scholarly journals mSphere of Influence: the Wild Genetic Diversity of Our Closest Yeast Companions

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Douda Bensasson
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Natural Variation ◽  
Field Survey ◽  
Population Genomics ◽  
Yeast Species ◽  
Natural Environments ◽  
Population Genetic Analysis ◽  
Content Type ◽  
Wild Yeast

ABSTRACT Douda Bensasson uses the population genomics of model yeast species to understand how wild yeast colonize new environments, such as humans or their food. In this mSphere of Influence article, she reflects on how the discovery of “Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity” (Q.-M. Wang, W.-Q. Liu, G. Liti, S.-A. Wang, and F.-Y. Bai, Mol Ecol 21:5404–5417, 2012, https://doi.org/10.1111/j.1365-294X.2012.05732.x) showed that a field survey and population genetic analysis of old growth forests could “unveil the hidden part of the iceberg” of natural variation in S. cerevisiae that went unnoticed for over a hundred years of yeast research.

scholarly journals Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date

2021 ◽  
Author(s):  
F. J. Canales ◽  
G. Montilla-Bascón ◽  
W. A. Bekele ◽  
C. J. Howarth ◽  
T. Langdon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Large Scale ◽  
Population Genomics ◽  
Heading Date ◽  
Population Genetic Analysis ◽  
High Genetic Diversity ◽  
A Genome ◽  
Interactive Map

Key messageGenomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement.AbstractDuring the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.

scholarly journals First Complete Genome Sequence of a Distinct Papaya Ringspot Virus Isolate from the Northeastern Region of India

2018 ◽  
Vol 6 (22) ◽  
Author(s):  
Ritesh Mishra ◽  
Basavaprabhu L. Patil
Keyword(s):  
Nucleotide Sequence Identity ◽  
Population Genetic ◽  
Virus Isolate ◽  
Ringspot Virus ◽  
Papaya Ringspot Virus ◽  
Population Genetic Analysis ◽  
Content Type ◽  
Northeastern Region ◽  
Sequence Identity ◽  
French Isolate

ABSTRACT This is the first report of a Papaya ringspot virus (PRSV) isolate from the northeastern region of India. The nucleotide sequence identity of PRSV-Meghalaya was in the range of 72.6 to 82.5% with other Indian PRSV isolates, and the highest identity of 84.4% was with a French isolate. Population genetic analysis indicated positive selection.

scholarly journals Population genetic analysis ofGiardia duodenalis: genetic diversity and haplotype sharing between clinical and environmental sources

2017 ◽  
Vol 6 (2) ◽  
pp. e00424 ◽  
Author(s):  
Mauricio Durigan ◽  
Maisa Ciampi-Guillardi ◽  
Ricardo C. A. Rodrigues ◽  
Juliane A. Greinert-Goulart ◽  
Isabel C. V. Siqueira-Castro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Haplotype Sharing ◽  
Population Genetic Analysis

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

scholarly journals Population genetic analysis of Indian SARS-CoV-2 isolates reveals a unique phylogenetic cluster

2020 ◽  
Author(s):  
Dhruv Das ◽  
V.S.S.N.R Akkipeddi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Polymorphism ◽  
Population Genetic ◽  
Vaccine Development ◽  
Viral Population ◽  
Population Genetic Analysis ◽  
Phylogenetic Cluster ◽  
Indian Study ◽  
Novel Virus

AbstractThe SARS-CoV-2 pandemic originated from Wuhan, China in December 2019 raised an alarming situation all over the globe. Sequencing of this novel virus provides an opportunity to evaluate the genetic polymorphism present in the viral population. Herein, we analysed 173 sequences isolated from Indian patients and performed SNP linkage, clustering and phylogenetic analysis to understand the local genetic diversity. We found that the SNP linkages that lead to the identification of some global clades, do not hold true for the local clade classification. In addition to the unique cluster, established by another Indian study, we identified a new cluster (I-20D) that encompasses 28% of the analysed sequences. This cluster is defined by two linked variations – C22444T and C28854T. A detailed study of such polymorphisms can be useful for drug and vaccine development.

scholarly journals Potential Probiotic Yeasts Sourced from Natural Environmental and Spontaneous Processed Foods

Foods ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 287 ◽  
Author(s):  
Alice Agarbati ◽  
Laura Canonico ◽  
Enrica Marini ◽  
Emanuele Zannini ◽  
Maurizio Ciani ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Yeast Species ◽  
Food Choices ◽  
Natural Environments ◽  
Processed Foods ◽  
Wild Yeast ◽  
Yeast Strains ◽  
Probiotic Yeast ◽  
Future Direction ◽  
Yeast Isolation

In the last decades, there has been a growing interest from consumers in their food choices. Organic, natural, less processed, functional, and pre-probiotic products were preferred. Although, Saccharomyces cerevisiae var. boulardii is the most well-characterized probiotic yeast available on the market, improvement in probiotic function using other yeast species is an attractive future direction. In the present study, un-anthropized natural environments and spontaneous processed foods were exploited for wild yeast isolation with the goal of amplifying the knowledge of probiotic aptitudes of different yeast species. For this purpose, 179 yeast species were isolated, identified as belonging to twelve different genera, and characterized for the most important probiotic features. Findings showed interesting probiotic characteristics for some yeast strains belonging to Lachancea thermotolerans, Metschnikowia ziziphicola, Saccharomyces cerevisiae, and Torulaspora delbrueckii species, although these probiotic aptitudes were strictly strain-dependent. These yeast strains could be proposed for different probiotic applications, such as a valid alternative to, or in combination with, the probiotic yeast S. cerevisiae var. boulardii.

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