Geoffrey C. Waldbieser
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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: Trematode parasitism increases mortality in marsh ramshorn snails <i>Planorbella trivolvis</i> exposed to repeated low-dose copper sulfate treatments in laboratory trials
Trematode parasitism increases mortality in marsh ramshorn snails <i>Planorbella trivolvis</i> exposed to repeated low-dose copper sulfate treatments in laboratory trials Open
Objective Controlling the trematode Bolbophorus damnificus in catfish aquaculture relies on disrupting the parasite life cycle by targeting the snail intermediate hosts. Copper sulfate pentahydrate (CSP) is a common and effective molluscic…
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: Correction: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture
Correction: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture Open
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: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture
Advancing genetic improvement in the omics era: status and priorities for United States aquaculture Open
Background The innovations of the “Omics Era” have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements we…
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: Tad pili contribute to the virulence and biofilm formation of virulent Aeromonas hydrophila
Tad pili contribute to the virulence and biofilm formation of virulent Aeromonas hydrophila Open
Type IV pili (T4P) are versatile proteinaceous protrusions that mediate diverse bacterial processes, including adhesion, motility, and biofilm formation. Aeromonas hydrophila , a Gram-negative facultative anaerobe, causes disease in a wide…
View article: Effect of strain and e<scp>nteric septicemia of catfish</scp> vaccine‐booster on production and processing traits of the Delta Select and Delta Control strains of channel catfish, <i>Ictalurus punctatus</i>
Effect of strain and e<span>nteric septicemia of catfish</span> vaccine‐booster on production and processing traits of the Delta Select and Delta Control strains of channel catfish, <i>Ictalurus punctatus</i> Open
The Delta Select channel catfish strain (DS) was developed by selection for increased growth and carcass yield. Progeny from DS and the Delta Control (DC) strain (a randomly bred strain from the same base population as DS) were compared in…
View article: Complete genome of <i>Vibrio harveyi</i> isolate K2014767 from the hepatopancreas of captive Caribbean spiny lobster ( <i>Panulirus argus</i> )
Complete genome of <i>Vibrio harveyi</i> isolate K2014767 from the hepatopancreas of captive Caribbean spiny lobster ( <i>Panulirus argus</i> ) Open
The complete genome sequence is reported for Vibrio harveyi isolate K2014767, isolated from a captive Caribbean spiny lobster ( Panulirus argus ) during a species-specific mortality event in a public display aquarium in the United States.
View article: Redefining piscine lactococcosis
Redefining piscine lactococcosis Open
Piscine lactococcosis is a significant threat to cultured and wild fish populations worldwide. The disease typically presents as a per-acute to acute hemorrhagic septicemia causing high morbidity and mortality, recalcitrant to antimicrobia…
View article: Pathology, microbiology, and genetic diversity associated with Erysipelothrix rhusiopathiae and novel Erysipelothrix spp. infections in southern sea otters (Enhydra lutris nereis)
Pathology, microbiology, and genetic diversity associated with Erysipelothrix rhusiopathiae and novel Erysipelothrix spp. infections in southern sea otters (Enhydra lutris nereis) Open
Erysipelothrix spp., including E. rhusiopathiae , are zoonotic bacterial pathogens that can cause morbidity and mortality in mammals, fish, reptiles, birds, and humans. The southern sea otter (SSO; Enhydra lutris nereis ) is a federally-li…
View article: Evaluating nanopore sequencing for microbial community characterization in catfish pond water
Evaluating nanopore sequencing for microbial community characterization in catfish pond water Open
In the United States, catfish are primarily farmed in earthen ponds, resulting in an aquatic environment influenced both by management practices and natural ecological processes. Profiling pond water microbiota can be useful for understand…
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: 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: Additional file 2 of Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions
Additional file 2 of Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions Open
Additional file 2: Supplementary Table S7. Shared markers between blue catfish and channel catfish. Supplementary Table S10. Gene annotation of 508 gene families that were specific to channel catfish and blue catfish compared with other 14…
View article: First Isolation of a Herpesvirus (Family Alloherpesviridae) from Great Lakes Lake Sturgeon (Acipenser fulvescens)
First Isolation of a Herpesvirus (Family Alloherpesviridae) from Great Lakes Lake Sturgeon (Acipenser fulvescens) Open
The lake sturgeon (Acipenser fulvescens; LST) is the only native sturgeon species in the Great Lakes (GL), but due to multiple factors, their current populations are estimated to be <1% of historical abundances. Little is known about infec…
View article: The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for 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 North American Atlantic salmon Open
Given the genetic and genomic differences between Atlantic salmon of European origin and North American (N.A.) origin, it is crucial to develop unique genomic resources for each lineage. Here we describe the resources that we recently deve…
View article: Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries
Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries Open
View article: Complete Genome Sequences of Francisella marina Strains E95-16 and E103-15, Isolated from Maricultured Spotted Rose Snapper ( <i>Lutjanus guttatus</i> ) on the Pacific Coast of Central America
Complete Genome Sequences of Francisella marina Strains E95-16 and E103-15, Isolated from Maricultured Spotted Rose Snapper ( <i>Lutjanus guttatus</i> ) on the Pacific Coast of Central America Open
In 2015 and 2016, a previously unrecognized Francisella sp. was isolated from disease outbreaks in maricultured spotted rose snapper ( Lutjanus guttatus ) on the Pacific coast of Central America. Polyphasic analysis demonstrated that these…
View article: A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout
A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout Open
Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originat…
View article: A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals structural genome variation in rainbow trout
A long reads-based <i>de-novo</i> assembly of the genome of the Arlee homozygous line reveals structural genome variation in rainbow trout Open
Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originat…
View article: Characterization of a Novel Conjugative Plasmid in Edwardsiella piscicida Strain MS-18-199
Characterization of a Novel Conjugative Plasmid in Edwardsiella piscicida Strain MS-18-199 Open
Edwardsiella piscicida is a pathogenic bacterium responsible for significant losses in important wild and cultured fish species. E. piscicida strain MS-18-199 recovered from a diseased hybrid catfish from East Mississippi and…
View article: The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish
The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish Open
View article: Complete genome sequence data of multidrug-resistant Aeromonas veronii strain MS-18-37
Complete genome sequence data of multidrug-resistant Aeromonas veronii strain MS-18-37 Open
View article: Additional file 1: of The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish
Additional file 1: of The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish Open
Table S1. Differentially expressed genes located on chromosome 4 10-14 dpf. Table S2. Differentially expressed genes located on chromosome 4 15-19 dpf. (XLSX 26 kb)
View article: Development of genomic predictions for harvest and carcass weight in channel catfish
Development of genomic predictions for harvest and carcass weight in channel catfish Open
Genomic evaluation improves the ability to predict future performance relative to traditional BLUP and will allow more accurate identification of genetically superior individuals within catfish families.
View article: Draft Genome Sequence of Fish Pathogen Aeromonas bestiarum GA97-22
Draft Genome Sequence of Fish Pathogen Aeromonas bestiarum GA97-22 Open
Aeromonas bestiarum is a Gram-negative mesophilic motile bacterium causing acute hemorrhagic septicemia or chronic skin ulcers in fish. Here, we report the draft genome sequence of A. bestiarum strain GA97-22, which was isolated from rainb…
View article: Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function
Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function Open
The microbiota of teleost fish has gained a great deal of research attention within the past decade, with experiments suggesting that both host-genetics and environment are strong ecological forces shaping the bacterial assemblages of fish…
View article: Identification of Four Distinct Phylogenetic Groups in Flavobacterium columnare With Fish Host Associations
Identification of Four Distinct Phylogenetic Groups in Flavobacterium columnare With Fish Host Associations Open
Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the most prevalent fish diseases worldwide. An exceptionally high level of genetic diversity among isolates of F. columnare has lon…