, particularly at the early stage, whereas the 3rd and 4th instar larvae were most tolerant and could survive up to 15 days of low O2. Strain SI was slightly more resistant than BF in egg and larval stages. Proteolytic activity prior to, during and after hypoxia treatment revealed remarkable metabolic plasticity of cowpea bruchids in response to modified atmosphere.

Structural and Genetic Investigation of the Egg and First-Instar Larva of an Egg-Laying Population of Blaesoxipha plinthopyga (Diptera: Sarcophagidae), a Species of Forensic Importance

Flies in the family Sarcophagidae incubate their eggs and are known to be ovoviviparous (i.e., ovolarviparous), but a laboratory-maintained colony of Blaesoxipha plinthopyga (Wiedemann) deposited clutches of viable eggs over 10 generations. A description of the egg and first-instar larva of this species is provided along with genetic data (genome size and cytochrome oxidase I sequences). The egg is similar to previously described eggs of other Sarcophagidae but differs in the configuration of the micropyle. In the first-instar larva, the oral ridges are much more developed than has been described for other species. B. plinthopyga has forensic importance, and the present descriptive information is critical for proper case management.

Strepsiptera, phylogenomics and the long branch attraction problem

Insect phylogeny has recently been the focus of renewed interest as advances in sequencing techniques make it possible to rapidly generate large amounts of genomic or transcriptomic data for a species of interest. However, large numbers of markers are not sufficient to guarantee accurate phylogenetic reconstruction, and the choice of the model of sequence evolution as well as adequate taxonomic sampling are as important for phylogenomic studies as they are for single-gene phylogenies. Recently, the sequence of the genome of a strepsipteran has been published and used to place Strepsiptera as sister group to Coleoptera. However, this conclusion relied on a data set that did not include representatives of Neuropterida or of coleopteran lineages formerly proposed to be related to Strepsiptera. Furthermore, it did not use models that are robust against the long branch attraction artifact. Here we have sequenced the transcriptomes of seven key species to complete a data set comprising 36 species to study the higher level phylogeny of insects, with a particular focus on Neuropteroidea (Coleoptera, Strepsiptera, Neuropterida), especially on coleopteran taxa considered as potential close relatives of Strepsiptera. Using models robust against the long branch attraction artifact we find a highly resolved phylogeny that confirms the position of Strepsiptera as a sister group to Coleoptera, rather than as an internal clade of Coleoptera, and sheds new light onto the phylogeny of Neuropteroidea.

Parthenogenesis in a whitetip reef shark Triaenodon obesus involves a reduction in ploidy

Genetic analysis of a female whitetip reef shark Triaenodon obesus and her stillborn pup, assumed to be of parthenogenetic origin, revealed that the pup was homozygous at all 24 nuclear-encoded microsatellites assayed, consistent with the idea that diploidy in the pup had been restored via terminal fusion. Flow cytometric analysis, however, indicated that the genome size of the pup was no more than half that of the mother, and microscopy revealed that nuclear volume was c. 1.73 times larger in the mother than in the pup. Together these data suggest that the pup was genetically haploid, developing directly from an unfertilized egg; as far as is known, this is the first observation of a spontaneously produced haploid vertebrate.

Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity

We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.

Genome size evolution is ubiquitous, and–even after decades of research–mysterious. There are two major classes of hypotheses regarding genome size evolution, those that attribute its causes to evolutionarily neutral processes and those that suggest a role for selection. Numerous correlations between genome size and fitness-related phenotypes have been documented, suggesting selection could play a role in genome size evolution. Unfortunately, many of the effects in those studies are confounded with factors that could provide alternative explanations. Here, we show that 211 inbred strains of Drosophila melanogaster exhibit abundant variation in genome size, which correlates with life history traits in a temperature-dependent manner. Gene expression analyses suggest a role for differences in metabolism between strains with large and small genomes. Thus, there is genetic variation in genome size within D. melanogaster, and this variation is connected to variation in environmentally dependent life history traits. These observations indicate that selection is indeed a potential mechanism by which genome size can evolve. Our results also suggest that higher levels of genetic architecture may explain some of the genetic contribution to biologically important complex traits and raise the possibility that nucleotide quantity can contribute to phenotype in addition to quality.

Stick insect genomes reveal natural selection's role in parallel speciation

Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis of parallel speciation remains poorly understood. We analyzed whole-genome divergence between replicate pairs of stick insect populations that are adapted to different host plants and undergoing parallel speciation. We found thousands of modest-sized genomic regions of accentuated divergence between populations, most of which are unique to individual population pairs. We also detected parallel genomic divergence across population pairs involving an excess of coding genes with specific molecular functions. Regions of parallel genomic divergence in nature exhibited exceptional allele frequency changes between hosts in a field transplant experiment. The results advance understanding of biological diversification by providing convergent observational and experimental evidence for selection's role in driving repeatable genomic divergence.

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.

Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms

Understanding the genetic mechanisms of adaptive population divergence is one of the most fundamental endeavours in evolutionary biology and is becoming increasingly important as it will allow predictions about how organisms will respond to global environmental crisis. This is particularly important for the honey bee, a species of unquestionable ecological and economical importance that has been exposed to increasing human-mediated selection pressures. Here, we conducted a single nucleotide polymorphism (SNP)-based genome scan in honey bees collected across an environmental gradient in Iberia and used four FST -based outlier tests to identify genomic regions exhibiting signatures of selection. Additionally, we analysed associations between genetic and environmental data for the identification of factors that might be correlated or act as selective pressures. With these approaches, 4.4% (17 of 383) of outlier loci were cross-validated by four FST -based methods, and 8.9% (34 of 383) were cross-validated by at least three methods. Of the 34 outliers, 15 were found to be strongly associated with one or more environmental variables. Further support for selection, provided by functional genomic information, was particularly compelling for SNP outliers mapped to different genes putatively involved in the same function such as vision, xenobiotic detoxification and innate immune response. This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human-mediated environmental changes.