Brian E. Scheffler
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View article: <i>De novo</i> Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference
<i>De novo</i> Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference Open
Rainbow trout ( Oncorhynchus mykiss ) exhibit extensive genomic diversity shaped by domestication, life history, and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemb…
View article: Independent Expansions Define Giant Hornet Genomes
Independent Expansions Define Giant Hornet Genomes Open
Background Body size and invasiveness are highly significant ecological and agricultural traits. The Vespalineage of hornets demonstrates extreme variation in both traits. In addition, many Vespa species destroy beehives and are of great c…
View article: Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts
Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts Open
The North American-native ornamental tree, flowering dogwood (Cornus florida L.), has a showy bract display that can range in color from white to pink to deep red. Although many trees have white bracts, there is consumer demand for novel p…
View article: Genome report: whole-genome assembly of the relapsing fever tick <i>Ornithodoros turicata</i> Dugès (Acari: Argasidae)
Genome report: whole-genome assembly of the relapsing fever tick <i>Ornithodoros turicata</i> Dugès (Acari: Argasidae) Open
The soft tick family Argasidae contains vectors of medical and veterinary importance, but few molecular resources are available compared to hard ticks (Ixodidae). One example is Ornithodoros turicata, a recognized vector of Borrelia turica…
View article: Pangenome analysis provides insights into the evolution of mango ( <i>Mangifera</i> spp.)
Pangenome analysis provides insights into the evolution of mango ( <i>Mangifera</i> spp.) Open
Mango ( Mangifera spp.) is a major tropical fruit crop of global economic importance, but advanced genomic resources are needed to support its breeding, conservation, and sustainable cultivation. In this study, a mango pangenome was constr…
View article: Genetic marker data for sweetpotato improvement
Genetic marker data for sweetpotato improvement Open
View article: The genome assembly of the westslope cutthroat trout, <i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout, <i>Oncorhynchus mykiss</i>
The genome assembly of the westslope cutthroat trout, <i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout, <i>Oncorhynchus mykiss</i> Open
Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genet…
View article: Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line
Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line Open
View article: Near-complete genome sequence of a type-A deformed wing virus discovered from <i>Solenopsis invicta</i> in Mississippi, USA
Near-complete genome sequence of a type-A deformed wing virus discovered from <i>Solenopsis invicta</i> in Mississippi, USA Open
Deformed wing virus (DWV) can cause a major disease in honeybees worldwide and has been detected in many other arthropods (S. J. Martin and L. E. Brettell, Annu Rev Virol 6:49–69, 2019, https://www.annualreviews.org/content/journals/10.114…
View article: A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium yellows resistance QTL
A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium yellows resistance QTL Open
Sugar beet (Beta vulgaris L.) is a global source of table sugar and animal fodder. Here we report a highly contiguous, haplotype phased genome assembly and annotation for sugar beet line FC309. Both assembled haplomes for FC309 represent t…
View article: The genome assembly of the westslope cutthroat trout,<i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout
The genome assembly of the westslope cutthroat trout,<i>Oncorhynchus lewisi</i>, reveals interspecific chromosomal rearrangements with the rainbow trout Open
Cutthroat trout ( Oncorhynchus clarkii ) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several gen…
View article: Chromosome-scale genome of the polyphagous pest <i>Anastrepha ludens</i> (Diptera: Tephritidae) provides insights on sex chromosome evolution in <i>Anastrepha</i>
Chromosome-scale genome of the polyphagous pest <i>Anastrepha ludens</i> (Diptera: Tephritidae) provides insights on sex chromosome evolution in <i>Anastrepha</i> Open
The Mexican fruit fly, Anastrepha ludens, is a polyphagous true fruit fly (Diptera: Tephritidae) considered 1 of the most serious insect pests in Central and North America to various economically relevant fruits. Despite its agricultural r…
View article: Chromosome-scale genome assembly of the hunt bumble bee, <i>Bombus huntii</i> Greene, 1860, a species of agricultural interest
Chromosome-scale genome assembly of the hunt bumble bee, <i>Bombus huntii</i> Greene, 1860, a species of agricultural interest Open
The Hunt bumble bee, Bombus huntii, is a widely distributed pollinator in western North America. The species produces large colony sizes in captive rearing conditions, experiences low parasite and pathogen loads, and has been demonstrated …
View article: A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium Yellows resistance QTL
A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium Yellows resistance QTL Open
Sugar beet (Beta vulgaris L.) is a global source for table sugar and animal fodder. Here we report a highly contiguous and haplotype phased genome assembly and annotation for sugar beet line FC309. Both assembled haplomes for FC309 represe…
View article: Chromosome-scale genome assembly of the Hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest
Chromosome-scale genome assembly of the Hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest Open
The Hunt bumble bee, Bombus huntii , is a widely distributed pollinator in western North America. The species produces large colony sizes in captive rearing conditions, experiences low parasite and pathogen loads, and has been demonstrated…
View article: Genome report: chromosome-scale genome assembly of the West Indian fruit fly <i>Anastrepha obliqua</i> (Diptera: Tephritidae)
Genome report: chromosome-scale genome assembly of the West Indian fruit fly <i>Anastrepha obliqua</i> (Diptera: Tephritidae) Open
The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the genome us…
View article: Discovery of a resistance gene cluster associated with smut resistance in peanut
Discovery of a resistance gene cluster associated with smut resistance in peanut Open
Peanut smut, caused by Thecaphora frezzii Carranza & J.C. Lindq., is an emerging threat for the global peanut industry. The disease’s destructive potential can be exemplified by pod incidence values as high as 70% and yield losses reaching…
View article: Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning
Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning Open
As sequencing costs decrease and availability of high fidelity long-read sequencing increases, generating experiment specific de novo genome assemblies becomes feasible. In many crop species, obtaining the genome of a hybrid or heterozygou…
View article: Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (<i>Hydrangea macrophylla</i>) and insights into Asterid evolution
Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (<i>Hydrangea macrophylla</i>) and insights into Asterid evolution Open
The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophy…
View article: Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp.
Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp. Open
Due to complex polyploid, sugarcane whole genome sequencing and characterization lag far behind other crops. PCR-based DNA markers are a viable low-cost option to evaluate genetic diversity and verify genotypes. In this study, the 5S ribos…
View article: Genome Report: Chromosome-scale Genome Assembly of the West Indian fruit fly<i>Anastrepha obliqua</i>(Diptera: Tephritidae)
Genome Report: Chromosome-scale Genome Assembly of the West Indian fruit fly<i>Anastrepha obliqua</i>(Diptera: Tephritidae) Open
The West Indian fruit fly, Anastrepha obliqua , is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua , we sequenced the genome …
View article: Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa
Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa Open
View article: Chromosome-scale genome assembly of the rusty patched bumble bee, <i>Bombus affinis</i> (Cresson) (Hymenoptera: Apidae), an endangered North American pollinator
Chromosome-scale genome assembly of the rusty patched bumble bee, <i>Bombus affinis</i> (Cresson) (Hymenoptera: Apidae), an endangered North American pollinator Open
The rusty patched bumble bee, Bombus affinis, is an important pollinator in North America and a federally listed endangered species. Due to habitat loss and large declines in population size, B. affinis is facing imminent extinction unless…
View article: The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon
The generation of the first chromosome-level de novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon Open
Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing and aquaculture industries. Large differences exist between the genomes of Atlantic salmon of European origin and North Ameri…
View article: Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa.
Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. Open
We assembled and annotated a new, long-read genome assembly for ‘Carlos’, a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We are awaiting release of the genome through …
View article: Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa.
Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. Open
We assembled and annotated a new, long-read genome assembly for ‘Carlos’, a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We are awaiting release of the genome through …
View article: Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions Open
Background Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F 1 hybrids can be produced through artificial spawning. F 1 hybrids produced by mating …
View article: Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture
Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture Open
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…
View article: Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL a New R/Shiny App to Streamline Genetic Mapping
Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci in Gossypium hirsutum and iCottonQTL a New R/Shiny App to Streamline Genetic Mapping Open
Cotton leaf curl virus (CLCuV) causes devastating losses to fiber production in Central Asia. Viral spread across Asia in the last decade is causing concern that the virus will spread further before resistant varieties can be bred. Current…
View article: Chromosome-scale genome assembly of the pink bollworm, <i>Pectinophora gossypiella</i> , a global pest of cotton
Chromosome-scale genome assembly of the pink bollworm, <i>Pectinophora gossypiella</i> , a global pest of cotton Open
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 c…