Dataset Information

Identification of essential and non-essential genes in Ambystoma tigrinum virus.

ABSTRACT: Members of the genus Ranavirus (family Iridoviridae) are large double-stranded (ds) DNA viruses that are found world-wide infecting fish, amphibian and reptile ectothermic hosts. Ranavirus genomes range from 105 to 155kbp in length and they are predicted to encode around 90-125 genes. Currently, our knowledge of the function of ?50% of these genes is known or inferred based on homology to orthologous genes characterized in other systems; however, the function of the remaining open reading frames (ORFS) is unknown. Therefore, in order to begin to uncover the function of unknown ORFs in ranaviruses we developed a standardized approach to generate a recombination cassette for any ORF in Ambystoma tigrinum virus (ATV). Our standardized approach quickly and efficiently assembles recombination cassettes and recombinant ATV. We have used this approach to identify two essential, one semi-essential and two non-essential genes in ATV.

SUBMITTER: Aron MM

PROVIDER: S-EPMC4985175 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Identification of essential and non-essential genes in Ambystoma tigrinum virus.

Aron Mariah M MM Allen Alexander G AG Kromer Mathew M Galvez Hector H Vigil Brianna B Jancovich James K JK

Virus research 20160326

Members of the genus Ranavirus (family Iridoviridae) are large double-stranded (ds) DNA viruses that are found world-wide infecting fish, amphibian and reptile ectothermic hosts. Ranavirus genomes range from 105 to 155kbp in length and they are predicted to encode around 90-125 genes. Currently, our knowledge of the function of ∼50% of these genes is known or inferred based on homology to orthologous genes characterized in other systems; however, the function of the remaining open reading frames ...[more]

PMID: 27025572

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Project description:BackgroundLoss of pond habitat is catastrophic to aquatic larval amphibians, but even reduction in the amount of time a breeding site holds water (hydroperiod) can influence amphibian development and limit reproductive success. Using the landscape variation of a glacial valley in the Greater Yellowstone Ecosystem as the context for a natural experiment, we examined variation in growth pattern and life history of the salamander Ambystoma tigrinum melanostictum and determined how these developmental characteristics varied with hydroperiod over several summers.ResultsIn ponds that dried early in the season, maximum larval size was reduced relative to the sizes achieved in permanent ponds. Ephemeral ponds were associated with early metamorphosis at small body sizes, while permanent ponds facilitated longer larval periods and later metamorphosis. Paedomorphosis resulted from indefinite metamorphic postponement, and was identified only in the most permanent environments. Patterns of growth and allometry were similar between ponds with different hydroperiods, but considerable life history variation was derived from modulating the timing of and size at metamorphosis. Considering maximum rates of growth and inferring the minimum size at metamorphosis across 25 ponds over the course of three years, we calculated that hydroperiods longer than three months are necessary to support these populations through metamorphosis and/or reproductive maturity.ConclusionsLandscape heterogeneity fosters life history variation in this natural population. Modulation of the complex ambystomatid life cycle allows this species to survive in unpredictable environments, but current trends towards rapid pond drying will promote metamorphosis at smaller sizes and could eliminate the paedomorphic phenotype from this region. Metamorphosis at small size is has been linked to altered fitness traits, including reduced survival and fecundity. Thus, widespread environmental truncation of larval periods may lead to decreased population persistence. We found that the hydroperiods of many ponds in this region are now shorter than the developmental period required for larvae to reach the minimum size for metamorphosis; these locations serve as reproductive sinks that may be detrimental for persistence of the species in the region.

Project description:Animals live in heterogeneous environments must navigate in order to forage or capture food, defend territories, and locate mates. These heterogeneous environments have a variety of substrates that differ in their roughness, texture, and other properties, all of which may alter locomotor performance. Despite such natural variation in substrate, many studies on locomotion use noncompliant surfaces that either are unrepresentative of the range of substrates experienced by species or underestimate maximal locomotor capabilities. The goal of this study was to determine the role of forefeet and hindfeet on substrates with different properties during walking in a generalized sprawling tetrapod, the tiger salamander (Ambystoma tigrinum). Adult salamanders (n = 4, SVL = 11.2-14.6 cm) walked across level dry sand (DS), semi-soft plaster of Paris (PoP), wet sand (WS), and a hard, noncompliant surface (table)-substrates that vary in compliance. Trials were filmed in dorsal and anterior views. Videos were analyzed to determine the number of digits and surface area of each foot in contact with the substrate. The surface area of the forelimbs contacting the substrate was significantly greater on DS and PoP than on WS and the table. The surface area of the hindlimbs contacting the substrate was significantly greater on DS than on all other substrates. There were no significant differences in the time that the fore- or hindfeet were in contact with the substrate as determined by the number of digits. We conclude that salamanders modulate the use of their feet depending on the substrate, particularly on DS which is known to increase the mechanical work and energy expended during locomotion owing to the fluid nature of its loose particles. More studies are needed to test a wider range of substrates and to incorporate behavioral data from field studies to get a better understanding of how salamanders are affected by different substrates in their natural environment.

Dataset Information

Identification of essential and non-essential genes in Ambystoma tigrinum virus.

Publications

Identification of essential and non-essential genes in Ambystoma tigrinum virus.

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