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At least 91 records · Page 5Linked to original sources
USGS2015

Isolation of a complete circular virus genome sequence from an Alaskan black-capped chickadee (Poecile atricapillus) gastrointestinal tract sample.

We report here the genome sequence of a circular virus isolated from samples of an Alaskan black-capped chickadee (Poecile atricapillus) gastrointestinal tract. The genome is 2,152 bp in length and is most similar (30 to 44.5% amino acid identity) to the genome sequences of other single-stranded DNA (ssDNA) circular viruses belonging to the gemycircularvirus group.

Genome Announcements↗
USGS2019

Coast to coast: High genomic connectivity in North American scoters

Dispersal shapes demographic processes and therefore is fundamental to understanding biological, ecological, and evolutionary processes acting within populations. However, assessing population connectivity in scoters ( Melanitta sp.) is challenging as these species have large spatial distributions that span remote landscapes, have varying nesting distributions (disjunct vs. continuous), exhibit unknown levels of dispersal, and vary in the timing of the formation of pair bonds (winter vs. fall/spring migration) that may influence the distribution of genetic diversity. Here, we used double‐digest restriction‐associated DNA sequence (ddRAD) and microsatellite genotype data to assess population structure within the three North American species of scoter (black scoter, M. americana ; white‐winged scoter, M. deglandi ; surf scoter, M. perspicillata ), and between their European congeners (common scoter, M. nigra ; velvet scoter, M. fusca ). We uncovered no or weak genomic structure (ddRAD Φ ST < 0.019; microsatellite F ST < 0.004) within North America but high levels of structure among European congeners (ddRAD Φ ST > 0.155, microsatellite F ST > 0.086). The pattern of limited genomic structure within North America is shared with other sea duck species and is often attributed to male‐biased dispersal. Further, migratory tendencies (east vs. west) of female surf and white‐winged scoters in central Canada are known to vary across years, providing additional opportunities for intracontinental dispersal and a mechanism for the maintenance of genomic connectivity across North America. In contrast, the black scoter had relatively elevated levels of divergence between Alaska and Atlantic sites and a second genetic cluster found in Alaska at ddRAD loci was concordant with its disjunct breeding distribution suggestive of a dispersal barrier (behavioral or physical). Although scoter populations appear to be connected through a dispersal network, a small percentage (<4%) of ddRAD loci had elevated divergence which may be useful in linking areas (nesting, molting, staging, and wintering) throughout the annual cycle.

North America↗
USGS2019

Genomic pedigree reconstruction identifies predictors of mating and reproductive success in an invasive vertebrate

The persistence of an invasive species is influenced by its reproductive ecology, and a successful control program must operate on this premise. However, the reproductive ecology of invasive species may be enigmatic due to factors that also limit their management, such as cryptic coloration and behavior. We explored the mating and reproductive ecology of the invasive Brown Treesnake (BTS : Boiga irregularis ) by reconstructing a multigenerational genomic pedigree based on 654 single nucleotide polymorphisms for a geographically closed population established in 2004 on Guam ( N = 426). The pedigree allowed annual estimates of individual mating and reproductive success to be inferred for snakes in the study population over a 14‐year period. We then employed generalized linear mixed models to gauge how well phenotypic and genomic data could predict sex‐specific annual mating and reproductive success. Average snout–vent length (SVL), average body condition index (BCI), and trappability were significantly related to annual mating success for males, with average SVL also related to annual mating success for females. Male and female annual reproductive success was positively affected by SVL, BCI, and trappability. Surprisingly, the degree to which individuals were inbred had no effect on annual mating or reproductive success. When juxtaposed with current control methods, these results indicate that baited traps, a common interdiction tool, may target fecund BTS in some regards but not others. Our study emphasizes the importance of reproductive ecology as a focus for improving BTS control and promotes genomic pedigree reconstruction for such an endeavor in this invasive species and others.

Ecology and Evolution↗
USGS2014

Genome complexity in the coelacanth is reflected in its adaptive immune system

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

Journal of Experimental Zoology Part B: Molecular ↗
USGS2020

Mitochondrial genome diversity and population mitogenomics of Polar cod (Boreogadus saida) and Arctic dwelling gadoids

High-latitude fish typically exhibit a narrow thermal tolerance window, which may pose challenges when coping with temperatures that shift outside of a species’ range of tolerance. Due to its role in aerobic metabolism and energy balance, the mitochondrial genome is likely critical for the acclimation and adaptation to differing temperature regimes in marine ectotherms. As oceans continue to warm, there is growing need to understand the ability of organisms to respond to changing environmental conditions given evidence that some species, in particular cold-water species, may already be experiencing difficulties. To assess how Arctic gadids in Alaska have responded to differential thermal preferences in the past and how regions are interconnected, we sequenced complete mitochondrial genomes for four Arctic gadids to determine the distribution of mitochondrial diversity and population-level structure as well as to detect signatures of selection acting on the mitochondrial genome. We found little population-level structure within all four species with the clear exception of Gulf of Alaska saffron cod ( Eleginus gracilis ). Northern localities exhibited higher levels of genetic diversity and primarily northern lineages were observed within polar cod ( Boreogadus saida ) and saffron cod, likely reflecting asymmetrical dispersal and potentially admixture of distinct lineages via ocean currents. The main evolutionary force shaping the evolution of the mitogenome appears to be purifying selection, but we also identified potential positive selection of candidate amino acid replacements primarily in complex I (ND genes) in polar cod. The high levels of mitochondrial diversity observed in our study and large population size may provide this species with the ability to respond evolutionarily (i.e. long-term) to a changing environment.

Alaska↗
USGS2023

Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods

Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex, Rana muscosa and Rana sierrae, inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also find that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.

California↗
USGS2021

Production of haploid gynogens to inform genomic resource development in the paleotetraploid pallid sturgeon (Scaphirhynchus albus)

Order Acipenseriformes (sturgeons and paddlefishes) is an ancient lineage of osteichthyan fishes (>200 million years old) with most extant species at conservation risk. A relatively basal species, the pallid sturgeon, Scaphirhynchus albus, is a federally endangered species native to the Mississippi and Missouri River basins. Hybridization with sympatric shovelnose sturgeon, S. platorynchus, is one of several threats to pallid sturgeon. Current molecular markers cannot reliably distinguish among pure species and multigenerational backcrosses. This information is critical for implementation of management strategies to increase populations through natural reproduction and artificial propagation. Genotypes from a large panel of unlinked single-nucleotide polymorphisms (SNPs) may provide greater resolution of the two species; however, paralogous sequence variants (PSVs) within individuals resulting from an ancient whole genome duplication event confound SNP development. The aim of this study was to produce pallid sturgeon gynogens that contain 100% homozygous DNA contributed by only the maternal parent and have enough DNA for future SNP marker development. When homozygous gynogens are sequenced, heterozygosity at a locus within an individual indicates the presence of incorrectly aligned sequences that contain PSVs; accurate identification of these multi-locus contigs can facilitate their exclusion when developing disomic markers. In this study, we attempted to produce two types of pallid sturgeon gynogens: a) haploid gynogens produced from the activation of pallid sturgeon eggs with ultraviolet-irradiated sperm from the distantly related paddlefish (Polyodon spathula), and b) doubled haploids produced from the activation of pallid sturgeon eggs with irradiated paddlefish milt followed by thermal shock to suppress the first mitotic division. Production of doubled haploids, gynogens with 100% homozygous DNA and double the genome content of haploid gynogens, was pursued because it was originally unknown if haploid gyongens would survive long enough to attain enough genetic material for SNP marker development. We performed flow cytometry and microsatellite genotyping on the specimens in order to confirm haploid and doubled haploid status. Our study was unable to successfully yield doubled haploids; however, we successfully produced haploid gynogens that contained enough nuclear DNA for our future SNP marker development study. Interestingly, this study also produced paddlefish × pallid sturgeon hybrids in the control groups in two separate years; this is the first study to report viable offspring between the paddlefish and a Scaphirhynchus sturgeon species and reflects on the malleability of the genomes of the species in this order.

Louisiana, Arkansas, Missouri, Nebraska, North Dak↗
USGS2020

Genomic architecture and repertoire of the rainbow trout immunoglobulin light chain genes

The genomic loci encoding the four immunoglobulin light chains (IgL1, IgL2, IgL3, and IgL4) in the Swanson trout genome assembly were annotated in order to provide a measurement of the potential IgL repertoire. IgL1 and IgL3 gene segments are co-localized on chromosomes 21, 18, 15, and 7 while IgL2 and IgL4 were found on chromosomes 13 and 17, respectively. In total, 48 constant (C L ), 87 variable (V L ), and 59 joining (J L ) productive genes are described. Pairwise alignment of the V L segments revealed that they belong to nine different families, three of which (kappa IV, V, and VI) are described for the first time in this study. V L and C L sequences on chromosome 15 and 21 and those on chromosomes 7 and 18 clustered together in phylogenetic analysis. PCR was used to examine IgL C L and V L genes in 9 lines of rainbow trout. IgL4 in the Hot Creek and Golden trout lines was missing 42 nucleotides resulting in a loss of 14 amino acids. The sigma IV variable family was completely absent from the Swanson, Arlee, Hot Creek, and wild type lines and silenced in the Skamania line with the addition of 176 bp mini-satellite insert. Similarly, the Whale Rock, Arlee, and wild type lines were all found to encode two sigma II products, a functional 252 bp product and a larger 425 bp product that contained a 172 bp insert. Results from this study indicate that there are genomic differences in IgL repertoire between different lines of trout that could affect humoral immune responses post vaccination and during disease.

Developmental and Comparative Immunology↗
USGS2021

Genomic comparison of carbapenem-resistant Enterobacteriaceae from humans and gulls in Alaska

Objectives Wildlife may harbor clinically important antimicrobial resistant (AMR) bacteria, but the role of wildlife in the epidemiology of AMR bacterial infections in humans is largely unknown. In this study, we aimed to assess dissemination of the bla KPC carbapenemase gene among humans and gulls in Alaska. Methods We performed whole genome sequencing to determine the genetic context of bla KPC in bacterial isolates from all four human carbapenemase-producing Enterobacteriaceae (CPE) infections reported in Alaska between 2013–2018 and to compare sequences to seven previously reported CPE isolates from gull feces within the same region and time period. Results Genomic analysis of CPE isolates suggested independent acquisition events among humans with no evidence for direct transmission of bla KPC between people and gulls. However, some isolates shared conserved genetic elements surrounding bla KPC , suggesting possible exchange between species. Conclusions Our results highlight the genomic plasticity associated with bla KPC and demonstrate that sampling of wildlife may be useful for identifying clinically relevant antimicrobial resistance not observed through local passive surveillance in humans.

Alaska↗
USGS2020

Conservation genomics in a changing arctic

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

Trends in Ecology and Evolution↗
USGS2025

Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation

Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure population shifts and pathogen distributions. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a 2-day turnaround from airborne sample collection to completed analysis by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed, including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus ) and a venomous spider (golden silk orb weaver, Trichonephila clavipes ), and haplotyping humans ( Homo sapiens ) from natural complex community settings, such as subtropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid simultaneous detection of all life and its genetic diversity from air, water and sediment samples for unbiased non-targeted information-rich genomics-empowered (1) biodiversity monitoring, (2) population genetics, (3) pathogen and disease-vector genomic surveillance, (4) allergen and narcotic surveillance, (5) antimicrobial resistance surveillance and (6) bioprospecting.

Nature Ecology & Evolution↗
USGS2022

Museum genomics provide evidence for persistent genetic differentiation in a threatened seabird species in the Western Atlantic

Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of Ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns ( Sterna dougallii ) with a breeding distribution in the Northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20 th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.

Integrative and Comparative Biology↗
USGS2023

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus , has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed “ring species” around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis , as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

Journal of Heredity↗
USGS2019

Replicated landscape genomics identifies evidence of local adaptation to urbanization in wood frogs

Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs ( Lithobates sylvaticus ). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an F ST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 F ST outlier loci. Discriminant analysis of principal components using the 37 F ST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 F ST outlier loci mapped to the American bullfrog ( Rana [Lithobates] catesbeiana ) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.

Maine↗
USGS2021

Mixed-stock analysis in the age of genomics: Rapture genotyping enables evaluation of stock-specific exploitation in a freshwater fish population with weak genetic structure

Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple spawning stocks that are weakly differentiated. Freshwater fisheries exemplify this problem, with many harvested populations supported by multiple stocks of young evolutionary age and that are isolated across small spatial scales. As a result, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing now offer the ability to discriminate among populations with weak population structure, by providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We demonstrate the use of genomic data to conduct a mixed-stock analysis of Lake Erie's commercial and recreational walleye (Sander vitreus) fisheries and estimate the relative harvest of weakly differentiated stocks (pairwise FST < 0.01). We used RAD-capture (Rapture) to sequence and genotype individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks with 95% reassignment accuracy. An outcome not possible in the past with microsatellite markers. Genetic assignment of 1,075 fish harvested from recreational and commercial fisheries in the eastern basin indicated that western basin stocks constituted the majority of individuals harvested during peak walleye fishing season (July – September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May – June). Clear spatial structure in stock-specific harvest existed; more easterly sites contained more individuals of east basin origin than did westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the power of genomic data to facilitate mixed-stock analysis in exploited fish populations with weak population structure or limited existing genetic resources.

Michigan, New York, Ohio, Pennsylvania↗
USGS2021

Genomic and environmental influences on resilience in a cold-water fish near the edge of its range

Small, isolated populations present a challenge for conservation. The dueling effects of selection and drift in a limited pool of genetic diversity make the responses of small populations to environmental perturbations erratic and difficult to predict. This is particularly true at the edge of a species range, where populations often persist at the limits of their environmental tolerances. Populations of cisco, Coregonus artedi , in inland lakes have experienced numerous extirpations along the southern edge of their range in recent decades, which are thought to result from environmental degradation and loss of cold, well-oxygenated habitat as lakes warm. Yet, cisco extirpations do not show a clear latitudinal pattern, suggesting that local environmental factors and potentially local adaptation may influence resilience. Here, we used genomic tools to investigate the nature of this pattern of resilience. We used restriction site-associated DNA capture (Rapture) sequencing to survey genomic diversity and differentiation in southern inland lake cisco populations and compared the frequency of deleterious mutations that potentially influence fitness across lakes. We also examined haplotype diversity in a region of the major histocompatibility complex involved in stress and immune system response. We correlated these metrics to spatial and environmental factors including latitude, lake size, and measures of oxythermal habitat and found significant relationships between genetic metrics and broad and local factors. High levels of genetic differentiation among populations were punctuated by a phylogeographic break and residual patterns of isolation-by-distance. Although the prevalence of deleterious mutations and inbreeding coefficients was significantly correlated with latitude, neutral and non-neutral genetic diversity were most strongly correlated with lake surface area. Notably, differences among lakes in the availability of estimated oxythermal habitat left no clear population genomic signature. Our results shed light on the complex dynamics influencing these isolated populations and provide valuable information for their conservation.

Wisconsin↗
USGS2009

Avian influenza at both ends of a migratory flyway: characterizing viral genomic diversity to optimize surveillance plans for North America

Although continental populations of avian influenza viruses are genetically distinct, transcontinental reassortment in low pathogenic avian influenza (LPAI) viruses has been detected in migratory birds. Thus, genomic analyses of LPAI viruses could serve as an approach to prioritize species and regions targeted by North American surveillance activities for foreign origin highly pathogenic avian influenza (HPAI). To assess the applicability of this approach, we conducted a phylogenetic and population genetic analysis of 68 viral genomes isolated from the northern pintail (Anas acuta) at opposite ends of the Pacific migratory flyway in North America. We found limited evidence for Asian LPAI lineages on wintering areas used by northern pintails in California in contrast to a higher frequency on breeding locales of Alaska. Our results indicate that the number of Asian LPAI lineages observed in Alaskan northern pintails, and the nucleotide composition of LPAI lineages, is not maintained through fall migration. Accordingly, our data indicate that surveillance of Pacific Flyway northern pintails to detect foreign avian influenza viruses would be most effective in Alaska. North American surveillance plans could be optimized through an analysis of LPAI genomics from species that demonstrate evolutionary linkages with European or Asian lineages and in regions that have overlapping migratory flyways with areas of HPAI outbreaks.

Alaska, California↗
USGS2024

Genome sequences of toxigenic cyanobacteria from a bloom in Lake Mattamuskeet, North Carolina (United States)

Lake Mattamuskeet, the largest lake in North Carolina, USA, has undergone decades-long eutrophication causing reduced water quality and promoting cyanobacterial blooms that may produce toxins. It is therefore necessary to evaluate the cyanobacterial diversity of the lake and their toxigenic potential. We present draft genomes of Microcystis , Pelatocladus , Raphidiopsis , and Umezakia strains isolated from Lake Mattamuskeet. The whole-genome shotgun projects for Umezakia ovalisporum BLCC-F208, Microcystis sp. BLCC-F209, Microcystis sp. BLCC-F210, Pelatocladus sp. BLCC-F211, U. ovalisporum BLCC-F215, and Raphidiopsis BLCC-F218 have been deposited in GenBank under accession numbers JBHFLK000000000, JBHFLL000000000, CP169647, JBHFLM000000000, JBHFLN000000000, and JBHFLO000000000, respectively. Based on the genomic analysis, several biosynthetic gene clusters (BCGs) with varying degrees of similarity to known toxic and bioactive compound gene clusters were identified across the different cyanobacterial strains.

North Carolina↗