scholarly journals Composite Bacterial Hopanoids and Their Microbial Producers across Oxygen Gradients in the Water Column of the California Current

2013 ◽  
Vol 79 (23) ◽  
pp. 7491-7501 ◽  
Author(s):  
Jenan J. Kharbush ◽  
Juan A. Ugalde ◽  
Shane L. Hogle ◽  
Eric E. Allen ◽  
Lihini I. Aluwihare
Keyword(s):  
Genetic Diversity ◽  
Water Column ◽  
Genetic Relationships ◽  
Structural Diversity ◽  
Low Oxygen ◽  
Structural Variations ◽  
Data Set ◽  
Pentacyclic Triterpenoid ◽  
History Of ◽  
Membrane Components

ABSTRACTHopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greatersqhCgenetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential “hot spots” of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.

scholarly journals Anthropological Genetics Perspectives on the Transatlantic Slave Trade

2020 ◽  
Author(s):  
Cesar Fortes-Lima ◽  
Paul Verdu
Keyword(s):  
Genetic Diversity ◽  
Native American ◽  
Cultural Landscape ◽  
Slave Trade ◽  
Genetic Relationships ◽  
Anthropological Genetics ◽  
15Th Century ◽  
African Descendants ◽  
Genome Wide Data ◽  
History Of

Abstract During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950’s mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socio-economic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.

scholarly journals Genetic structure and differentiation in cultivated grape, Vitis vinifera L.

2003 ◽  
Vol 81 (3) ◽  
pp. 179-192 ◽  
Author(s):  
MALLIKARJUNA K. ARADHYA ◽  
GERALD S. DANGL ◽  
BERNARD H. PRINS ◽  
JEAN-MICHEL BOURSIQUOT ◽  
M. ANDREW WALKER ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Vitis Vinifera ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Vitis Vinifera L ◽  
Significant Heterogeneity ◽  
Multivariate Relationships ◽  
History Of ◽  
Single Complex ◽  
Grape Cultivars

222 cultivated (Vitis vinifera) and 22 wild (V. vinifera ssp. sylvestris) grape accessions were analysed for genetic diversity and differentiation at eight microsatellite loci. A total of 94 alleles were detected, with extensive polymorphism among the accessions. Multivariate relationships among accessions revealed 16 genetic groups structured into three clusters, supporting the classical eco-geographic grouping of grape cultivars: occidentalis, pontica and orientalis. French cultivars appeared to be distinct and showed close affinity to the wild progenitor, ssp. sylvestris from south-western France (Pyrenees) and Tunisia, probably reflecting the origin and domestication history of many of the old wine cultivars from France. There was appreciable level of differentiation between table and wine grape cultivars, and the Muscat types were somewhat distinct within the wine grapes. Contingency χ2 analysis indicated significant heterogeneity in allele frequencies among groups at all loci. The observed heterozygosities for different groups ranged from 0·625 to 0·9 with an overall average of 0·771. Genetic relationships among groups suggested hierarchical differentiation within cultivated grape. The gene diversity analysis indicated narrow divergence among groups and that most variation was found within groups (∼85%). Partitioning of diversity suggested that the remaining variation is somewhat structured hierarchically at different levels of differentiation. The overall organization of genetic diversity suggests that the germplasm of cultivated grape represents a single complex gene pool and that its structure is determined by strong artificial selection and a vegetative mode of reproduction.

scholarly journals Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward W. Davis ◽  
Javier F. Tabima ◽  
Alexandra J. Weisberg ◽  
Lucas Dantas Lopes ◽  
Michele S. Wiseman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Immune System ◽  
The United States ◽  
Genomic Diversity ◽  
Data Set ◽  
Important Species ◽  
Content Type ◽  
Low Genetic Diversity ◽  
History Of ◽  
Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

scholarly journals Worldwide phylogeography and history of wheat genetic diversity

2019 ◽  
Vol 5 (5) ◽  
pp. eaav0536 ◽  
Author(s):  
François Balfourier ◽  
Sophie Bouchet ◽  
Sandra Robert ◽  
Romain De Oliveira ◽  
Hélène Rimbert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism Array ◽  
Human Migration ◽  
Structural Variations ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Allele Distribution ◽  
Fertile Crescent ◽  
History Of ◽  
New Alleles

Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.

Genetic diversity of Asian and European common wheat lines assessed by fluorescence in situ hybridization

Genome ◽  
2021 ◽  
Author(s):  
Xiu Yang ◽  
Binwen Tan ◽  
Yulu Yang ◽  
Xiaohui Zhang ◽  
Wei Zhu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Common Wheat ◽  
Genetic Relationships ◽  
Structural Variations ◽  
D Genome ◽  
Western Asia ◽  
Wheat Lines

Understanding the genetic diversity of wheat is important for wheat breeding and improvement. However, there have been limited attempts to evaluate wheat diversity using fluorescence in situ hybridization (FISH). In this study, the chromosomal structures of 149 wheat accessions from 13 countries located between the latitudes of 30° and 45°N, the principal growing region for wheat, were characterized using FISH with pTa535 and pSc119.2 probes. The ranges of the numbers of FISH types in the A-, B-, and D-genomes were 2–8, 3–7, and 2–4, respectively, and the average numbers in the A- and B-genomes were greater than in the D-genome. Chromosomal translocations were detected by these probes, and previously undescribed translocations were also observed. Using the FISH, the genetic relationships among the 149 common wheat lines were divided into three groups (G1, G2, and G3). G1 mainly consisted of Southern European lines, G2 consisted of most lines from Japan and some lines from Western Asia, China, and Korea, and G3 consisted of the other lines from Southern Europe and most of the lines from Western Asia, China, and Korea. FISH karyotypes of wheat chromosomes distinguished chromosomal structural variations, revealed the genetic diversity among wheat varieties. Furthermore, these results provide valuable information for the further genetic improvement of wheat in China.

scholarly journals Worldwide phylogeography and history of wheat genetic diversity

2018 ◽  
Author(s):  
François Balfourier ◽  
Sophie Bouchet ◽  
Sandra Robert ◽  
Romain De Oliveira ◽  
Hélène Rimbert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Snp Array ◽  
Wild Relatives ◽  
Human Migration ◽  
Structural Variations ◽  
Breeding Programs ◽  
Allele Distribution ◽  
Fertile Crescent ◽  
History Of ◽  
New Alleles

AbstractSince its domestication in the Fertile Crescent ~8,000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4,506 landraces and cultivars originating from 105 different countries genotyped with a high-density SNP array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the apparition of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960.One Sentence SummaryA phylogeographical study reveals the complex history of wheat genetic diversity through time and space.

scholarly journals The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

2021 ◽  
Vol 7 (17) ◽  
pp. eabf6106
Author(s):  
Weiwei He ◽  
Yen-Lin Chen ◽  
Lois Pollack ◽  
Serdal Kirmizialtin
Keyword(s):  
Structural Diversity ◽  
Conformational Ensemble ◽  
Structural Variations ◽  
Dna And Rna ◽  
X Ray Scattering ◽  
Double Stranded Dna ◽  
Binding Partners ◽  
Rna Duplexes ◽  
Dynamics Simulations ◽  
Integrate Solution

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

Economics of respiratory disease in dairy replacement heifers

2020 ◽  
Vol 21 (2) ◽  
pp. 143-148
Author(s):  
Michael W. Overton
Keyword(s):  
Respiratory Disease ◽  
Milk Production ◽  
Incident Case ◽  
Data Set ◽  
Dairy Heifers ◽  
The Usa ◽  
History Of ◽  
On Farm ◽  
The Impact ◽  
Selective Culling

AbstractBovine respiratory disease (BRD) is a frequent disease concern in dairy cattle and is most commonly diagnosed in young dairy heifers. The impact of BRD is highly variable, depending on the accuracy and completeness of detection, effectiveness of treatment, and on-farm culling practices. Consequences include decreased rate of weight gain, a higher culling risk either as heifers or as cows, delayed age at first service, delayed age at first calving, and in some cases, lower future milk production. In this data set of 104,100 dairy replacement heifers from across the USA, 36.6% had one or more cases diagnosed within the first 120 days of age with the highest risk of new cases occurring prior to weaning. Comparison of the raising cost for heifers with BRD and those without a recorded history of BRD resulted in an estimated cost per incident case occurring in the first 120 days of age of $252 or $282, depending upon whether anticipated future milk production differences were considered or not. Current market conditions contributed to a cost estimate that is significantly higher than previously published estimates, driven in part by the losses associated with selective culling of a subset of heifers that experienced BRD.

scholarly journals Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Sierra Leone ◽  
Evolutionary History ◽  
Molecular Diversity ◽  
Genomic Data ◽  
Gene Recombination ◽  
Necrosis Virus ◽  
History Of ◽  
Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital

2021 ◽  
Author(s):  
Michael Brilhante ◽  
Stefanie Gobeli Brawand ◽  
Andrea Endimiani ◽  
Helene Rohrbach ◽  
Sonja Kittl ◽  
...  
Keyword(s):  
High Risk ◽  
Klebsiella Pneumoniae ◽  
Genetic Relationships ◽  
Clinical Environment ◽  
Structural Variations ◽  
Veterinary Clinic ◽  
Antimicrobial Resistance Genes ◽  
Carbapenemase Gene ◽  
Genetic Features ◽  
Almost All

Abstract Objectives Infections with carbapenem-resistant Enterobacterales (CRE) are an emerging problem in pets and a major threat to public health. We determined the genetic relationships among carbapenemase-producing Klebsiella pneumoniae (CPKp) strains causing infections in hospitalized pets in a veterinary clinic and those found in the environment. Methods WGS was performed with both the Illumina and Nanopore platforms. Searches of genetic features were performed using several databases and bioinformatics tools, and phylogeny was assessed by whole-genome MLST (wgMLST) using SeqSphere and SNP calling with Snippy. Results WGS analysis of the CPKp strains identified all environmental and almost all animal strains as the high-risk clone ST11, with the exception of two strains that belonged to ST307. All CPKp belonged to novel complex types (CTs) and carried a conjugative 63 kb IncL plasmid encoding the carbapenemase gene blaOXA-48, yersiniabactin and other virulence factors. Although all CPKp ST11 strains carried additional similar IncR plasmids harbouring multiple antimicrobial resistance genes (ARGs), such as the plasmid-mediated blaDHA-1 AmpC gene, some structural variations were observed. The two ST307 strains carried identical 156 kb MDR IncFIB(K) plasmids with several ARGs, including the blaCTX-M-15 ESBL gene. Both wgMLST and cgSNP analysis confirmed that CPKp strains of the same ST were genetically highly related independent of the source of isolation. Conclusions This study demonstrated that the clinical CPKp strains were highly related to those contaminating the clinical environment. These findings confirmed nosocomial spread and highlight veterinary hospitals as a source of CPKp, which may further spread to animals, the environment and humans.

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