Biology subjects

Childers, A. K.

Publications and source records attributed to Childers, A. K..

11 recordsLinked to original sources

bioRxiv2026

Multiple roads to swarming: divergent molecular machineries drive the repeated evolution of locusts

Locust swarming, one of nature's most spectacular examples of a repeated emergent polyphenism, has long been suspected to rely on conserved "swarming genes" or shared genomic features. By applying a model-clade approach comparing six species that vary in their degrees of plasticity and collective behavior, we show that the evolution of swarming locusts is not driven by shared genomic features or a universal set of swarming genes. In contrast, we find that this phenomenon evolved through flexible regulatory architectures, in which the degree of behavioral plasticity directly correlates with the total scale of density-responsive gene expression. While different locust species recruit largely non-overlapping gene sets to achieve the same syndrome, these divergent molecular machineries converge on similar higher-level biological functions. Thus, multiple molecular pathways achieve locust swarming, challenging the preconceived notion about the genetic prerequisites to transition from solitary to collective states. Further, we establish that a complex syndrome such as locust swarming emerges through modular regulatory systems that can be amplified, modified, or attenuated across the tree of life.

evolutionary biology↗

bioRxiv2022

Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton

The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), is a major global pest of cotton. Current management practices include chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). These strategies have contributed to eradication of P. gossypiella from the cotton growing areas of the United States and northern Mexico. However, this pest has evolved resistance to Bt cotton in Asia, where it remains a critical pest, and the benefits of using transgenic Bt crops have been lost. A complete annotated reference genome is needed to improve global Bt resistance management of the pink bollworm. We generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S) using PacBio continuous long reads for contig generation, Illumina Hi-C for scaffolding, and Illumina whole-genome re-sequencing for error-correction. The psuedohaploid assembly consists of 29 autosomes and the Z sex chromosome. The assembly exceeds the minimum Earth BioGenome Project quality standards, has a low error-rate, is highly contiguous at both the contig and scaffold level (L/N50 of 18/8.26 MB and 14/16.44 MB, respectively), and complete, with 98.6% of lepidopteran single-copy orthologs represented without duplication. The genome was annotated with 50% repeat content and 14,107 protein-coding genes, further assigned to 41,666 functional annotations. This assembly represents the first publicly available complete annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.

genomics↗

bioRxiv2022

A chromosome-scale genome assembly of a Bacillus thuringiensis Cry1Ac insecticidal protein resistant strain of Helicoverpa zea

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. H. zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single-copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices. SignificanceWe established a chromosome-level reference assembly for Helicoverpa zea, an insect pest of multiple cultivated crops in the Americas. This assembly of a Bacillus thuringiensis insecticidal protein resistant strain, HzStark_Cry1AcR, will facilitate future research in areas such as population genomics and adaptations to agricultural control practices.

genomics↗

bioRxiv2022

polishCLR: a Nextflow workflow for polishing PacBio CLR genome assemblies

Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) Continuous Long Reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.

bioinformatics↗

bioRxiv2021

Workflows for rapid functional annotation of diverse arthropod genomes

Genome sequencing of a diverse array of arthropod genomes is already underway and these genomes will be used to study human health, agriculture, biodiversity and ecology. These new genomes are intended to serve as community resources and provide the foundational information that is required to apply omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related but distinct processes: demarcating genes and other elements present in genome sequences (structural annotation); and associating function with genetic elements (functional annotation). While there are well established and freely available workflows for structural annotation of gene identification in newly assembled genomes, workflows for providing the functional annotation required to support functional genomics studies are less well understood. Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.) and a first-pass genome-wide functional annotation effort can rapidly identify under-represented gene sets for focused community annotation efforts. We present an open source, open access and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to a diverse range of arthropod species. We show that the performance of the predictions is consistent across a set of arthropod genomes with varying assembly and annotation quality.Complete instructions for running each component of the functional annotation pipeline on the command line, a high performance computing cluster and the CyVerse Discovery Environment can be found at the readthedocs site (https://agbase-docs.readthedocs.io/en/latest/agbase/workflow.html). Simple summaryGenomic technologies are accumulating information about genes at a faster rate than ever before, and sequencing initiatives like the Earth Biogenome Project, i5k and Ag100Pest are expected to increase this rate of acquisition. However, if genomic sequencing is to be used for improvement of human health, agriculture and our understanding of biological systems, it is necessary to identify genes and understand how they contribute to biological outcomes. While there are several well-established workflows for assembling genomic sequences and identifying genes, understanding gene function is essential to create actionable knowledge. Moreover this functional annotation process must be easily accessible and provide information at a genomic scale to keep up with new sequence data. We report a well defined workflow for rapid functional annotation of whole proteomes to produce Gene Ontology and pathways information. We test this workflow on a diverse set of arthropod genomes and compare it to common arthropod reference genomes. The workflow we described is freely and publicly available via a web interface on CyVerse or as biocontainers that can be deployed scalably on local computing systems.

bioinformatics↗

bioRxiv2019

Deformed wing virus type A, a major honey bee pathogen, is vectored by the mite Varroa destructor in a non-propagative manner.

Honey bees, the primary managed insect pollinator, suffer considerable losses due to Deformed wing virus (DWV), an RNA virus vectored by the mite Varroa destructor. Mite vectoring has resulted in the emergence of virulent DWV variants. The basis for such changes in DWV is poorly understood. Most importantly, it remains unclear whether replication of DWV occurs in the mite. In this study, we exposed Varroa mites to DWV type A via feeding on artificially infected honey bees. A significant, 357-fold increase in DWV load was observed in these mites after 2 days. However, after 8 additional days of passage on honey bee pupae with low viral loads, the DWV load dropped by 29-fold. This decrease significantly reduced the mites ability to transmit DWV to honey bees. Notably, negative-strand DWV RNA, which could indicate viral replication, was detected only in mites collected from pupae with high DWV levels but not in the passaged mites. We also found that Varroa mites contain honey bee mRNAs, consistent with the acquisition of honey bee cells which would additionally contain DWV replication complexes with negative-strand DWV RNA. We propose that transmission of DWV type A by Varroa mites occurs in a non-propagative manner.

microbiology↗

bioRxiv2019

Dynamic evolution in the key honey bee pathogen Deformed wing virus

The impacts of invertebrate RNA virus population dynamics on virulence and infection outcomes are poorly understood. Deformed wing virus (DWV), the main viral pathogen of honey bees, negatively impacts bee health which can lead to colony death. Despite previous reports on the reduction of DWV diversity following the arrival of the parasitic mite Varroa destructor, the key DWV vector, we found high genetic diversity of DWV in infested United States (US) honey bee colonies. Phylogenetic analysis showed that the divergent US DWV genotypes are of monophyletic origin, which were likely generated as a result of diversification after a genetic bottleneck. To investigate the population dynamics of this divergent DWV, we designed a series of novel infectious cDNA clones corresponding to co-existing DWV genotypes, thereby devising a reverse genetic system for an invertebrate RNA virus quasispecies. Equal replication rates were observed for all clone-derived DWV variants in single infections. Surprisingly, individual clones replicated to the same high levels as their mixtures and even the parental highly diverse natural DWV population, suggesting that complementation between genotypes was not required to replicate to high levels. Mixed clone-derived infections showed a lack of strong competitive exclusion, suggesting that the DWV genotypes were adapted to co-exist. Mutational and recombination events were observed across clone progeny providing new insights into the forces that drive and constrain virus diversification. Accordingly, herein we propose a new model of Varroa-induced DWV dynamics whereby an initial selective sweep is followed by virus diversification fueled by negative frequency-dependent selection for new genotypes. This selection likely reflects the ability of rare lineages to evade host defenses, specifically antiviral RNA interference (RNAi). In support of this, we show that RNAi induced against one DWV strain is less effective against an alternate strain from the same population.\n\nAuthor SummaryVirulence of Deformed wing virus (DWV), a major pathogen of honey bees, showed a sharp and significant increase following the introduction of its vector, the mite Varroa destructor. Varroa vectoring resulted in genetic changes of DWV, including reduction of DWV diversity to nearly clonal levels in the UK and Hawaii. Contrary to the previous reports, we discovered that virulent DWV populations circulating across the Varroa-infested United States included many divergent genotypes generated following a strong bottleneck event. We designed a series of the full-length infectious cDNA clones that captured the diversity of a typical virulent DWV population from a declining Varroa-infested colony, effectively establishing first reverse genetic system for an invertebrate RNA virus quasispecies, in order to investigate interactions between the virus genotypes. We demonstrated that individual co-existing DWV genotypes and diverse natural DWV populations replicated equally well indicating that complementation between isolates was not required to enable DWV replication to high levels. Also, no obvious competitive exclusion was detected between genotypes in mixed infections suggesting DWV genotypes are adapted to co-exist to maintain overall population diversity. We suggest that introduction of Varroa resulted in an initial selective sweep of DWV diversity which was followed by DWV diversification driven by selection for new genotypes capable of evading host defenses, specifically antiviral RNA interference.

microbiology↗

bioRxiv2019

A High-Quality Genome Assembly from a Single, Field collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies, however, long-read methods have historically had greater input DNA requirements and higher costs than next generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell. The Spotted Lanternfly is an invasive species recently discovered in the northeastern United States, threatening to damage economically important crop plants in the region. The DNA from one individual was used to make one standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on one Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing approximately 36-fold coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Further, it was possible to segregate more than half of the diploid genome into the two separate haplotypes. The assembly also recovered two microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

genomics↗

bioRxiv2019

Genomic analyses of sibling honey bee ectoparasitic mite species show divergent strategies of adaptation

Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association between honey bees and ectoparasitic mites by sequencing the genomes of the sister mite species Varroa destructor and Varroa jacobsoni. These genomes were closely related, with 99.7% sequence identity. Among the 9,628 orthologous genes, 4.8% showed signs of positive selection in at least one species. Divergent selective trajectories were discovered in conserved chemosensory gene families (IGR, SNMP), and Halloween genes (CYP) involved in moulting and reproduction. However, there was little overlap in these gene sets and associated GO terms, indicating different selective regimes operating on each of the parasites. Based on our findings, we suggest that species-specific strategies may be needed to combat evolving parasite communities.

genomics↗

bioRxiv2018

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

BackgroundThe ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.\n\nResultsEach of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.\n\nConclusionsThe improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.

genomics↗

bioRxiv2017

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

genomics↗