scholarly journals Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli mice allows protection from multiple retroviruses

2019 ◽  
Author(s):  
Melvyn W. Yap ◽  
George R. Young ◽  
Renata Varnaite ◽  
Serge Morand ◽  
Jonathan P. Stoye
Keyword(s):  
Equine Infectious Anemia Virus ◽  
Nuclear Dna ◽  
Foamy Virus ◽  
Genetic Material ◽  
Natural Resistance ◽  
Nucleotide Polymorphisms ◽  
Restriction Factors ◽  
Extra Copy ◽  
Wild Mice ◽  
Mus Caroli

AbstractViruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. To begin to understand how restriction factors evolve, we surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice (Mus caroli, M. cervicolor and M. cookii). The presence of flanking repeats suggested it arose by LINE-mediated retrotransposition. A high degree of natural variation was observed in both Fv1 and Fv7, including numerous single nucleotide polymorphisms resulting in altered amino acids, as well as insertions and deletions that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes with activities directed against feline foamy virus (FFV), equine infectious anemia virus (EIAV) and MLV. It seems likely, at least in the case of M. caroli, that the observed gene duplication confers protection against multiple viruses not possible with a single restriction factor. We suggest that EIAV-, FFV- and MLV-like viruses are endemic within these populations, driving the evolution of the Fv1 and Fv7 genes.Author SummaryDuring the passage of time all vertebrates will be exposed to infection by a variety of different kinds of virus. To meet this threat, a variety of genes for natural resistance to viral infection have evolved. The prototype of such so-called restriction factors is encoded by the mouse Fv1 gene, which acts to block the life cycle of retroviruses at a stage between virus entry into the cell and integration of the viral genetic material into the nuclear DNA. We have studied the evolution of this gene in certain species of wild mice from South East Asia and describe an example where a duplication of the Fv1 gene has taken place. The two copies of the gene, initially identical, have evolved separately allowing the development of resistance to two rather different kinds of retroviruses, lentiviruses and spumaviruses. Independent selection for resistance to these two kinds of retrovirus suggests that such mice are repeatedly exposed to never-before-reported pathogenic retroviruses of these genera.

scholarly journals Non-Destructive Genotyping of Honeybee Queens to Support Selection and Breeding

Insects ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 896
Author(s):  
Jernej Bubnič ◽  
Katarina Mole ◽  
Janez Prešern ◽  
Ajda Moškrič
Keyword(s):  
Nuclear Dna ◽  
Time Window ◽  
Genetic Material ◽  
Relevant Information ◽  
Nucleotide Polymorphisms ◽  
Tissue Samples ◽  
Reliable Determination ◽  
Honeybee Queen ◽  
Non Destructive

In traditional bee breeding, the honeybee queen is chosen for breeding based on the performance of the colony produced by its mother. However, we cannot be entirely certain that a specific queen will produce offspring with desirable traits until we observe the young queen’s new colony. Collecting the queen’s genetic material enables quick and reliable determination of the relevant information. We sampled exuviae, feces, and wingtips for DNA extraction to avoid fatally injuring the queen when using tissue samples. Quantity and purity of extracted DNA were measured. Two mitochondrial markers were used to determine the lineage affiliation and exclude possible contamination of DNA extracts with non-honeybee DNA. dCAPS (derived Cleaved Amplified Polymorphic Sequences) markers allowed detection of single nucleotide polymorphisms (SNPs) in nuclear DNA regions presumably associated with Varroa sensitive hygiene and set the example of successful development of genotyping protocol from non-destructive DNA sources. One of the logical future steps in honeybee breeding is introducing genomic selection and non-destructive sampling methods of genetic material may be the prerequisite for successful genotyping. Our results demonstrate that the extraction of DNA from feces and exuviae can be introduced into practice. The advantage of these two sources over wingtips is reducing the time window for processing the samples, thus enabling genotyping directly after the queen’s emergence.

scholarly journals Fast genetic mapping using insertion-deletion polymorphisms in Caenorhabditis elegans

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ho-Yon Hwang ◽  
Jiou Wang
Keyword(s):  
Caenorhabditis Elegans ◽  
Genetic Mapping ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Material ◽  
Mapping Method ◽  
Forward Genetics ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Large Populations

AbstractGenetic mapping is used in forward genetics to narrow the list of candidate mutations and genes corresponding to the mutant phenotype of interest. Even with modern advances in biology such as efficient identification of candidate mutations by whole-genome sequencing, mapping remains critical in pinpointing the responsible mutation. Here we describe a simple, fast, and affordable mapping toolkit that is particularly suitable for mapping in Caenorhabditis elegans. This mapping method uses insertion-deletion polymorphisms or indels that could be easily detected instead of single nucleotide polymorphisms in commonly used Hawaiian CB4856 mapping strain. The materials and methods were optimized so that mapping could be performed using tiny amount of genetic material without growing many large populations of mutants for DNA purification. We performed mapping of previously known and unknown mutations to show strengths and weaknesses of this method and to present examples of completed mapping. For situations where Hawaiian CB4856 is unsuitable, we provide an annotated list of indels as a basis for fast and easy mapping using other wild isolates. Finally, we provide rationale for using this mapping method over other alternatives as a part of a comprehensive strategy also involving whole-genome sequencing and other methods.

GENETIC VARIATION IN RARE AND WIDESPREAD LOMATIUM SPECIES (APIACEAE): A COMPARISON OF AFLP AND SSCP DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 347-356 ◽  
Author(s):  
M. A. GITZENDANNER ◽  
P. S. SOLTIS
Keyword(s):  
Rare Species ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Allelic Variation ◽  
Plant Conservation ◽  
Single Copy ◽  
Small Populations ◽  
Nucleotide Polymorphisms ◽  
Widespread Species ◽  
Low Levels

Plant conservation genetics has been hampered by a lack of markers for studies of levels and patterns of variation in rare species. We investigated the levels of variation in several rare and widespread species of the western North American genus Lomatium Raf. (Apiaceae) using two relatively new molecular markers: AFLPs and single-strand conformation polymorphisms (SSCPs). For each species, approximately 150 AFLP loci have been scored, yielding estimates of species-level percent polymorphic loci in rare species ranging from near zero to over 80%. Levels of AFLP diversity were similar in two of the rare species, L. bradshawii (Rose ex Mathias) Mathas & Constance and L. ochocense Helliwell & Constance, and the widespread species. The third rare species, L. cookii Kagan, which has small populations, has low levels of diversity based on AFLPs. We also examined nucleotide diversity at the single-copy nuclear-DNA locus glyceraldehyde 3-phosphate dehydrogenase (Gap-C). PCR-amplified segments were analysed for allelic variation using SSCPs, and intrapopulational nucleotide polymorphisms were identified in both L. bradshawii and L. cookii. In the 211bp segment of Gap-C analysed, five nucleotide sites were segregating within populations of L. bradshawii and two in L. cookii.

scholarly journals Susceptibility of the Iranian population to severe acute respiratory syndrome coronavirus 2 infection based on variants of angiotensin I converting enzyme 2

2020 ◽  
Vol 15 (8) ◽  
pp. 507-514
Author(s):  
Alireza Mohebbi ◽  
Fatemeh Sana Askari ◽  
Mohsen Ebrahimi ◽  
Mana Zakeri ◽  
Mohammad Yasaghi ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Single Nucleotide Polymorphisms ◽  
Resistance Mutation ◽  
Iranian Population ◽  
Natural Resistance ◽  
Missense Mutations ◽  
Nucleotide Polymorphisms ◽  
Converting Enzyme ◽  
Viral Glycoprotein ◽  
Single Nucleotide

Background: Variations in the viral receptor human angiotensin-converting enzyme 2 (ACE2) may specify the susceptibility of a certain population to severe acute respiratory syndrome coronavirus 2. Objective: Evaluation of the affinity of severe acute respiratory syndrome coronavirus 2 spike glycoprotein to the Iranian genetic variants of ACE2. Materials & methods: Single nucleotide polymorphisms of ACE2 among the Iranian population were collected from the Iranome database. Missense mutations in the N-terminal peptidase domain were selected for in silico analysis. Results: 17 missense single nucleotide polymorphisms were found at ACE2. Viral glycoprotein had the lowest affinity to ACE2 mutant V485L. Discussion: The V485L variant of ACE2 could be a natural resistance mutation among the Iranian population. In addition, variant S331F can increase slightly the susceptibility to infection with the virus.

scholarly journals Structure and phylogeography of two tropical predators, spinner ( Stenella longirostris ) and pantropical spotted ( S. attenuata ) dolphins, from SNP data

2018 ◽  
Vol 5 (4) ◽  
pp. 171615 ◽  
Author(s):  
Matthew S. Leslie ◽  
Phillip A. Morin
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
Nuclear Dna ◽  
Population Level ◽  
Genetic Connectivity ◽  
Nucleotide Polymorphisms ◽  
Stenella Longirostris ◽  
Spinner Dolphin ◽  
Spinner Dolphins ◽  
Almost All

Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin ( Stenella longirostris ) and the pantropical spotted dolphin ( Stenella attenuata ), using more than 3000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species. Bayesian phylogeographic analyses of spinner dolphins showed deep divergence between Indo-Pacific, Atlantic and eastern tropical Pacific Ocean (ETP) lineages. Despite high morphological variation, our results show very close relationships between endemic ETP spinner subspecies in relation to global diversity. The dwarf spinner dolphin is a monophyletic subspecies nested within a major clade of pantropical spinner dolphins from the Indian and western Pacific Ocean populations. Population-level division among the dwarf spinner dolphins was detected—with the northern Australia population being very different from that in Indonesia. In contrast to spinner dolphins, the major boundary for spotted dolphins is between offshore and coastal habitats in the ETP, supporting the current subspecies-level taxonomy. Comparing these species underscores the different scale at which population structure can arise, even in species that are similar in habitat (i.e. pelagic) and distribution.

scholarly journals Genomic Comparison of Two O111:H−Enterohemorrhagic Escherichia coli Isolates from a Historic Hemolytic-Uremic Syndrome Outbreak in Australia

2016 ◽  
Vol 84 (3) ◽  
pp. 775-781 ◽  
Author(s):  
Lauren J. McAllister ◽  
Stephen J. Bent ◽  
Nicola K. Petty ◽  
Elizabeth Skippington ◽  
Scott A. Beatson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Hemolytic Uremic Syndrome ◽  
Sequence Data ◽  
Enterohemorrhagic Escherichia Coli ◽  
Nucleotide Polymorphisms ◽  
Extra Copy ◽  
Content Type ◽  
Shiga Toxin 2 ◽  
Uremic Syndrome ◽  
Insertion Sites

EnterohemorrhagicEscherichia coli(EHEC) is an important cause of diarrhea and hemolytic-uremic syndrome (HUS) worldwide. Australia's worst outbreak of HUS occurred in Adelaide in 1995 and was one of the first major HUS outbreaks attributed to a non-O157 Shiga-toxigenicE. coli(STEC) strain. Molecular analyses conducted at the time suggested that the outbreak was caused by an O111:H−clone, with strains from later in the outbreak harboring an extra copy of the genes encoding the potent Shiga toxin 2 (Stx2). Two decades later, we have used next-generation sequencing to compare two isolates from early and late in this important outbreak. We analyzed genetic content, single-nucleotide polymorphisms (SNPs), and prophage insertion sites; for the latter, we demonstrate how paired-end sequence data can be leveraged to identify such insertion sites. The two strains are genetically identical except for six SNP differences and the presence of not one but two additional Stx2-converting prophages in the later isolate. Isolates from later in the outbreak were associated with higher levels of morbidity, suggesting that the presence of the additional Stx2-converting prophages is significant in terms of the virulence of this clone.

scholarly journals Asymmetric hybridization of roach Rutilus rutilus and common bream Abramis brama in controlled backcrosses: Genetic and morphological patterns

2020 ◽  
Vol 28 (4) ◽  
pp. 376-383
Author(s):  
V. V. Stolbunova ◽  
V. V. Pavlova ◽  
Y. V. Kodukhova
Keyword(s):  
Cytochrome B ◽  
Nuclear Dna ◽  
Morphological Variability ◽  
Genetic Material ◽  
Nuclear Genome ◽  
Rutilus Rutilus ◽  
F1 Hybrids ◽  
Abramis Brama ◽  
Roach Rutilus Rutilus ◽  
Bream Abramis Brama

In most cases in natural environments, hybrids of roach Rutilus rutilus L. and bream Abramis brama L. possess mitochondrial DNA of bream. Presumably, the genetic basis for unidirectional hybridization of roach and bream is the high level of divergence in the genes of the mitochondrial electron transport chain (cytochrome b and cytochrome c oxidase subunits I, III). Disruption of the interaction of the products of these genes leads to nuclear-cytoplasmic incompatibility of alien genomes, what is shown in a decrease of viability and developmental abnormalities in hybrids. In the present work we studied the viability and morphology of hybrid underyearlings obtained by crossing of hybrid females of first generation (RA and AR) with males of roach R. rutilus and bream A. brama. The method of genotyping (ITS1 ribosomal DNA, cytochrome b mtDNA) and comparative analysis of the complex of 23 plastic and meristic characteristics of backcrossed hybrids are used. All progenies showed an increase in morphological variability compared to parental species and F1 hybrids. In progenies with introgression of mtDNA, a violation of associations between traits and the formation of transgressive phenotypes that go beyond the parental populations were found. In RAA backcrosses (combining mtDNA of R. rutilus and nuclear genome of A. brama) a decrease in viability with impaired recovery of external traits of bream was found. Conversely, ARR backcrosses (combining mtDNA of A. brama and the nuclear genome of R. rutilus) have a high viability and completely restore the morphotype of roach, which indicates the stable development of hybrids when they include alien genetic material. The differences in viability and morphology between backcrossed hybrids with the mtDNA of R. rutilus and A. brama evidence varying degrees of nuclear-cytoplasmic compatibility of the genomes of roach and bream. The complete interaction between mitochondrial and nuclear DNA from different species (wild-type-like) happens in direction of introgression mtDNA of A. brama, the less polymorphic of the two parental genomes. In the direction of introgression of highly polymorphic mtDNA of R. rutilus the formation of a reproductive barrier occurs. Our results show that the main reason for the asymmetry of hybridization of R. rutilus and A. brama is unequal rates of mitochondrial evolution and the priority of the introgression of mtDNA belongs a species with a lower rate of changes in mtDNA.

scholarly journals Genetic variability of farmed fur animals of the Canidae family assessed by nuclear and mitochondrial DNA analysis

2016 ◽  
Vol 72 (8) ◽  
pp. 505-510 ◽  
Author(s):  
Sylwia Nisztuk-Pacek
Keyword(s):  
Mitochondrial Dna ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Mitochondrial Gene ◽  
Genetic Material ◽  
Cox1 Gene ◽  
Phylogenetic Distance ◽  
Raccoon Dog ◽  
Study Results ◽  
Fur Animals

The aim of the study was to assess the biodiversity of farmed fur animals from the Canidae family (common fox, polar fox, and raccoon dog) using nuclear and mitochondrial markers. The study involved 434 animals. The biological material included whole peripheral blood or skin tissue. The isolated genetic material was subjected to qualitative and quantitative analyses. Mitochondrial DNA (mtDNA) gene fragments (COX1, COX2, CYTB) and nuclear DNA (nDNA) gene fragments (MSTN1, MSTN2, MSTN3, IGF1, GHR) were amplified with the PCR (polymerase chain reaction) technique. The amplicons obtained were sequenced or subjected to PCR-RFLP (restriction fragment length polymorphism) reaction, and bioinformatics analyses were performed. The interspecific analysis of the nDNA sequences revealed a total of 25 polymorphisms. On the other hand, the interspecific analysis of the mtDNA gene fragments identified 277 polymorphisms. The COX1 gene fragment exhibited the greatest variability. It was shown that the frequency of polymorphisms within the mitochondrial genome was almost 20-fold higher than that in the nuclear genome of the raccoon dog. It was found that the genetic distances revealed by the analysis of the mitochondrial gene fragments were similar to the results obtained by the nDNA analysis. The genetic distance between the raccoon and common fox was the greatest. The smallest phylogenetic distance was revealed between the two fox species. The study results indicate mitochondrial and nuclear genes may be alternatively used for determining the phylogenetic relationships between fur animals from the Canidae family.

scholarly journals Optical characterization of epidermal cells and their relationship to DNA recovery from touch samples

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1360 ◽  
Author(s):  
Cristina E. Stanciu ◽  
M. Katherine Philpott ◽  
Ye Jin Kwon ◽  
Eduardo E. Bustamante ◽  
Christopher J. Ehrhardt
Keyword(s):  
Nuclear Dna ◽  
Genetic Material ◽  
Epidermal Cells ◽  
Extracellular Dna ◽  
Biological Information ◽  
Forensic Evidence ◽  
Dna Recovery ◽  
Genetic Components ◽  
Cell Pellet

The goal of this study was to investigate the relative contributions of different cellular and genetic components to biological samples created by touch or contact with a surface – one of the most challenging forms of forensic evidence. Touch samples were generated by having individuals hold an object for five minutes and analyzed for quantity of intact epidermal cells, extracellular DNA, and DNA from pelleted cell material after elution from the collection swab. Comparisons were made between samples where individuals had washed their hands immediately prior to handling and those where hand washing was not controlled. The vast majority (84-100%) of DNA detected in these touch samples was extracellular and was uncorrelated to the number of epidermal cells detected. Although little to no extracellular or cell pellet-associated DNA was detected when individuals washed their hands prior to substrate handling, we found that a significant number of epidermal cells (between ~5x103 and ~1x105) could still be recovered from these samples, suggesting that other types of biological information may be present even when no amplifiable nuclear DNA is present. These results help to elucidate the biological context for touch samples and characterize factors that may contribute to patterns of transfer and persistence of genetic material in forensic evidence.

Sign in / Sign up

Export Citation Format

Share Document