Extensive genome-wide duplications in the eastern oyster (
            Crassostrea virginica
            )

Genomic structural variation is an important source of genetic and phenotypic diversity, playing a critical role in evolution. The recent availability of a high-quality reference genome for the eastern oyster, Crassostrea virginica , and whole-genome sequence data of samples from across the species range in the USA, provides an opportunity to explore structural variation across the genome of this species. Our analysis shows significantly greater individual-level duplications of regions across the genome than that of most model vertebrate species. Duplications are widespread across all ten chromosomes with variation in frequency per chromosome. The eastern oyster shows a large interindividual variation in duplications as well as particular chromosomal regions with a higher density of duplications. A high percentage of duplications seen in C. virginica lie completely within genes and exons, suggesting the potential for impacts on gene function. These results support the hypothesis that structural changes may play a significant role in standing genetic variation in C. virginica , and potentially have a role in their adaptive and evolutionary success. Altogether, these results suggest that copy number variation plays an important role in the genomic variation of C. virginica . This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

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Identification of misclassified ClinVar variants using disease population prevalence

10.1101/075416 ◽

2016 ◽

Cited By ~ 4

Author(s):

Naisha Shah ◽

Ying-Chen Claire Hou ◽

Hung-Chun Yu ◽

Rachana Sainger ◽

Eric Dec ◽

...

Keyword(s):

Genetic Risk ◽

Rare Variants ◽

Sequence Data ◽

Critical Role ◽

Significant Proportion ◽

Whole Genome Sequence ◽

Supporting Evidence ◽

Level Of Evidence ◽

Population Prevalence

ABSTRACTThere is a significant interest in the standardized classification of human genetic variants. The availability of new large datasets generated through genome sequencing initiatives provides a ground for the computational evaluation of the supporting evidence. We used whole genome sequence data from 8,102 unrelated individuals to analyze the adequacy of estimated rates of disease on the basis of genetic risk and the expected population prevalence of the disease. Analyses included the ACMG recommended 56 gene-condition sets for incidental findings and 631 genes associated with 348 OrphaNet conditions. A total of 21,004 variants were used to identify patterns of inflation (i.e. excess genetic risk). Inflation, i.e., misclassification, increases as the level of evidence in ClinVar supporting the pathogenic nature of the variant decreases. The burden of rare variants was a main contributing factor of the observed inflation indicating misclassified benign private mutations. We also analyzed the dynamics of re-classification of variant pathogenicity in ClinVar over time. The study strongly suggests that ClinVar includes a significant proportion of wrongly ascertained variants, and underscores the critical role of ClinVar to contrast claims, and foster validation across submitters.

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Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.1441 ◽

2021 ◽

Vol 288 (1961) ◽

Author(s):

Anna Brüniche-Olsen ◽

Kenneth F. Kellner ◽

Jerrold L. Belant ◽

J. Andrew DeWoody

Keyword(s):

Life History ◽

Life History Traits ◽

Management Practices ◽

Sequence Data ◽

Extinction Risk ◽

Conservation Status ◽

Genomic Variation ◽

Genomic Diversity ◽

Whole Genome Sequence ◽

Habitat Availability

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes ( N e ) and current genomic variability ( H ), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that N e and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.

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Diverse endogenous retroviruses generate structural variation between human genomes via LTR recombination

10.1101/382630 ◽

2018 ◽

Cited By ~ 1

Author(s):

Jainy Thomas ◽

Hervé Perron ◽

Cédric Feschotte

Keyword(s):

Structural Variation ◽

Genomic Variation ◽

Endogenous Retroviruses ◽

Interindividual Variation ◽

Sequencing Data ◽

Long Terminal Repeats ◽

Substantial Fraction ◽

Human Endogenous Retroviruses ◽

Solo Ltrs ◽

Human Genomes

ABSTRACTHuman endogenous retroviruses (HERVs) occupy a substantial fraction of the genome and impact cellular function with both beneficial and deleterious consequences. The vast majority of HERV sequences descend from ancient retroviral families no longer capable of infection or genomic propagation. In fact, most are no longer represented by full-length proviruses but by solitary long terminal repeats (solo LTRs) that arose via non-allelic recombination events between the two LTRs of a proviral insertion. Because LTR-LTR recombination events may occur long after proviral insertion but are challenging to detect in resequencing data, we hypothesize that this mechanism produces an underappreciated amount of genomic variation in the human population. To test this idea, we develop a computational pipeline specifically designed to capture such dimorphic HERV alleles from short-read genome sequencing data. When applied to 279 individuals sequenced as part of the Simons Genome Diversity Project, the pipeline retrieves most of the dimorphic variants previously reported for the HERV-K(HML2) subfamily as well as dozens of additional candidates, including members of the HERV-H and HERV-W families. We experimentally validate several of these candidates, including the first reported instance of an unfixed HERV-W provirus. These data indicate that human proviral content exhibit more extensive interindividual variation than previously recognized. These findings have important implications for our understanding of the contribution of HERVs to human physiology and disease.

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Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2025453118 ◽

2021 ◽

Vol 118 (15) ◽

pp. e2025453118

Author(s):

Malin L. Pinsky ◽

Anne Maria Eikeset ◽

Cecilia Helmerson ◽

Ian R. Bradbury ◽

Paul Bentzen ◽

...

Keyword(s):

Atlantic Cod ◽

Sequence Data ◽

Genomic Variation ◽

Whole Genome Sequence ◽

Phenotypic Change ◽

Rapid Decline ◽

Effective Population ◽

Genomic Change ◽

Early 21St Century ◽

Intensive Exploitation

The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

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Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

eLife ◽

10.7554/elife.26255 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 40

Author(s):

John A Lees ◽

Nicholas J Croucher ◽

David Goldblatt ◽

François Nosten ◽

Julian Parkhill ◽

...

Keyword(s):

Low Income ◽

Genome Wide Association Study ◽

Sequence Data ◽

Theoretical Models ◽

Invasive Disease ◽

Genomic Variation ◽

Whole Genome Sequence ◽

Pneumococcal Carriage ◽

Genome Wide ◽

Significant Locus

Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.

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Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

10.1101/107086 ◽

2017 ◽

Cited By ~ 1

Author(s):

John A. Lees ◽

Nicholas J. Croucher ◽

Goldblatt David ◽

Nosten Francois ◽

Parkhill Julian ◽

...

Keyword(s):

Environmental Factors ◽

Low Income ◽

Genome Wide Association Study ◽

Sequence Data ◽

Genomic Variation ◽

Whole Genome Sequence ◽

Vaccine Response ◽

Pneumococcal Carriage ◽

Genome Wide ◽

A Genome

AbstractStreptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, and the duration of carriage is an important consideration in modelling transmission dynamics and vaccine response. Existing studies of carriage duration variability are based at the serotype level only, and do not probe variation within lineages or fully quantify interactions with other environmental factors.Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data. By combining these results with whole genome sequence data we estimate that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas host traits accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). For the locus effects, a genome-wide association study identified 16 loci which may have an effect on carriage duration independent of serotype. Hits at a genome-wide level of significance were to prophage sequences, suggesting infection by such viruses substantially affects carriage duration.These results show that both serotype and non-serotype specific effects alter carriage duration in infants and young children and are more important than other environmental factors such as host genetics. This has implications for models of pneumococcal competition and antibiotic resistance, and leads the way for the analysis of heritability of complex bacterial traits.Significance statementOther than serotype, the genetic determinants of pneumococcal carriage duration are unknown. In this study we used longitudinal sampling to measure the duration of carriage in infants, and searched for any associated variation in the pan-genome. While we found that the pathogen genome explains most of the variability in duration, serotype did not fully account for this. Recent theoretical work has proposed the existence of alleles which alter carriage duration to explain the puzzle of continued coexistence of antibiotic-resistant and sensitive strains. Here we have shown that these alleles do exist in a natural population, and also identified candidates for the loci which fulfil this role. Together these findings have implications for future modelling of pneumococcal epidemiology and resistance.

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An atomic resolution study of a carbide phase in platinum

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100120503 ◽

1992 ◽

Vol 50 (1) ◽

pp. 20-21

Author(s):

M.J. Witcomb ◽

M.A. O'Keefe ◽

CJ. Echer ◽

C. Nelson ◽

J.H. Turner ◽

...

Keyword(s):

Solid Solution ◽

Carbon Atom ◽

Carbide Phase ◽

Structural Changes ◽

Critical Role ◽

Alloy System ◽

Atomic Resolution ◽

Excess Carbon ◽

Interstitial Carbon ◽

Resolution Study

Under normal circumstances, Pt dissolves only a very small amount of interstitial carbon in solid solution. Even so, an appropriate quench/age treatment leads to the formation of stable Pt2C {100} plate precipitates. Excess (quenched-in) vacancies play a critical role in the process by accommodating the volume and structural changes that accompany the transformation. This alloy system exhibits other interesting properties. Due to a large vacancy/carbon atom binding energy, Pt can absorb excess carbon at high temperatures in a carburizing atmosphere. In regions rich in carbon and vacancies, another carbide phase, Pt7C which undergoes an order-disorder reaction was formed. The present study of Pt carburized at 1160°C and aged at 515°C shows that other carbides in the PtxC series can be produced.

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Effects of resuspension of eastern oyster Crassostrea virginica biodeposits on phytoplankton community structure

Marine Ecology Progress Series ◽

10.3354/meps13277 ◽

2020 ◽

Vol 640 ◽

pp. 79-105

Author(s):

ET Porter ◽

E Robins ◽

S Davis ◽

R Lacouture ◽

JC Cornwell

Keyword(s):

Water Quality ◽

Community Structure ◽

Crassostrea Virginica ◽

Skeletonema Costatum ◽

Eastern Oyster ◽

Energy Dissipation Rate ◽

Negative Effects ◽

Cell Densities ◽

Sediment Bottom ◽

Nitrite Nitrate

Anthropogenic disturbances in the Chesapeake Bay (USA) have depleted eastern oyster Crassostrea virginica abundance and altered the estuary’s environment and water quality. Efforts to rehabilitate oyster populations are underway; however, the effect of oyster biodeposits on water quality and plankton community structure are not clear. In July 2017, we used 6 shear turbulence resuspension mesocosms (STURMs) to determine differences in plankton composition with and without the daily addition of oyster biodeposits to a muddy sediment bottom. STURM systems had a volume-weighted root mean square turbulent velocity of 1.08 cm s-1, energy dissipation rate of ~0.08 cm2 s-3, and bottom shear stress of ~0.36-0.51 Pa during mixing-on periods during 4 wk of tidal resuspension. Phytoplankton increased their chlorophyll a content in their cells in response to low light in tanks with biodeposits. The diatom Skeletonema costatum bloomed and had significantly longer chains in tanks without biodeposits. These tanks also had significantly lower concentrations of total suspended solids, zooplankton carbon, and nitrite +nitrate, and higher phytoplankton carbon concentrations. Results suggest that the absence of biodeposit resuspension initiates nitrogen uptake for diatom reproduction, increasing the cell densities of S. costatum. The low abundance of the zooplankton population in non-biodeposit tanks suggests an inability of zooplankton to graze on S. costatum and negative effects of S. costatum on zooplankton. A high abundance of the copepod Acartia tonsa in biodeposit tanks may have reduced S. costatum chain length. Oyster biodeposit addition and resuspension efficiently transferred phytoplankton carbon to zooplankton carbon, thus supporting the food web in the estuary.

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