A potential model system for studying the genetics of domestication: behavioral variation among wild and domesticated strains of zebra danio (Danio rerio)

2005 ◽  
Vol 62 (9) ◽  
pp. 2046-2054 ◽  
Author(s):  
Barrie D Robison ◽  
William Rowland
Keyword(s):  
Growth Rate ◽  
Danio Rerio ◽  
Laboratory Strain ◽  
Model System ◽  
Population Declines ◽  
Behavioral Differences ◽  
Large Space ◽  
Genetic Changes ◽  
Phenotypic Differences ◽  
Domestication Process

The process of domestication in fish is fundamentally important to conservation efforts because of the extensive use of hatcheries to mitigate population declines. Research into the genetic changes associated with the domestication process in many endangered species is impeded by a lack of genomic tools, long generation times, and large space requirements. The study of the genetics of fish domestication could therefore benefit from the introduction of a model system. In this paper, we document behavioral and growth rate differences observed between a domesticated laboratory strain of zebra danio (Danio rerio) and a strain newly introduced into the laboratory from its native habitat in India. Domesticated zebra danio showed a higher degree of surface orientation, a reduced startle response, and higher growth rate compared with wild zebra danio. Wild–domesticated interstrain hybrids were intermediate in phenotype for all traits. When strains were reared together, most interstrain behavioral differences were maintained, indicating a genetic basis underlying the interstrain phenotypic variation. Phenotypic differences observed in this study are consistent with the effects of domestication in other fish species, indicating that the zebra danio can be used as a model system for studying the genetics of the domestication process in fish.

scholarly journals Genome sequences of human cytomegalovirus strain TB40/E variants propagated in fibroblasts and epithelial cells

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Ahmed Al Qaffas ◽  
Salvatore Camiolo ◽  
Mai Vo ◽  
Alexis Aguiar ◽  
Amine Ourahmane ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Human Cytomegalovirus ◽  
Viral Entry ◽  
Sequence Data ◽  
Laboratory Strain ◽  
Serial Passage ◽  
Wild Type Virus ◽  
Protein Coding ◽  
Genetic Changes ◽  
Long Read

AbstractThe advent of whole genome sequencing has revealed that common laboratory strains of human cytomegalovirus (HCMV) have major genetic deficiencies resulting from serial passage in fibroblasts. In particular, tropism for epithelial and endothelial cells is lost due to mutations disrupting genes UL128, UL130, or UL131A, which encode subunits of a virion-associated pentameric complex (PC) important for viral entry into these cells but not for entry into fibroblasts. The endothelial cell-adapted strain TB40/E has a relatively intact genome and has emerged as a laboratory strain that closely resembles wild-type virus. However, several heterogeneous TB40/E stocks and cloned variants exist that display a range of sequence and tropism properties. Here, we report the use of PacBio sequencing to elucidate the genetic changes that occurred, both at the consensus level and within subpopulations, upon passaging a TB40/E stock on ARPE-19 epithelial cells. The long-read data also facilitated examination of the linkage between mutations. Consistent with inefficient ARPE-19 cell entry, at least 83% of viral genomes present before adaptation contained changes impacting PC subunits. In contrast, and consistent with the importance of the PC for entry into endothelial and epithelial cells, genomes after adaptation lacked these or additional mutations impacting PC subunits. The sequence data also revealed six single noncoding substitutions in the inverted repeat regions, single nonsynonymous substitutions in genes UL26, UL69, US28, and UL122, and a frameshift truncating gene UL141. Among the changes affecting protein-coding regions, only the one in UL122 was strongly selected. This change, resulting in a D390H substitution in the encoded protein IE2, has been previously implicated in rendering another viral protein, UL84, essential for viral replication in fibroblasts. This finding suggests that IE2, and perhaps its interactions with UL84, have important functions unique to HCMV replication in epithelial cells.

scholarly journals A wood-warbler produced through both interspecific and intergeneric hybridization

2018 ◽  
Vol 14 (11) ◽  
pp. 20180557 ◽  
Author(s):  
David P. L. Toews ◽  
Henry M. Streby ◽  
Lowell Burket ◽  
Scott A. Taylor
Keyword(s):  
Intergeneric Hybridization ◽  
Population Declines ◽  
Morphometric Traits ◽  
Early Generation ◽  
Phenotypic Differences ◽  
Vermivora Chrysoptera ◽  
Hybridization Event ◽  
Wood Warblers ◽  
Declining Populations ◽  
Female Hybrid

Hybridization between divergent taxa can provide insight into the breakdown of characters used in mate choice, as well as reproductive compatibility across deep evolutionary timescales. Hybridization can also occur more frequently in declining populations, as there is a smaller pool of conspecific mates from which to choose. Here, we report an unusual combination of factors that has resulted in a rare, three-species hybridization event among two genera of warblers, one of which is experiencing significant population declines. We use bioacoustic, morphometric and genetic data, to demonstrate that an early generation female hybrid between a golden-winged warbler ( Vermivora chrysoptera ) and a blue-winged warbler ( V. cyanoptera ) went on to mate and successfully reproduce with a chestnut-sided warbler ( Setophaga pensylvanica ) . We studied the product of this event—a putative chrysoptera × cyanoptera × pensylvanica hybrid—and show that this male offspring sang songs like S. pensylvanica , but had morphometric traits similar to Vermivora warblers. The hybrid's maternal parent had V. chrysoptera mitochondrial DNA and , with six plumage-associated loci, we predicted the maternal parent's phenotype to show that it was likely an early generation Vermivora hybrid . That this hybridization event occurred within a population of Vermivora warblers in significant decline suggests that females may be making the best of a bad situation, and that wood-warblers in general have remained genetically compatible long after they evolved major phenotypic differences.

scholarly journals Comparative genomics reveals the molecular determinants of rapid growth of the cyanobacteriumSynechococcus elongatusUTEX 2973

2018 ◽  
Vol 115 (50) ◽  
pp. E11761-E11770 ◽  
Author(s):  
Justin Ungerer ◽  
Kristen E. Wendt ◽  
John I. Hendry ◽  
Costas D. Maranas ◽  
Himadri B. Pakrasi
Keyword(s):  
Growth Rate ◽  
Photosynthetic Rate ◽  
Rapid Growth ◽  
Mutational Analysis ◽  
Specific Activity ◽  
Synechococcus Elongatus ◽  
Fast Growth ◽  
Close Relative ◽  
Genetic Changes ◽  
Photosynthetic Productivity

Cyanobacteria are emerging as attractive organisms for sustainable bioproduction. We previously describedSynechococcus elongatusUTEX 2973 as the fastest growing cyanobacterium known.Synechococcus2973 exhibits high light tolerance and an increased photosynthetic rate and produces biomass at three times the rate of its close relative, the model strainSynechococcus elongatus7942. The two strains differ at 55 genetic loci, andsome of these loci must contain the genetic determinants of rapid photoautotrophic growth and improved photosynthetic rate. Using CRISPR/Cpf1, we performed a comprehensive mutational analysis ofSynechococcus2973 and identified three specific genes,atpA,ppnK, andrpaA, with SNPs that confer rapid growth. The fast-growth–associated allele of each gene was then used to replace the wild-type alleles inSynechococcus7942. Upon incorporation, each allele successively increased the growth rate ofSynechococcus7942; remarkably, inclusion of all three alleles drastically reduced the doubling time from 6.8 to 2.3 hours. Further analysis revealed that our engineering effort doubled the photosynthetic productivity ofSynechococcus7942. We also determined that the fast-growth–associated allele ofatpAyielded an ATP synthase with higher specific activity, while that ofppnKencoded a NAD+kinase with significantly improved kinetics. TherpaASNPs cause broad changes in the transcriptional profile, as this gene is the master output regulator of the circadian clock. This pioneering study has revealed the molecular basis for rapid growth, demonstrating that limited genetic changes can dramatically improve the growth rate of a microbe by as much as threefold.

The use of zebrafish (Danio rerio) as a model system in neurobehavioral toxicology

2004 ◽  
Vol 26 (6) ◽  
pp. 707-708 ◽  
Author(s):  
Frank M. Scalzo ◽  
Edward D. Levin
Keyword(s):  
Danio Rerio ◽  
Model System

scholarly journals Genome Sequence Resource of Magnaporthe oryzae Laboratory Strain 2539

2020 ◽  
Vol 33 (8) ◽  
pp. 1029-1031
Author(s):  
Meilian Chen ◽  
Baohua Wang ◽  
Guodong Lu ◽  
Zhenhui Zhong ◽  
Zonghua Wang
Keyword(s):  
Genome Sequence ◽  
Magnaporthe Oryzae ◽  
Genome Assembly ◽  
Laboratory Strain ◽  
Model System ◽  
Blast Disease ◽  
High Quality ◽  
Host Pathogen Interaction ◽  
Host Pathogen ◽  
High Quality Genome

Magnaporthe oryzae causes blast disease on more than 50 species of monocot plants, including important crops such as rice, millet, and most recently wheat. Additionally, it is an important model system for studying host-pathogen interaction. Here, we report a high-quality genome assembly and annotation of a laboratory strain 2539 of M. oryzae, which is a widely used progeny of a rice-infecting isolate and a grass-infecting isolate. The genome sequence of strain 2539 will be useful for studying the evolution, host adaption, and pathogenicity of M. oryzae, which will be beneficial for a better understanding of the mechanisms of host-pathogen interaction.

scholarly journals Induction of ovarian cancer by defined multiple genetic changes in a mouse model system

Cancer Cell ◽  
2002 ◽  
Vol 1 (1) ◽  
pp. 53-62 ◽  
Author(s):  
Sandra Orsulic ◽  
Yi Li ◽  
Robert A. Soslow ◽  
Lynn A. Vitale-Cross ◽  
J.Silvio Gutkind ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Mouse Model ◽  
Model System ◽  
Genetic Changes ◽  
Mouse Model System

scholarly journals Laboratory Strains of Murine Cytomegalovirus Are Genetically Similar to but Phenotypically Distinct from Wild Strains of Virus

2008 ◽  
Vol 82 (13) ◽  
pp. 6689-6696 ◽  
Author(s):  
L. M. Smith ◽  
A. R. McWhorter ◽  
L. L. Masters ◽  
G. R. Shellam ◽  
A. J. Redwood
Keyword(s):  
Inbred Mice ◽  
Laboratory Strain ◽  
Murine Cytomegalovirus ◽  
Phenotypic Characteristics ◽  
Phenotypic Differences ◽  
Resistance Patterns ◽  
Wild Strains ◽  
Clinical Models ◽  
Low Passage

ABSTRACT Murine cytomegalovirus (MCMV) is widely used to model human cytomegalovirus (HCMV) infection. However, it is known that serially passaged laboratory strains of HCMV differ significantly from recently isolated clinical strains of HCMV. It is therefore axiomatic that clinical models of HCMV using serially passaged strains of MCMV may not be able to fully represent the complexities of the system they are attempting to model and may not fully represent the complex biology of MCMV. To determine whether genotypic and phenotypic differences also exist between laboratory strains of MCMV and wild derived strains of MCMV, we sequenced the genomes of three low-passage strains of MCMV, plus the laboratory strain, K181. We coupled this genetic characterization to their phenotypic characteristics. In contrast to what is seen with HCMV (and rhesus CMV), there were no major genomic rearrangements in the MCMV genomes. In addition, the genome size was remarkably conserved between MCMV strains with no major insertions or deletions. There was, however, significant sequence variation between strains of MCMV, particularly at the genomic termini. These more subtle genetic differences led to considerable differences in in vivo replication with some strains of MCMV, such as WP15B, replicating preferentially in otherwise-MCMV-resistant C57BL/6 mice. CBA mice were no more resistant to MCMV than C57BL/6 mice and for some MCMV strains appeared to control infection less well than C57BL/6 mice. It is apparent that the previously described host resistance patterns of inbred mice and MCMV are not consistently applicable for all MCMV strains.

scholarly journals Dietary Strontium Increases Bone Mineral Density in Intact Zebrafish (Danio rerio): A Potential Model System for Bone Research

Zebrafish ◽  
2010 ◽  
Vol 7 (3) ◽  
pp. 267-273 ◽  
Author(s):  
Anthony J. Siccardi ◽  
Steve Padgett-Vasquez ◽  
Heath W. Garris ◽  
Tim R. Nagy ◽  
Louis R. D'Abramo ◽  
...  
Keyword(s):  
Bone Mineral Density ◽  
Bone Mineral ◽  
Danio Rerio ◽  
Potential Model ◽  
Model System ◽  
Mineral Density ◽  
Bone Research

scholarly journals The fish watch: Zebrafish: a clock in every cell

2005 ◽  
Vol 27 (6) ◽  
pp. 23-26
Author(s):  
Amanda-Jayne F. Carr ◽  
David Whitmore
Keyword(s):  
Circadian Rhythms ◽  
Danio Rerio ◽  
Biological Process ◽  
Genetic Model ◽  
Model System ◽  
Biological Processes ◽  
Powerful Method ◽  
Dark Cycle ◽  
Environmental Light ◽  
The One

The environmental light–dark cycle is one of the most reliable rhythmic signals, and many organisms have evolved a circadian (circa diem, ‘about a day’) system to co-ordinate biological processes with this predictable environmental change. These rhythms are endogenous and persist even in constant conditions, the light–dark cycle serving to synchronize these rhythms precisely to 24 hours. Genetic approaches have proved invaluable in increasing our understanding of the circadian clock. The ability to isolate a mutant with a defect in a rhythmic process is a very powerful method, which depends on no prior assumptions about the biological process under investigation. Consequently, Drosophila and the mouse have become the most powerful genetic models to study circadian rhythms in animals. The one alternative vertebrate genetic model system to the mouse is the zebrafish (Danio rerio).

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