Warmwater Aquaculture Research Unit

Tupelo, MS, United States

Warmwater Aquaculture Research Unit

Tupelo, MS, United States
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News Article | May 1, 2017
Site: phys.org

Catfish is an important dietary protein source and is the third most commonly farmed fish worldwide. While more than 2,500 species of catfish are known to exist, the channel catfish dominates U.S. aquaculture, accounting for more than 60 percent of fish and seafood production. In 2015, production sales for U.S. catfish growers totaled $361 million, up 3 percent from the previous year, according to USDA's National Agricultural Statistics Service. Research at the Agricultural Research Service (ARS) Warmwater Aquaculture Research Unit (WARU) in Stoneville, Mississippi, helps catfish producers improve the quality and quantity of their products. Recently, a team led by WARU molecular biologist Geoff Waldbieser and Auburn University scientist John Liu produced the first genome-sequence assembly for the channel catfish. It's also the first for any type of catfish. The total complement of DNA in the cell is called the "genome," and the catfish genome, like an instruction manual, contains the information needed to make and "operate" each fish. The catfish genome-sequence assembly gives scientists the ability to read the instruction manual for each individual catfish and look for differences that make some animals grow faster or resist disease better. Waldbieser used a special breeding technique called "gynogenesis" to produce the genome donor, Coco, so that she contained two copies of DNA—like other animals—except that both copies were completely identical. "I named her after Coco Chanel, because she's Channel No. 1," Waldbieser says. Collaborating with ARS scientists at the Genomics and Bioinformatics Research Unit in Stoneville and the Bovine Functional Genomics Laboratory in Beltsville, Maryland, Waldbieser produced about 800 million DNA sequences from Coco's DNA. "Those sequences were like puzzle pieces. It took 2 months on a 64-processor computer workstation to align them and produce the genome assembly," Waldbieser says. Waldbieser and WARU geneticist Brian Bosworth recently used Coco's genome to identify variation in DNA sequences between individual catfish within the Delta Select line—an improved catfish line being developed at WARU for use by farmers. "Now that we know where the genetic variations in the DNA sequences are located, we will be able to analyze different parts of the genome inherited by different individual catfish," Waldbieser says. "We can identify those segments, propagate them to our fish population, and improve meat production and production efficiency for farmers." This is important, because improving catfish growth rate, fillet yield, meat quality, and disease resistance will greatly benefit fish farmers, Waldbieser adds. More information: Qifan Zeng et al. Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence, Scientific Reports (2017). DOI: 10.1038/srep40347


Kumru S.,Mississippi State University | Tekedar H.C.,Mississippi State University | Gulsoy N.,Marmara University | Waldbieser G.C.,Warmwater Aquaculture Research Unit | And 2 more authors.
Frontiers in Microbiology | Year: 2017

Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here, we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90.71% similar) and DNA-DNA Hybridization (42.6% similar). Genome alignment indicated the two genomes have a large number of rearrangements. However, function-based comparative genomics analysis indicated that the two strains have similar functional capabilities with 2,263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391. Both strains carry type I secretion system, type VI secretion system, and type IX secretion system. The two genomes also have similar CRISPR capacities. The F. columnare strain ATCC 49512 genome contains a higher number of insertion sequence families and phage regions, while the F. columnare strain 94-081 genome has more genomic islands and more regulatory gene capacity. Transposon mutagenesis using Tn4351 in pathogenic strain 94-081 yielded six mutants, and experimental infections of fish showed hemolysin and glycine cleavage protein mutants had 15 and 10% mortalities, respectively, while the wild-type strain caused 100% mortalities. Our comparative and mutational analysis yielded important information on classification of genomovars I and II F. columnare as well as potential virulence genes in F. columnare strain 94-081. © 2017 Kumru, Tekedar, Gulsoy, Waldbieser, Lawrence and Karsi.


Griffin M.J.,Mississippi State University | Quiniou S.,Warmwater Aquaculture Research Unit | Khoo L.,Mississippi State University | Bollinger T.K.,Canadian Cooperative Wildlife Health Center
Journal of Fish Diseases | Year: 2015

The goal of this study was to identify a myxosporidian parasite infecting the central nervous system of yellow perch Perca flavescens (Mitchell, 1814) observed while investigating a fish kill in Saskatchewan, Canada. Fish were collected from seven different lakes, from two distinct watersheds. Sixty-four per cent (54/86) of yellow perch contained myxozoan pseudocysts located throughout the spinal cord and brain. Myxospores measured 16.5 μm (range 16.2-16.8) long and 8.2 μm (range 7.9-8.4) wide and contained two pyriform, mildly dissymmetrical, polar capsules measuring 7.7 μm (range 7.3-8.1) long and 2.7 μm (range 2.4-3.0) wide. The polar capsules each contained a single polar filament, with 7-9 turns per polar filament coil. Sequencing of the 18S SSU rDNA gene demonstrated >99% similarity to Myxobolus neurophilus. In 60% of infected fish, there was a mild to moderate, non-suppurative myelitis or encephalitis, or both, associated with myxospores. Axonal degeneration was present in rare cases. These findings extend the geographical distribution of M. neurophilus and suggest it may be widespread in yellow perch populations in Saskatchewan. © 2014 John Wiley & Sons Ltd.


Chatakondi N.G.,U.S. Department of Agriculture | Chatakondi N.G.,Warmwater Aquaculture Research Unit
Journal of the World Aquaculture Society | Year: 2014

Hormone-induced spawning of channel catfish held communally in tanks is a reliable method to produce channel catfish, Ictalurus punctatus ♀ × blue catfish, Ictalurus furcatus ♂, F1 hybrid catfish fry. However, mature catfish are crowded, and repeatedly handled during the process of induced ovulation. Repeated handling of gravid females is stressful and may impair ovulation, egg quality, and reproductive performance. Three trials were conducted to evaluate the effects of two methods of confining post-hormone-injected female channel catfish on stress response (cortisol concentrations) and reproductive performance: fish were either held individually while suspended in soft, nylon-mesh bags or communally in a concrete tank. Percent of females ovulated to hormone treatment, relative fecundity, percent egg viability, and latency of channel catfish did not differ for fish in the two treatments. However, percent hatch and fry/kg of females was higher (P < 0.05) for fish held in bags that for fish held communally in tanks. Mean plasma cortisol response immediately prior to the first hormone injection (0h) did not differ among fish groups in the two treatments. However, mean plasma cortisol concentrations were significantly lower (P < 0.05) for fish in the bag treatment at 16 and 36h compared to fish held communally in tanks. Plasma estradiol levels (measure of oocyte maturation) were assessed at 0, 16, and 36 h after hormone injection; concentrations were (P<0.05) higher at 16h compared to 0 and 36h; however, estradiol concentrations did not differ for fish held in the two treatments (P > 0.05). Suspending hormone-injected broodfish individually in soft bags reduced stress response, improved egg hatching rate, and increased hybrid fry produced per kg weight of female broodfish. Using this simple technology, farmers can improve the efficiency of hatcheries producing hybrid catfish fry. © by the World Aquaculture Society 2014.


PubMed | Warmwater Aquaculture Research Unit, U.S. Department of Agriculture and Mississippi State University
Type: Journal Article | Journal: Genome announcements | Year: 2015

Aeromonas hydrophila occurs in freshwater environments and infects fish and mammals. Here, we report the complete genome sequence of Aeromonas hydrophila AL06-06, which was isolated from diseased goldfish and is being used for comparative genomic studies with A.hydrophila strains that cause bacterial septicemia in channel catfish aquaculture.


Schroeter J.C.,Southern Illinois University Carbondale | Peterson B.C.,Warmwater Aquaculture Research Unit | Small B.C.,University of Idaho
Aquaculture | Year: 2016

Large-scale, gene expression profiling methods allow for high throughput analysis of physiological pathways at a fraction of the cost of individual gene expression analysis. Systems, such as the Fluidigm quantitative PCR array described here, can provide powerful assessments of the effects of diet, environment, and management on physiological pathways affecting production parameters. A targeted microfluidic PCR array was designed and validated, for channel catfish (Ictalurus punctatus) representing key pathways involved in appetite, growth, metabolism, and intestinal inflammation for their potential to provide insight into the effects of diet and dietary supplements on these important physiological processes regulating feed efficiency and growth. With few exceptions, PCR primers were designed from Ictaluridae gene sequences published in GenBank. PCR amplicons from primers designed outside of Ictaluridae were sequenced to verify gene identity. All target gene primers were initially validated via conventional real-time qPCR (RT-qPCR). Combined hypothalamus/pituitary, hepatic, stomach, and intestinal tissue were used validate a 48.48 microfluidic PCR array to analyze multitissue gene expression. Use of the Fluidigm array resulted in reliable cycle threshold levels (Ct), efficiencies (E), and quality threshold scores (QS) for all but eight genes examined. Of the potential reference genes included in the panel, alpha-tubulin (TUBA) had a high QS, E, and acceptable Ct. The high throughput application of this technology, relative to conventional RT-qPCR, for assessing dietary effects on these pathways is demonstrated. Development of this targeted multi-tissue microfluidic array paves the way for the rapid evaluation of regulatory pathways in response to alternative feeding strategies, dietary formulations, and supplementation, as well as environmental and management effects for improving channel catfish culture and validates a cost-effective, dynamic, gene expression platform for use with other cultured fishes. © 2016 Elsevier B.V.


Rosser T.G.,Mississippi State University | Griffin M.J.,Mississippi State University | Quiniou S.M.A.,Warmwater Aquaculture Research Unit | Greenway T.E.,Mississippi State University | And 3 more authors.
Journal of Parasitology | Year: 2014

The actinospore diversity of infected Dero digitata was surveyed (May 2011) from a channel catfish (Ictalurus punctatus) production pond in the Mississippi Delta region for the elucidation of unknown myxozoan life cycles. At present, only 2 myxozoan life cycles have been molecularly confirmed in channel catfish, linking the actinospore stage from an aquatic oligochaete (D. digitata) and the myxospore stage from the catfish. In this study D. digitata (n = 2,592) were isolated from oligochaetes collected from the bottom sediment of a channel catfish production pond. After 1 wk of daily observation, a total of 6 genetically different actinospore types were observed. The collective groups were classified as 2 aurantiactinomyxons, 2 helioactinomyxons, 1 raabeia, and 1 triactinomyxon. Overall prevalence of myxozoan infections in the isolated oligochaetes was 4.4%. Actinospores were photographed and measured for morphological characterization. Four previously undescribed actinospore types were identified and characterized molecularly and morphologically. Phylogenetic analysis revealed the raabeia and one of the helioactinomyxon (type 1) actinospores were closely related to the group of myxozoans known to parasitize ictalurids in North America. To date, no myxospores have been linked to the newly sequenced actinospores reported in this survey. The morphological and molecular data generated from this study will assist in the identification of myxospore counterparts for these actinospore stages and aid in the elucidation of unknown myxozoan life cycles in closed production systems. © 2014 American Society of Parasitologists.


Rosser T.G.,Mississippi State University | Griffin M.J.,Mississippi State University | Quiniou S.M.A.,Warmwater Aquaculture Research Unit | Khoo L.H.,Mississippi State University | Pote L.M.,Mississippi State University
Parasitology Research | Year: 2014

In the southeastern USA, the channel catfish Ictalurus punctatus is a host to at least eight different species of myxozoan parasites belonging to the genus Henneguya, four of which have been characterized molecularly using sequencing of the small subunit ribosomal RNA (SSU rRNA) gene. However, only two of these have confirmed life cycles that involve the oligochaete Dero digitata as the definitive host. During a health screening of farm-raised channel catfish, several fish presented with deformed primary lamellae. Lamellae harbored large, nodular, white pseudocysts 1.25 mm in diameter, and upon rupturing, these pseudocysts released Henneguya myxospores, with a typical lanceolate-shaped spore body, measuring 17.1 ± 1.0 μm (mean ± SD; range = 15.0–19.3 μm) in length and 4.8 ± 0.4 μm (3.7–5.6 μm) in width. Pyriform-shaped polar capsules were 5.8 ± 0.3 μm in length (5.1–6.4 μm) and 1.7 ± 0.1 μm (1.4–1.9 μm) in width. The two caudal processes were 40.0 ± 5.1 μm in length (29.5–50.0 μm) with a spore length of 57.2 ± 4.7 (46.8–66.8 μm). The contiguous SSU rRNA gene sequence obtained from myxospores of five excised cysts did not match any Henneguya sp. in GenBank. The greatest sequence homology (91 % over 1,900 bp) was with Henneguya pellis, associated with blister-like lesions on the skin of blue catfish Ictalurus furcatus. Based on the unique combination of pseudocyst and myxospore morphology, tissue location, host, and SSU rRNA gene sequence data, we report this isolate to be a previously unreported species, Henneguya bulbosus sp. nov. © 2014, Springer-Verlag Berlin Heidelberg.


Rosser T.G.,Mississippi State University | Griffin M.J.,Mississippi State University | Quiniou S.M.A.,Warmwater Aquaculture Research Unit | Khoo L.H.,Mississippi State University | And 3 more authors.
Parasitology Research | Year: 2015

There are more than 200 species of Henneguya described from fish. Of these, only three life cycles have been determined, identifying the actinospore and myxospore stages from their respective hosts. Two of these life cycles involve the channel catfish (Ictalurus punctatus) and the freshwater oligochaete Dero digitata. Herein, we molecularly confirm the life cycle of a previously undescribed Henneguya sp. by matching 18S ribosomal RNA (rRNA) gene sequence of the myxospore stage from channel catfish with the previously described actinospore stage (Aurantiactinomyxon mississippiensis) from D. digitata. Gill tissue from naturally infected channel catfish contained pseudocysts restricted to the apical end of the primary lamellae. Myxospores were morphologically consistent with Henneguya spp. from ictalurid fishes in North America. The spores measured 48.8 ± 4.8 μm (range = 40.7–61.6 μm) in total spore length. The lanceolate spore body was 17.1 ± 1.0 μm (14.4–19.3 μm) in length and 5.0 ± 0.3 μm (4.5–5.5 μm) in width. The two polar capsules were 6.2 ± 0.4 μm (5.8–7.0 μm) long and 5.0 ± 0.3 μm (4.5–5.5 μm) wide. The polar capsule contained eight to nine coils in the polar filament. The two caudal processes were of equal length, measuring 31.0 ± 4.1 μm (22.9–40.6 μm). The 1980-bp 18S rRNA gene sequence obtained from two excised cysts shared 99.4 % similarity (100 % coverage) to the published sequence of A. mississippiensis, an actinospore previously described from D. digitata. The sequence similarity between the myxospore from channel catfish and actinospore from D. digitata suggests that they are conspecific, representing alternate life stages of Henneguya mississippiensis n. sp. © 2015, Springer-Verlag Berlin Heidelberg.


PubMed | Warmwater Aquaculture Research Unit and Mississippi State University
Type: Journal Article | Journal: Systematic parasitology | Year: 2016

The smallmouth buffalo Ictiobus bubalus Rafinesque (Catostomidae) is native to North American waterways and occasionally grown in pond aquaculture. Species of Myxobolus Btschli, 1882 have been reported from the gills, integument, and intestinal tract of buffalo fish, although there is ambiguity in some host records. In the summer of 2013, thirteen adult smallmouth buffalo were seined from a 0.1-acre (0.04-hectare) experimental research pond at the Thad Cochran National Warmwater Aquaculture Center in Stoneville, Mississippi, USA, and examined for the presence of parasitic infection. Two previously unknown species of Myxobolus were observed parasitising the gills. Plasmodia of the two species differed from each other in both size and shape. Morphologically the two species were distinct from one another and from other Myxobolus spp. previously reported from buffalo fish. Myxospores of Myxobolus ictiobus n. sp. were spherical and measured 12.7-14.5 (13.9 0.4) m in length and 10.7-13.6 (12.5 0.7) m in width with a thickness of 10.3-14.8 (12.6 2.3) m. Polar capsules measured 5.6-7.4 (6.6 0.4) m in length and 3.7-4.9 (4.5 0.8) m in width and each contained a coiled polar filament with 5-6 turns. Myxospores of Myxobolus minutus n. sp. were circular in shape and measured 7.4-9.6 (8.6 0.7) m in length and 7.5-9.9 (8.8 0.7) m in width with a thickness of 6.5-7.3 (6.7 0.3) m. Polar capsules measured 3.6-4.9 (4.3 0.3) m in length and 2.8-3.8 (3.3 0.3) m and each contained a coiled polar filament with 5-6 turns. Supplemental 18S rRNA gene sequencing identified unique sequences for each isolate. Phylogenetic analysis of 18S rRNA sequences demonstrated a strong clustering of both isolates with other species of Myxobolus from cypriniform fish.

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