Are Shell Strength Phenotypic Traits in Mussels Associated with Species Alone?

Mussels often hybridise to form the Mytilus species complex comprised of M. edulis and M. galloprovincialis as the main species cultivated in Europe and, where their geographical distribution overlaps, the species M. trossulus. It has been suggested that M. trossulus have a weaker shell than the UK native M. edulis and hybridisation reduces farmed mussel yields and overall fitness. Here, we investigate the hypothesised link between species and shell weakness, employing multi-locus genotyping combined with measurements of six different phenotypes indicative of shell strength (shell thickness, flexural strength, Young’s modulus, Vicker’s hardness, fracture toughness, calcite and aragonite crystallographic orientation). Historic evidence from shell strength studies assumed species designation based on geographical origin, single locus DNA marker or allozyme genetic techniques that are limited in their ability to discern hybrid individuals. Single nucleotide polymorphic markers have now been developed with the ability to better distinguish between the species of the complex and their hybrids. Our study indicates that shell strength phenotypic traits are less associated with species than previously thought. The application of techniques outlined in this study challenges the historic influence of M. trossulus hybridisation on mussel yields and opens up potential for the environment to determine mussel shell fitness.

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Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

Plants ◽

10.3390/plants10040656 ◽

2021 ◽

Vol 10 (4) ◽

pp. 656

Author(s):

Evangelia Stavridou ◽

Georgios Lagiotis ◽

Parthena Kalaitzidou ◽

Ioannis Grigoriadis ◽

Irini Bosmali ◽

...

Keyword(s):

Ssr Markers ◽

Geographical Origin ◽

Expressed Sequence Tag ◽

Phenotypic Diversity ◽

Molecular Data ◽

Phenotypic Traits ◽

Dissimilarity Matrix ◽

Heterotic Groups ◽

Hrm Analysis ◽

Sesame Genotypes

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

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Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections

Microorganisms ◽

10.3390/microorganisms9071416 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1416

Author(s):

Karen Leth Nielsen ◽

Marc Stegger ◽

Kristoffer Kiil ◽

Berit Lilje ◽

Karen Ejrnæs ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract ◽

Urinary Tract Infections ◽

Genomic Variation ◽

Whole Genome Sequencing Data ◽

Phenotypic Traits ◽

Recurrent Infections ◽

Single Nucleotide ◽

Recurrent Urinary Tract Infections ◽

Tract Infections

Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.

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Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Biomedicines ◽

10.3390/biomedicines9070808 ◽

2021 ◽

Vol 9 (7) ◽

pp. 808

Author(s):

Laura Pérez-Lago ◽

Teresa Aldámiz-Echevarría ◽

Rita García-Martínez ◽

Leire Pérez-Latorre ◽

Marta Herranz ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Evolutionary Dynamics ◽

Viral Evolution ◽

Special Focus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

New Variant ◽

History Of ◽

Evolution Dynamics ◽

The Uk

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

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Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Animals ◽

10.3390/ani11061510 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1510

Author(s):

Salvatore Mastrangelo ◽

Rosalia Di Gerlando ◽

Maria Teresa Sardina ◽

Anna Maria Sutera ◽

Angelo Moscarelli ◽

...

Keyword(s):

Conservation Status ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Local Populations ◽

Genomic Technologies ◽

Fitness Traits ◽

Genome Wide ◽

Breeding Schemes ◽

Genomic Inbreeding

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

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Detection of a single nucleotide polymorphism (SNP) DNA marker linked to cocoon traits in the mulberry silkworm, Bombyx mori (Lepidoptera: Bombycidae)

European Journal of Entomology ◽

10.14411/eje.2011.043 ◽

2011 ◽

Vol 108 (3) ◽

pp. 347-354 ◽

Cited By ~ 3

Author(s):

Sivaramakurup SREEKUMAR ◽

Southekal K. ASHWATH ◽

Monika SLATHIA ◽

Sundaramurthy N. KUMAR ◽

Syed M.H. QADRI

Keyword(s):

Single Nucleotide Polymorphism ◽

Bombyx Mori ◽

Dna Marker ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Mulberry Silkworm ◽

Silkworm Bombyx Mori

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Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows

10.1101/2020.07.24.220582 ◽

2020 ◽

Cited By ~ 1

Author(s):

Dan Sun ◽

Thomas S. Layman ◽

Hyeonsoo Jeong ◽

Paramita Chatterjee ◽

Kathleen Grogan ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Chromosome Pair ◽

Dna Methyltransferases ◽

Model Organisms ◽

Phenotypic Traits ◽

Zonotrichia Albicollis ◽

Single Nucleotide ◽

Genome Wide ◽

Nucleotide Resolution

ABSTRACTDNA methylation is known to play critical roles in key biological processes. Most of our knowledge on regulatory impacts of DNA methylation has come from laboratory-bred model organisms, which may not exhibit the full extent of variation found in wild populations. Here, we investigated naturally-occurring variation in DNA methylation in a wild avian species, the white-throated sparrow (Zonotrichia albicollis). This species offers exceptional opportunities for studying the link between genetic differentiation and phenotypic traits because of a non-recombining chromosome pair linked to both plumage and behavioral phenotypes. Using novel single-nucleotide resolution methylation maps and gene expression data, we show that DNA methylation and the expression of DNA methyltransferases are significantly higher in adults than in nestlings. Genes for which DNA methylation varied between nestlings and adults were implicated in development and cell differentiation and were located throughout the genome. In contrast, differential methylation between plumage morphs was localized to the non-recombining chromosome pair. One subset of CpGs on the non-recombining chromosome was extremely hypomethylated and localized to transposable elements. Changes in methylation predicted changes in gene expression for both chromosomes. In summary, we demonstrate changes in genome-wide DNA methylation that are associated with development and with specific functional categories of genes in white-throated sparrows. Moreover, we observe substantial DNA methylation reprogramming associated with the suppression of recombination, with implications for genome integrity and gene expression divergence. These results offer an unprecedented view of ongoing epigenetic reprogramming in a wild population.

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Reproducibility in the UK Biobank of Genome-Wide Significant Signals Discovered in Earlier Genome-wide Association Studies

10.1101/2020.06.24.20139576 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jack W. O’Sullivan ◽

John P. A. Ioannidis

Keyword(s):

Effect Size ◽

Association Studies ◽

Genome Wide Association ◽

P Value ◽

Genome Wide Association Studies ◽

Uk Biobank ◽

Single Nucleotide ◽

Genome Wide ◽

The Uk ◽

Open Question

AbstractWith the establishment of large biobanks, discovery of single nucleotide polymorphism (SNPs) that are associated with various phenotypes has been accelerated. An open question is whether SNPs identified with genome-wide significance in earlier genome-wide association studies (GWAS) are replicated also in later GWAS conducted in biobanks. To address this question, the authors examined a publicly available GWAS database and identified two, independent GWAS on the same phenotype (an earlier, “discovery” GWAS and a later, replication GWAS done in the UK biobank). The analysis evaluated 136,318,924 SNPs (of which 6,289 had reached p<5e-8 in the discovery GWAS) from 4,397,962 participants across nine phenotypes. The overall replication rate was 85.0% and it was lower for binary than for quantitative phenotypes (58.1% versus 94.8% respectively). There was a18.0% decrease in SNP effect size for binary phenotypes, but a 12.0% increase for quantitative phenotypes. Using the discovery SNP effect size, phenotype trait (binary or quantitative), and discovery p-value, we built and validated a model that predicted SNP replication with area under the Receiver Operator Curve = 0.90. While non-replication may often reflect lack of power rather than genuine false-positive findings, these results provide insights about which discovered associations are likely to be seen again across subsequent GWAS.

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Lifestyle factors and genetic variants on two biological age measures: evidence from 94,443 Taiwan Biobank participants

The Journals of Gerontology Series A ◽

10.1093/gerona/glab251 ◽

2021 ◽

Author(s):

Wan-Yu Lin

Keyword(s):

Genetic Variants ◽

Genome Wide Association Study ◽

Lifestyle Factors ◽

Biological Age ◽

Biological Aging ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

A Genome ◽

The Uk

Abstract Background Biological age (BA) can be estimated by phenotypes and is useful for predicting lifespan and healthspan. Levine et al. proposed a PhenoAge and a BioAge to measure BA. Although there have been studies investigating the genetic predisposition to BA acceleration in Europeans, little has been known regarding this topic in Asians. Methods I here estimated PhenoAgeAccel (age-adjusted PhenoAge) and BioAgeAccel (age-adjusted BioAge) of 94,443 Taiwan Biobank (TWB) participants, wherein 25,460 TWB1 subjects formed a discovery cohort and 68,983 TWB2 individuals constructed a replication cohort. Lifestyle factors and genetic variants associated with PhenoAgeAccel and BioAgeAccel were investigated through regression analysis and a genome-wide association study (GWAS). Results A unit (kg/m 2) increase of BMI was associated with a 0.177-year PhenoAgeAccel (95% C.I. = 0.163~0.191, p = 6.0×) and 0.171-year BioAgeAccel (95% C.I. = 0.165~0.177, p = 0). Smokers on average had a 1.134-year PhenoAgeAccel (95% C.I. = 0.966~1.303, p = 1.3×) compared with non-smokers. Drinkers on average had a 0.640-year PhenoAgeAccel (95% C.I. = 0.433~0.847, p = 1.3×) and 0.193-year BioAgeAccel (95% C.I. = 0.107~0.279, p = 1.1×) relative to non-drinkers. A total of 11 and 4 single-nucleotide polymorphisms (SNPs) were associated with PhenoAgeAccel and BioAgeAccel (p<5× in both TWB1 and TWB2), respectively. Conclusions A PhenoAgeAccel-associated SNP (rs1260326 in GCKR) and two BioAgeAccel-associated SNPs (rs7412 in APOE; rs16998073 near FGF5) were consistent with the finding from the UK Biobank. The lifestyle analysis shows that prevention from obesity, cigarette smoking, and alcohol consumption is associated with a slower rate of biological aging.

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Equid alphaherpesvirus 1 from Italian Horses: Evaluation of the Variability of the ORF30, ORF33, ORF34 and ORF68 Genes

Viruses ◽

10.3390/v11090851 ◽

2019 ◽

Vol 11 (9) ◽

pp. 851 ◽

Cited By ~ 1

Author(s):

Preziuso ◽

Sgorbini ◽

Marmorini ◽

Cuteri

Keyword(s):

Nested Pcr ◽

Economic Losses ◽

Single Nucleotide ◽

Diagnostic Pcr ◽

History Of ◽

Conserved Region ◽

The Uk

Equid alphaherpesvirus 1 (EHV-1) is an important pathogen of horses. It is spread worldwide and causes significant economic losses. The ORF33 gene has a conserved region that is often used as target in diagnostic PCR protocols. Single nucleotide point (SNP) mutations in ORF30 are usually used to distinguish between neuropathogenic and non-neuropathogenic genotypes. An ORF68 SNP-based scheme has been used for grouping different isolates. Recently, the highest number of variable sites in EHV-1 from the UK has been found in ORF34. In this study, EHV-1 positive samples from Italian horses with a history of abortion were investigated by amplifying and sequencing the ORF30, ORF33, ORF34 and ORF68 genes. Most animals were infected by the neuropathogenic type A2254G. A 118 bp deletion was found at nucleotide positions 701–818 of the ORF68 gene, making impossible to assign the samples to a known group. Sequencing of the ORF34 gene with a newly designed nested PCR showed new SNPs. Analysis of these sequences and of those obtained from genetic databases allowed the identification of at least 12 groups. These data add depth to the knowledge of EHV-1 genotypes circulating in Italy.

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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Nature Communications ◽

10.1038/s41467-019-11581-3 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 24

Author(s):

Hongzhong Lu ◽

Feiran Li ◽

Benjamín J. Sánchez ◽

Zhengming Zhu ◽

Gang Li ◽

...

Keyword(s):

Model Organism ◽

Metabolic Model ◽

Phenotypic Traits ◽

Cell Factory ◽

Scale Level ◽

Single Nucleotide ◽

Multi Scale ◽

Yeast Strains ◽

Single Nucleotide Variations ◽

Genome Scale

Abstract Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae––an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.

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