Genetic variation of populations of Citrus psorosis virus

Citrus psorosis virus (CPsV), the type species of genus Ophiovirus, has a segmented, negative-stranded RNA genome. We examined the population structure and genetic variation of CPsV in three coding regions located in RNAs 1, 2 and 3, analysing 22 isolates from Argentina, California, Florida, Italy and Spain. Most isolates contained a predominant sequence and some minor variants. Estimations of the genetic diversity and phylogenetic clustering of isolates disclosed two populations, one comprising isolates from Spain, Italy, Florida and California and the other including the Argentinean isolates. Isolate CPV-4 (from Texas) included for comparison was distant from both groups, suggesting that it belongs to a third group. The low ratio between non-synonymous and synonymous nucleotide substitutions indicated strong selection for amino acid sequence conservation, particularly in the coat protein gene. Incongruent phylogenetic relationships in different genomic regions suggested that exchange of genomic segments may have contributed to CPsV evolution.

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A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽

10.11646/zootaxa.4748.1.10 ◽

2020 ◽

Vol 4748 (1) ◽

pp. 182-194 ◽

Cited By ~ 1

Author(s):

JING ZHANG ◽

ERNST BROCKMANN ◽

QIAN CONG ◽

JINHUI SHEN ◽

NICK V. GRISHIN

Keyword(s):

Dna Sequences ◽

Type Species ◽

Phylogenetic Trees ◽

Type Specimens ◽

African Species ◽

Protein Coding ◽

Coding Regions ◽

As Species ◽

Close Relatives ◽

Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]).

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Genetic diversity of a natural population of Cucurbit yellow stunting disorder virus

Journal of General Virology ◽

10.1099/vir.0.80584-0 ◽

2005 ◽

Vol 86 (3) ◽

pp. 815-822 ◽

Cited By ~ 50

Author(s):

C. F. Marco ◽

M. A. Aranda

Keyword(s):

Coat Protein ◽

Nucleotide Diversity ◽

Protein Gene ◽

Virus Genome ◽

Plant Viruses ◽

The Other ◽

Single Amino Acid ◽

Coding Regions ◽

Single Amino Acid Change ◽

Genomic Regions

An analysis of nucleotide sequences in five coding and one non-coding genomic regions of 35 Cucurbit yellow stunting disorder virus (CYSDV) isolates collected on a local scale over an 8 year period is reported here. In total, 2277 nt were sequenced for each isolate, representing about 13 % of the complete virus genome. Mean nucleotide diversity for the whole population in synonymous positions in the coding regions was 0·00068, whilst in the 5′ untranslated region (5′ UTR) of genomic RNA2, it was 0·00074; both of these values are very small, compared with estimates of nucleotide diversity for populations of other plant viruses. Nucleotide diversity was also determined independently for each of the ORFs and for the 5′ UTR of RNA2; the data showed that variability is not distributed evenly among the different regions of the viral genome, with the coat protein gene showing more diversity than the other four coding regions that were analysed. However, the low variability found precluded any inference of selection differences among gene regions. On the other hand, no evidence of selection associated with host adaptation was found. In contrast, at least a single amino acid change in the coat protein appears to have been selected with time.

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Genetic variation in heat tolerance of the coral Platygyra daedalea offers the potential for adaptation to ocean warming

10.1101/2020.10.13.337089 ◽

2020 ◽

Author(s):

Holland Elder ◽

Virginia Weis ◽

Jose Montalvo-Proano ◽

Veronique J.L Mocellin ◽

Andrew H. Baird ◽

...

Keyword(s):

Genetic Variation ◽

Heat Stress ◽

Heat Tolerance ◽

Nucleotide Polymorphisms ◽

Narrow Sense Heritability ◽

Coding Regions ◽

Genomic Tools ◽

Coral Reef Ecosystems ◽

Few Data ◽

Genomic Regions

AbstractReef-building corals are foundational species in coral reef ecosystems and are threatened by many stressors including rising ocean temperatures. In 2015/16 and 2016/17, corals around the world experienced consecutive bleaching events and most coral populations are projected to experience temperatures above their current bleaching thresholds annually by 2050. Adaptation to higher temperatures is therefore necessary if corals are to persist in a warming future. While many aspects of heat stress have been well studied, few data are available for predicting the capacity for adaptive cross-generational responses in corals. To address this knowledge gap, we quantified the heritability and genetic variation associated with heat tolerance in Platygyra daedalea from the Great Barrier Reef (GBR). We tracked the survival of replicate quantitative genetic crosses (or families) of coral larvae from six parents in a heat stress selection experiment. We also identified allelic shifts in heat-selected survivors versus paired, non-selected controls of the same coral crosses. We estimated narrow sense heritability to be 0.66 and detected a total of 1,069 single nucleotide polymorphisms (SNPs) associated with heat tolerance. An overlap of 148 unique SNPs shared between experimental crosses indicates that specific genomic regions are responsible for heat tolerance of P. daedalea and some of these SNPs fall in coding regions. These findings suggest that this P. daedalea population has the genetic prerequisites for adaptation to increasing temperatures. This study also provides knowledge for the development of high throughput genomic tools to screen for variation within and across populations to harness or enhance adaptation through assisted gene flow and assisted migration.

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Discovery of an autoimmunity-associated IL2RA enhancer by unbiased targeting of transcriptional activation

10.1101/091843 ◽

2016 ◽

Cited By ~ 2

Author(s):

Dimitre R. Simeonov ◽

Benjamin G. Gowen ◽

Mandy Boontanrart ◽

Theodore Roth ◽

Youjin Lee ◽

...

Keyword(s):

Genetic Variation ◽

Transcriptional Activation ◽

Gene Activation ◽

Interleukin 2 ◽

General Mechanism ◽

Enhancer Activity ◽

Extracellular Signals ◽

Coding Regions ◽

Cell Type Specific ◽

Genomic Regions

The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell type-specific transcriptional programs and responses to specific extracellular cues 1-3. In order to understand the mechanisms by which non-coding genetic variation contributes to disease, systematic mapping of functional enhancers and their biological contexts is required. Here, we develop an unbiased discovery platform that can identify enhancers for a target gene without prior knowledge of their native functional context. We used tiled CRISPR activation (CRISPRa) to synthetically recruit transcription factors to sites across large genomic regions (>100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA (interleukin-2 receptor alpha; CD25). We identified several CRISPRa responsive elements (CaREs) with stimulation-dependent enhancer activity, including an IL2RA enhancer that harbors an autoimmunity risk variant. Using engineered mouse models and genome editing of human primary T cells, we found that sequence perturbation of the disease-associated IL2RA enhancer does not block IL2RA expression, but rather delays the timing of gene activation in response to specific extracellular signals. This work develops an approach to rapidly identify functional enhancers within non-coding regions, decodes a key human autoimmunity association, and suggests a general mechanism by which genetic variation can cause immune dysfunction.

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Comparing Genetic Variation within Red Winter Wheat Populations with and without Image-Based Optical Sorter Selection

Al-Qadisiyah Journal For Agriculture Sciences (QJAS) (P-ISSN 2077-5822 E-ISSN 2617-1479) ◽

10.33794/qjas.vol9.iss2.82 ◽

2019 ◽

Vol 9 (2) ◽

pp. 266-277

Author(s):

Hussein M. Khaeim ◽

Anthony Clark ◽

Tom Pearson ◽

Dr. David Van Sanford

Keyword(s):

Genetic Variation ◽

Fusarium Head Blight ◽

Heading Date ◽

Fusarium Head Blight Resistance ◽

Gibberella Zeae ◽

Mass Selection ◽

Head Blight ◽

Red Winter Wheat ◽

Two Populations ◽

Head Scab

Head scab is historically a devastating disease affecting not just all classes of wheat but also barley and other small grains around the world. Fusarium head blight (FHB), or head scab, is caused most often by Fusarium graminearum (Schwabe), (sexual stage – Gibberella zeae) although several Fusarium spp. can cause the disease. This study was conducted to determine the effect of mass selection for FHB resistance using an image-based optical sorter. lines were derived from the C0 and C2 of two populations to compare genetic variation within populations with and without sorter selection. Our overall hypothesis is that sorting grain results in improved Fusarium head blight resistance. Both of the used wheat derived line populations have genetic variation, and population 1 has more than population 17. They are significantly different from each other for fusarium damged kernel (FDK), deoxynivalenol (DON), and other FHB traits. Although both populations are suitable to be grown for bulks, population 1 seems better since it has more genetic variation as well as lower FDK and DON, and earlier heading date. Lines within each population were significantly different and some lines in each population had significantly lower FDK and DON after selection using an optical sorter. Some lines had significant reduction in both FDK and DON, and some others had either FDK or DON reduction. Lines of population 1 that had significant reduction, were more numerous than in population 17, and FDK and DON reduction were greater.

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Genetic variation in recombination rate in the pig

Genetics Selection Evolution ◽

10.1186/s12711-021-00643-0 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Martin Johnsson ◽

Andrew Whalen ◽

Roger Ros-Freixedes ◽

Gregor Gorjanc ◽

Ching-Yi Chen ◽

...

Keyword(s):

Genetic Variation ◽

Recombination Rate ◽

Large Scale ◽

Genome Wide Association Study ◽

Genetic Material ◽

A Genome ◽

Pig Genome ◽

Genetic Length ◽

Trait Locus ◽

Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

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VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections

Journal of Medical Microbiology ◽

10.1099/jmm.0.001457 ◽

2021 ◽

Vol 70 (12) ◽

Author(s):

Letícia T. Oliveira ◽

Lívia A. Alves ◽

Erika N. Harth-Chu ◽

Ryota Nomura ◽

Kazuhiko Nakano ◽

...

Keyword(s):

Streptococcus Mutans ◽

Type Species ◽

Virulence Gene ◽

Common Species ◽

Oral Microbiome ◽

Nucleotide Polymorphisms ◽

Content Type ◽

Virulence Gene Expression ◽

Coding Regions ◽

Link Type

Introduction. Streptococcus mutans , a common species of the oral microbiome, expresses virulence genes promoting cariogenic dental biofilms, persistence in the bloodstream and cardiovascular infections. Gap statement. Virulence gene expression is variable among S. mutans strains and controlled by the transcription regulatory systems VicRK and CovR. Aim. This study investigates polymorphisms in the vicRK and covR loci in S. mutans strains isolated from the oral cavity or from the bloodstream, which were shown to differ in expression of covR, vicRK and downstream genes. Methodology. The transcriptional activities of covR, vicR and vicK were compared by RT-qPCR between blood and oral strains after exposure to human serum. PCR-amplified promoter and/or coding regions of covR and vicRK of 18 strains (11 oral and 7 blood) were sequenced and compared to the reference strain UA159. Results. Serum exposure significantly reduced covR and vicR/K transcript levels in most strains (P<0.05), but reductions were higher in oral than in blood strains. Single-nucleotide polymorphisms (SNPs) were detected in covR regulatory and coding regions, but SNPs affecting the CovR effector domain were only present in two blood strains. Although vicR was highly conserved, vicK showed several SNPs, and SNPs affecting VicK regions important for autokinase activity were found in three blood strains. Conclusions. This study reveals transcriptional and structural diversity in covR and vicR/K, and identifies polymorphisms of functional relevance in blood strains, indicating that covR and vicRK might be important loci for S. mutans adaptation to host selective pressures associated with virulence diversity.

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Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

Australian Journal of Botany ◽

10.1071/bt11223 ◽

2012 ◽

Vol 60 (1) ◽

pp. 32 ◽

Cited By ~ 15

Author(s):

Laurence J. Clarke ◽

Duncan I. Jardine ◽

Margaret Byrne ◽

Kelly Shepherd ◽

Andrew J. Lowe

Keyword(s):

Genetic Variation ◽

New Species ◽

Genetic Structure ◽

Western Australia ◽

Sequence Data ◽

Isolation By Distance ◽

Conservation Strategies ◽

New Taxon ◽

Near Surface ◽

Two Populations

Atriplex sp. Yeelirrie Station (L. Trotter & A. Douglas LCH 25025) is a highly restricted, potentially new species of saltbush, known from only two sites ~30 km apart in central Western Australia. Knowledge of genetic structure within the species is required to inform conservation strategies as both populations occur within a palaeovalley that contains significant near-surface uranium mineralisation. We investigate the structure of genetic variation within populations and subpopulations of this taxon using nuclear microsatellites. Internal transcribed spacer sequence data places this new taxon within a clade of polyploid Atriplex species, and the maximum number of alleles per locus suggests it is hexaploid. The two populations possessed similar levels of genetic diversity, but exhibited a surprising level of genetic differentiation given their proximity. Significant isolation by distance over scales of less than 5 km suggests dispersal is highly restricted. In addition, the proportion of variation between the populations (12%) is similar to that among A. nummularia populations sampled at a continent-wide scale (several thousand kilometres), and only marginally less than that between distinct A. nummularia subspecies. Additional work is required to further clarify the exact taxonomic status of the two populations. We propose management recommendations for this potentially new species in light of its highly structured genetic variation.

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Genetic variation in fatty acid composition of subcutaneous fat in cattle

Animal Production Science ◽

10.1071/an12154 ◽

2013 ◽

Vol 53 (2) ◽

pp. 129 ◽

Cited By ~ 17

Author(s):

M. J. Kelly ◽

R. K. Tume ◽

S. Newman ◽

J. M. Thompson

Keyword(s):

Fatty Acids ◽

Genetic Variation ◽

Fatty Acid Composition ◽

Fatty Acid ◽

Acid Composition ◽

Saturated Fatty Acids ◽

Genetic Correlations ◽

Subcutaneous Fat ◽

Monounsaturated Fatty Acids ◽

Selection For

Genetic parameters were estimated for fatty acid composition of subcutaneous beef fat of 1573 animals which were the progeny of 157 sires across seven breeds grown out on pasture and then finished on either grain or grass in northern New South Wales or in central Queensland. There was genetic variation in individual fatty acids with estimates of heritability for the proportions of C14 : 0, C14 : 1c9, C16 : 0, C16 : 1c9, C18 : 0 and C18 : 1c9 fatty acids in subcutaneous beef fat of the order of 0.4 or above. Also substantial correlations between some fatty acids were observed. Genetic correlations between fatty acids and fat depth at the P8 site suggested that much of the genetic variation in fatty acid composition was related to changes in fatness. Selection for decreased fatness resulted in decreased proportions of C18 : 1c9 with concomitant increases in C18 : 0, C14 : 0 and C16 : 0. This suggested that selection for decreased fatness at a given weight will result in a decrease in the proportions of monounsaturated fatty acids in the subcutaneous fat in the carcass with a corresponding increase in the proportions of saturated fatty acids.

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Selection for Ethanol Tolerance in Two Populations of Drosophila Melanogaster Segregating Alcohol Dehydrogenase Allozymes

Australian Journal of Biological Sciences ◽

10.1071/bi9790387 ◽

1979 ◽

Vol 32 (3) ◽

pp. 387 ◽

Cited By ~ 36

Author(s):

John B Gibson ◽

NigeI Lewis ◽

MichaeI Adena ◽

Susan R Wilson

Keyword(s):

Drosophila Melanogaster ◽

Alcohol Dehydrogenase ◽

Ethanol Tolerance ◽

Selection For ◽

Two Populations

Selection for ethanol tolerance was equally successful in two populations of D. melanogaster in both of which the frequency of AdhF was 0�5 at the start of the experiment.

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