scholarly journals New insights into homoeologous copy number variations in the hexaploid wheat genome

2020 ◽  
Author(s):  
Caroline Juery ◽  
Lorenzo Concia ◽  
Romain De Oliveira ◽  
Nathan Papon ◽  
Ricardo Ramírez-González ◽  
...  
Keyword(s):  
Hexaploid Wheat ◽  
Core Genome ◽  
Diploid Species ◽  
Housekeeping Genes ◽  
Copy Number Variations ◽  
List Type ◽  
The Core ◽  
History Of ◽  
Function Expression ◽  
Dispensable Genome

AbstractBread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.Core ideasOnly one half of hexaploid wheat genes are in triads, i.e. in a 1:1:1 ratio across subgenomesTriads are likely part of the core genome; dyads and tetrads belong to the dispensable genomeSubgenome dominance and biased fractionation are absent in hexaploid wheatSubgenome differences are related to two successive waves of post-polyploid diploidization

scholarly journals Evolution of the Core Genome of Pseudomonas syringae, a Highly Clonal, Endemic Plant Pathogen

2004 ◽  
Vol 70 (4) ◽  
pp. 1999-2012 ◽  
Author(s):  
Sara F. Sarkar ◽  
David S. Guttman
Keyword(s):  
Genetic Variation ◽  
Pseudomonas Syringae ◽  
Core Genome ◽  
Demographic History ◽  
Housekeeping Genes ◽  
The United States ◽  
Plant Diseases ◽  
Endemic Plant ◽  
Host Association ◽  
The Core

ABSTRACT Pseudomonas syringae is a common foliar bacterium responsible for many important plant diseases. We studied the population structure and dynamics of the core genome of P. syringae via multilocus sequencing typing (MLST) of 60 strains, representing 21 pathovars and 2 nonpathogens, isolated from a variety of plant hosts. Seven housekeeping genes, dispersed around the P. syringae genome, were sequenced to obtain 400 to 500 nucleotides per gene. Forty unique sequence types were identified, with most strains falling into one of four major clades. Phylogenetic and maximum-likelihood analyses revealed a remarkable degree of congruence among the seven genes, indicating a common evolutionary history for the seven loci. MLST and population genetic analyses also found a very low level of recombination. Overall, mutation was found to be approximately four times more likely than recombination to change any single nucleotide. A skyline plot was used to study the demographic history of P. syringae. The species was found to have maintained a constant population size over time. Strains were also found to remain genetically homogeneous over many years, and when isolated from sites as widespread as the United States and Japan. An analysis of molecular variance found that host association explains only a small proportion of the total genetic variation in the sample. These analyses reveal that with respect to the core genome, P. syringae is a highly clonal and stable species that is endemic within plant populations, yet the genetic variation seen in these genes only weakly predicts host association.

scholarly journals Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential

2020 ◽  
Vol 21 (9) ◽  
pp. 3393
Author(s):  
Mengmeng Wang ◽  
Han Zhu ◽  
Zhijian Kong ◽  
Tuo Li ◽  
Lei Ma ◽  
...  
Keyword(s):  
Core Genome ◽  
Agricultural Waste ◽  
Environmental Parameters ◽  
Housekeeping Genes ◽  
Ecological Diversity ◽  
Thermostable Enzymes ◽  
Genetic Characteristics ◽  
Evolutionary Mechanism ◽  
The Core ◽  
Pan Genome

The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two Geobacillus genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of Geobacillus strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the Geobacillus strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of Geobacillus seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different Geobacillus species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and Geobacillus’ evolution was directed by the environment and HGT events.

scholarly journals The Aquilegia genome reveals a hybrid origin of core eudicots

2018 ◽  
Author(s):  
Gökçe Aköz ◽  
Magnus Nordborg
Keyword(s):  
Evolutionary History ◽  
Genetic Material ◽  
Diploid Species ◽  
Hybrid Origin ◽  
The Core ◽  
Whole Genome Duplications ◽  
Core Eudicots ◽  
Eventual Return ◽  
Genome Duplications ◽  
History Of

AbstractBackgroundWhole-genome duplications (WGD) have dominated the evolutionary history of plants. One consequence of WGD is a dramatic restructuring of the genome as it undergoes diploidization, a process under which deletions and rearrangements of various sizes scramble the genetic material, leading to a repacking of the genome and eventual return to diploidy. Here, we investigate the history of WGD in the columbine genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots.ResultsWithin-genome synteny confirms that columbines are ancient tetraploids, and comparison with the grape genome reveals that this tetraploidy appears to be shared with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots must have involved a two-step process: first tetraploidy in the ancestry of all eudicots, then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of synteny sharing suggests that the latter involved allopolyploidization, and that core eudicots thus have a hybrid origin.ConclusionsNovel analyses of synteny sharing together with the well-preserved structure of the columbine genome reveal that the gamma hexaploidy at the root of core eudicots is likely a result of hybridization between a tetraploid and a diploid species.

scholarly journals The Aquilegia genome reveals a hybrid origin of core eudicots

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Gökçe Aköz ◽  
Magnus Nordborg
Keyword(s):  
Evolutionary History ◽  
Genetic Material ◽  
Diploid Species ◽  
Hybrid Origin ◽  
The Core ◽  
Whole Genome Duplications ◽  
Core Eudicots ◽  
Eventual Return ◽  
Genome Duplications ◽  
History Of

Abstract Background Whole-genome duplications (WGDs) have dominated the evolutionary history of plants. One consequence of WGD is a dramatic restructuring of the genome as it undergoes diploidization, a process under which deletions and rearrangements of various sizes scramble the genetic material, leading to a repacking of the genome and eventual return to diploidy. Here, we investigate the history of WGD in the columbine genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots. Results Within-genome synteny confirms that columbines are ancient tetraploids, and comparison with the grape genome reveals that this tetraploidy appears to be shared with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots must have involved a two-step process: first, tetraploidy in the ancestry of all eudicots, then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of synteny sharing suggests that the latter involved allopolyploidization and that core eudicots thus have a hybrid origin. Conclusions Novel analyses of synteny sharing together with the well-preserved structure of the columbine genome reveal that the gamma hexaploidy at the root of core eudicots is likely a result of hybridization between a tetraploid and a diploid species.

THE CORE AND PERIPHERY OF THE CURRENT CULTURE OF ARTISTIC CREATION ABOUT THE GREAT PATRIOTIC WAR IN THE STUDENTS’ VIEWS

2020 ◽  
Vol 6 (3) ◽  
pp. 130-149
Author(s):  
Elena N. NARKHOVA ◽  
Dmitry Yu. NARKHOV
Keyword(s):  
Historical Memory ◽  
Soviet Period ◽  
Russian Society ◽  
Student Culture ◽  
The Core ◽  
Musical Works ◽  
Great Patriotic War ◽  
History Of ◽  
Current Student ◽  
Historical Periods

This article analyzes the degree of demand for works of art (films and television films and series, literary and musical works, works of monumental art) associated with the history of the Great Patriotic War among contemporary students. This research is based on the combination of two theories, which study the dynamics and statics of culture in the society — the theory of the nucleus and periphery by Yu. M. Lotman and the theory of actual culture by L. N. Kogan. The four waves of research (2005, 2010, 2015, 2020) by the Russian Society of Socio¬logists (ROS) have revealed a series of works in various genres on this topic in the core structure and on the periphery of the current student culture; this has also allowed tracing the dynamics of demand and the “movement” of these works in the sociocultural space. The authors introduce the concept of the archetype of the echo of war. The high student recognition of works of all historical periods (from wartime to the present day) is shown. A significant complex of works has been identified, forming two contours of the periphery. Attention is drawn to the artistic work of contemporary students as a way to preserve the historical memory of the Great Patriotic War. This article explains the necessity of preserving the layer of national culture in order to reproduce the national identity in the conditions of informational and ideological pluralism of the post-Soviet period. The authors note the differentiation of youth due to the conditions and specifics of socialization in the polysemantic sociocultural space.

Indexicality of Grammar: The Case of Japanese Transgender Speakers

2019 ◽  
Author(s):  
Hideko Abe
Keyword(s):  
Gender Identity ◽  
Gender Identity Disorder ◽  
Grammatical Gender ◽  
Core Structure ◽  
Subject Positions ◽  
Transgender Identity ◽  
The Core ◽  
History Of ◽  
History Of Scholarship ◽  
Grammatical Structures

This article discusses how the intersection of grammatical gender and social gender, entwined in the core structure of language, can be analyzed to understand the dynamic status of selfhood. After reviewing a history of scholarship that demonstrates this claim, the discussion analyzes the language practices of transgender individuals in Japan, where transgender identity is currently understood in terms of sei-dōitsusei-shōgai (gender identity disorder). Based on fieldwork conducted between 2011 and 2017, the analysis reveals how individuals identifying with sei-dōitsusei-shōgai negotiate subject positions by manipulating the specific indexical meanings attached to grammatical structures.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

scholarly journals A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

2008 ◽  
Vol 191 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Marc Deloger ◽  
Meriem El Karoui ◽  
Marie-Agnès Petit
Keyword(s):  
Dna Sequences ◽  
Dna Content ◽  
Core Genome ◽  
Biological Diversity ◽  
Bacterial Species ◽  
Genomic Distance ◽  
The Core ◽  
Intraspecies Diversity ◽  
Genome Level ◽  
Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

Dead-Ends and New Directions

2021 ◽  
Vol 15 (4) ◽  
pp. 327-347
Author(s):  
Jean Francesco A.L. Gomes
Keyword(s):  
Natural History ◽  
Scientific Theory ◽  
Good Science ◽  
Orthodox Christian ◽  
The Core ◽  
The Earth ◽  
New Directions ◽  
History Of ◽  
Evolutionary Science ◽  
Doctrine Of Creation

Abstract The aim of this article is to investigate how Abraham Kuyper and some late neo-Calvinists have addressed the doctrine of creation in light of the challenges posed by evolutionary scientific theory. I argue that most neo-Calvinists today, particularly scholars from the Vrije Universiteit Amsterdam (VU), continue Kuyper’s legacy by holding the core principles of a creationist worldview. Yet, they have taken a new direction by explaining the natural history of the earth in evolutionary terms. In my analysis, Kuyper’s heirs at the VU today offer judicious parameters to guide Christians in conversation with evolutionary science, precisely because of their high appreciation of good science and awareness of the nonnegotiable elements that make up the orthodox Christian narrative.

ЦЕННОСТИ И СМЫСЛЫ НЕНАСИЛИЯ В ПОЛИТИЧЕСКОМ ПРОТЕСТЕ

2021 ◽  
Vol 15 (4) ◽  
pp. 58
Author(s):  
Л. Ю. Логунова ◽  
Е. А. Маженина
Keyword(s):  
Political Culture ◽  
New Left ◽  
Political Protest ◽  
Self Awareness ◽  
Sociological Study ◽  
The Core ◽  
Long Term Study ◽  
History Of ◽  
The Individual ◽  
Left Movement

The article presents the results of a long-term study of protest as a cultural phenomenon, the transformation of values, realized in the activities of the best people of the planet and their followers. These values have absorbed the experience of many generations and the behavior of people defending the rights of an individual to dignity, equality before the law, fair attitude, freedom of thought. In the history of the development of political thought, values have formed that constitute the core of civil culture. The genesis of the birth of the nucleus of civil culture from the thinkers of Antiquity, ideologists of nonviolent resistance, leaders of the French bourgeois revolution, activists of the “new left” movement to the protests of our time is shown. The basis for updating the protection of these values is the socio-political situation, characterized by the divergence of interests of civil society and ruling political groups. The values of the core of civil culture (freedom of speech, freedom of conscience, freedom of assembly, human rights) acquire an acute urgency in situations of power crisis. This is the time of the birth of new values that will mobilize new generations of protesters. Protest, as an act of protecting the values of the individual, is a measure of the level of development of political culture in the state. The protest — it's not just a mass exit of dissent on the area. This is an indicator of the level of self-awareness of citizens and the development of the political culture of society. The symbols of political protest actions are a special text that expresses the meanings of values. The authors present the results of a sociological study, which used comparative, value-semantic, interpretive approaches, studied the meanings and values of political protests of the 20th — early 19th centuries, analyzed visual and publicistic evidence of protest actions: photo and video materials, publications in the press.

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