Biology subjects

Dikow, R. B.

Publications and source records attributed to Dikow, R. B..

4 recordsLinked to original sources

bioRxiv2024

Rapid adaptation to a globally introduced virulent pathogen in a keystone species

Emerging infectious diseases are one of the foremost contemporary threats to biodiversity conservation. Outbreaks of novel pathogens can lead to extinction of host populations, loss of gene flow due to extirpation, and bottlenecks in host populations with surviving individuals. In outbreaks with survivors, pathogens can exert strong selection on hosts, in some cases leading to the evolution of resistance or tolerance in the host population. The pathogen causing sylvatic plague, Yersinia pestis, was introduced to North America in the early 20th century and caused rapid population declines in prairie dogs (genus Cynomys), which experience >95% mortality during epizootics. Recently, survival from plague has been documented in a small number of black-tailed prairie dogs (C. ludovicianus) in natural populations in Colorado (USA). We performed whole-genome sequencing on 7 individuals from 3 colonies that survived infection with plague and 7 individuals from the same colonies that likely died during a plague epizootic. Using genome-wide association tests, FST outlier tests, and other inferences of selection, we detected SNPs on 5 scaffolds that were strongly associated with survivorship from plague in the wild. Some genes associated with these scaffolds also differ in humans that survived versus died in the plague pandemic in London, UK, suggesting conservation of gene function across taxonomically diverse lineages. Understanding the genetic basis of immunity can enable genetically-informed management actions such as targeted relocation to protect prairie dogs and the species that rely on them. More generally, understanding how rapid adaptation to pathogens occurs can help us predict the time frame and spatial scale at which adaptation may occur, during which other interventions are needed. Significance StatementEmerging infectious diseases are one of the foremost threats to global biodiversity, causing extinctions and population crashes on all continents. Introduced pathogens can exert strong selection on hosts for the evolution of tolerance or resistance, yet these evolutionary events are rare and it remains challenging to identify and sample both immune and susceptible individuals during an epizootic. This study leverages one of the only documented examples of prairie dogs surviving infection from introduced sylvatic plague in nature and compares their genomes to those of individuals that perished. We find strong signatures of selection in a small number of immune and non-immune genes, one of which has been implicated in survival from plague in humans. These findings suggest that adaptation to novel pathogens may occur via a combination of conserved genes and the co-opting of genes outside of classical immune pathways. Finally, it provides evidence that in native species with sufficient standing genetic variation, there is potential for adaptation to introduced pathogens.

evolutionary biology↗

bioRxiv2022

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

Insect silk is an incredibly versatile biomaterial. Lepidoptera and their sister lineage, Trichoptera, display some of the most diverse uses of silk with varying strength, adhesive qualities and elastic properties. It is well known that silk fibroin genes are long (> 20 kb) and have many repetitive motifs. These features make these genes challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (Plodia interpunctella) and genomic sequences for the caddisfly, Eubasilissa regina. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO Complete = 99.3%/95.2%), with complete and contiguous recovery of silk heavy fibroin gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.

genomics↗

bioRxiv2020

Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylaxmagnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-making Caddisflies (Insecta: Trichoptera)

Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. While Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving [~]275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read based de novo genome assemblies of two tube case-making Trichoptera from the suborder Integripalpia, Agrypnia vestita Walker and Hesperophylax magnus Banks. We find that these tube case-making caddisflies have genome sizes that are at least three-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. In H. magnus, long interspersed nuclear elements (LINEs) alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages. SignificanceThere is a lack of genomic resources for aquatic insects. So far, only three high-quality genomes have been assembled, all from individuals in the retreat-making suborder Annulipalpia. In this article, we report the first high-quality genomes of two case-making species from the suborder Integripalpia, which are essential for studying genomic diversity across this ecologically diverse insect order. Our research reveals larger genome sizes in the tube case-makers (suborder Integripalpia, infraorder Phryganides), accompanied by a disproportionate increase of repetitive DNA. This suggests that genome size is at least partly driven by a major expansion of repetitive elements. Our work shows that caddisflies have high potential as a model for understanding how genomic diversity might be linked to functional diversification and forms the basis for detailed studies on genome size evolution in caddisflies. Data depositionThis project has been deposited at NCBI under the Bioproject ID: PRJNA668166

genomics↗

bioRxiv2019

Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps

Polydnaviruses (PDVs) are mutualistic endogenous viruses associated with some lineages of parasitoid wasps that allow successful development of the wasps within their hosts. PDVs include two taxa resulting from independent virus acquisitions in braconid (bracoviruses) and ichneumonid wasps (ichnoviruses). PDV genomes are fully incorporated into the wasp genomes and comprise (1) virulence genes located on proviral segments that are packaged into the viral particle, and (2) genes involved in the production of the viral particles, which are not encapsidated. Whereas the genomic organization of bracoviruses within the wasp genome is relatively well known, the architecture of endogenous ichnoviruses remains poorly understood. We sequenced the genome of two ichnovirus-carrying wasp species, Hyposoter didymator and Campoletis sonorensis. Complete assemblies with long scaffold sizes allowed identification of the integrated ichnovirus, highlighting an extreme dispersion within the wasp genomes of the viral loci, i.e. isolated proviral segments and clusters of replication genes. Comparing the two wasp species, proviral segments harbor distinct gene content and variable genomic environment, whereas viral machinery clusters show conserved gene content and order, and can be inserted in collinear wasp genomic regions. This distinct architecture is consistent with the biological properties of the two viral elements: proviral segments producing virulence proteins allowing parasitism success are fine-tuned to the host physiology, while an ancestral viral architecture was likely maintained for the genes involved in virus particle production. Finding a distinct genomic architecture of ichnoviruses and bracoviruses highlights different evolutionary trajectories leading to virus domestication in the two wasp lineages.

genomics↗