scholarly journals Impact of transposable elements on genome structure and evolution in bread wheat

2018 ◽  
Author(s):  
Thomas Wicker ◽  
Heidrun Gundlach ◽  
Manuel Spannagl ◽  
Cristobal Uauy ◽  
Philippa Borrill ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Bread Wheat ◽  
Genome Structure ◽  
Reference Sequence ◽  
Structural Level ◽  
Gene Promoters ◽  
Genome Wide ◽  
Intergenic Regions ◽  
History Of ◽  
First Time

AbstractBackgroundTransposable elements (TEs) are ubiquitous components of genomes and they are the main contributors to genome evolution. The reference sequence of the hexaploid bread wheat (Triticum aestivum L.) genome enabled for the first time a comprehensive genome-wide view of the dynamics of TEs that have massively proliferated in the A, B, and D subgenomes.ResultsTEs represent 85% of the genome. We traced back TE amplification dynamics in the evolutionary history of wheat and did not find large bursts in the wake of either the tetra- or the hexaploidization. Despite the massive turnover of TEs since A, B, and D diverged, 76% of TE families are present in similar proportions in the three subgenomes. Moreover, spacing between homeologous genes was also conserved. TE content around genes is very different from the TE space comprising large intergenic regions and families that are enriched or depleted from gene promoters are the same in the three subgenomes.ConclusionsThe chromosome-scale assembly of the wheat genome provided an unprecedented genome-wide view of the organization and impact of TEs in such a complex genome. Our results suggest that TEs play a role at the structural level and that the overall chromatin structure is likely under selection pressure.

scholarly journals Variation in VKORC1 Is Associated with Vascular Dementia

2021 ◽  
Vol 80 (3) ◽  
pp. 1329-1337
Author(s):  
Jure Mur ◽  
Daniel L. McCartney ◽  
Daniel I. Chasman ◽  
Peter M. Visscher ◽  
Graciela Muniz-Terrera ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Vascular Dementia ◽  
Genetic Variant ◽  
Warfarin Dose ◽  
Uk Biobank ◽  
Parental History ◽  
Genome Wide ◽  
History Of ◽  
First Time ◽  
The Relationship

Background: The genetic variant rs9923231 (VKORC1) is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has been linked in a gene-based test to dementia/Alzheimer’s disease in the parents of participants, with suggestive evidence for an association for rs9923231 (p = 1.8×10–7), which was included in the genome-wide significant KAT8 locus. Objective: Our study aimed to investigate whether the relationship between rs9923231 and dementia persists only for certain dementia sub-types, and if those taking warfarin are at greater risk. Methods: We used logistic regression and data from 238,195 participants from UK Biobank to examine the relationship between VKORC1, risk of dementia, and the interplay with warfarin use. Results: Parental history of dementia, APOE variant, atrial fibrillation, diabetes, hypertension, and hypercholesterolemia all had strong associations with vascular dementia (p < 4.6×10–6). The T-allele in rs9923231 was linked to a lower warfarin dose (βperT - allele = –0.29, p < 2×10–16) and risk of vascular dementia (OR = 1.17, p = 0.010), but not other dementia sub-types. However, the risk of vascular dementia was not affected by warfarin use in carriers of the T-allele. Conclusion: Our study reports for the first time an association between rs9923231 and vascular dementia, but further research is warranted to explore potential mechanisms and specify the relationship between rs9923231 and features of vascular dementia.

scholarly journals Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes

2020 ◽  
Vol 8 (7) ◽  
pp. 1001
Author(s):  
Daniel Vieira ◽  
Soraia Esteves ◽  
Carolina Santiago ◽  
Eduardo Conde-Sousa ◽  
Ticiana Fernandes ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Yeast Species ◽  
Phenotypic Diversity ◽  
Population Analysis ◽  
Nuclear Genome ◽  
Reference Sequence ◽  
Evolutionary Analysis ◽  
Novel Approach ◽  
History Of ◽  
First Time

The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between the two, mainly regarding strains’ technological uses and/or geographical distribution. In the current work, we proposed a new method to align and analyze yeast mitogenomes, overcoming current difficulties that make it impossible to obtain comparable mitogenomes for a large number of isolates. To this end, 12,016 mitogenomes were considered, and we developed a novel approach consisting of the design of a reference sequence intended to be comparable between all mitogenomes. Subsequently, the population structure of 6646 Saccharomyces cerevisiae mitogenomes was assessed. Results revealed the existence of particular clusters associated with the technological use of the strains, in particular regarding clinical isolates, laboratory strains, and yeasts used for wine-associated activities. As far as we know, this is the first time that a positive concordance between nuclear and mitogenomes has been reported for S. cerevisiae, in terms of strains’ technological applications. The results obtained highlighted the importance of including the mtDNA genome in evolutionary analysis, in order to clarify the origin and history of yeast species.

scholarly journals Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lianyu Lin ◽  
Anupma Sharma ◽  
Qingyi Yu
Keyword(s):  
Transposable Elements ◽  
Inverted Repeat ◽  
Sequence Similarity ◽  
Genome Structure ◽  
Terminal Inverted Repeat ◽  
Essential Information ◽  
Dna Transposon ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. Results We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. Conclusions Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

scholarly journals Impact of transposable elements on genome structure and evolution in bread wheat

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Thomas Wicker ◽  
◽  
Heidrun Gundlach ◽  
Manuel Spannagl ◽  
Cristobal Uauy ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Bread Wheat ◽  
Genome Structure

scholarly journals Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 711
Author(s):  
Mian Faisal Nazir ◽  
Yinhua Jia ◽  
Haris Ahmed ◽  
Shoupu He ◽  
Muhammad Shahid Iqbal ◽  
...  
Keyword(s):  
Upland Cotton ◽  
Population Genomics ◽  
Association Studies ◽  
Genome Structure ◽  
Morphological Characteristics ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
History Of ◽  
Fibre Yield ◽  
Insight Into

Upland cotton is the most economically important fibre crop. The human-mediated selection has resulted in modern upland cultivars with higher yield and better fibre quality. However, changes in genome structure resulted from human-mediated selection are poorly understood. Comparative population genomics offers us tools to dissect the genetic history of domestication and helps to understand the genome-wide effects of human-mediated selection. Hereby, we report a comprehensive assessment of Gossypium hirsutum landraces, obsolete cultivars and modern cultivars based on high throughput genome-wide sequencing of the core set of genotypes. As a result of the genome-wide scan, we identified 93 differential regions and 311 selection sweeps associated with domestication and improvement. Furthermore, we performed genome-wide association studies to identify traits associated with the differential regions and selection sweeps. Our study provides a genetic basis to understand the domestication process in Chinese cotton cultivars. It also provides a comprehensive insight into changes in genome structure due to selection and improvement during the last century. We also identified multiple genome-wide associations (GWAS associations) for fibre yield, quality and other morphological characteristics.

Adam Zalužanský’s “De sexu plantarum” (1592): an early pioneering chapter on plant sexuality

2013 ◽  
Vol 40 (2) ◽  
pp. 244-256 ◽  
Author(s):  
Holger Funk
Keyword(s):  
Nineteenth Century ◽  
English Translation ◽  
History Of Botany ◽  
Main Work ◽  
Botanical History ◽  
History Of ◽  
The University ◽  
First Time

In the history of botany, Adam Zalužanský (d. 1613), a Bohemian physician, apothecary, botanist and professor at the University of Prague, is a little-known personality. Linnaeus's first biographers, for example, only knew Zalužanský from hearsay and suspected he was a native of Poland. This ignorance still pervades botanical history. Zalužanský is mentioned only peripherally or not at all. As late as the nineteenth century, a researcher would be unaware that Zalužanský’s main work Methodi herbariae libri tres actually existed in two editions from two different publishers (1592, Prague; 1604, Frankfurt). This paper introduces the life and work of Zalužanský. Special attention is paid to the chapter “De sexu plantarum” of Zalužanský’s Methodus, in which, more than one hundred years before the well-known De sexu plantarum epistola of R. J. Camerarius, the sexuality of plants is suggested. Additionally, for the first time, an English translation of Zalužanský’s chapter on plant sexuality is provided.

A Confrontation between Two Doctrines: The Birth of Struggle for Hegemony in Hebrew Children's Literature during the 1930s and 1940s

2008 ◽  
Vol 1 (2) ◽  
pp. 139-155 ◽  
Author(s):  
YAEL DARR
Keyword(s):  
Children's Literature ◽  
Educational System ◽  
Single Channel ◽  
Children’S Literature ◽  
The Political ◽  
Literary Creation ◽  
History Of ◽  
High Level ◽  
First Time ◽  
Literary Quality

This article describes a crucial and fundamental stage in the transformation of Hebrew children's literature, during the late 1930s and 1940s, from a single channel of expression to a multi-layered polyphony of models and voices. It claims that for the first time in the history of Hebrew children's literature there took place a doctrinal confrontation between two groups of taste-makers. The article outlines the pedagogical and ideological designs of traditionalist Zionist educators, and suggests how these were challenged by a group of prominent writers of adult poetry, members of the Modernist movement. These writers, it is argued, advocated autonomous literary creation, and insisted on a high level of literary quality. Their intervention not only dramatically changed the repertoire of Hebrew children's literature, but also the rules of literary discourse. The article suggests that, through the Modernists’ polemical efforts, Hebrew children's literature was able to free itself from its position as an apparatus controlled by the political-educational system and to become a dynamic and multi-layered field.

Digging the history. Absolute chronology of the settlement complex at Czermno-Cherven’ (eastern Poland). Research status and perspectives

2020 ◽  
Vol 72 (2) ◽  
Author(s):  
Tomasz Dzieńkowski ◽  
Marcin Wołoszyn ◽  
Iwona Florkiewicz ◽  
Radosław Dobrowolski ◽  
Jan Rodzik ◽  
...  
Keyword(s):  
Interdisciplinary Research ◽  
Qualitative Change ◽  
Archaeological Research ◽  
Research Status ◽  
History Of ◽  
Absolute Dating ◽  
First Time ◽  
Radiocarbon Datings

The article discusses the results of the latest interdisciplinary research of Czermno stronghold and its immediate surroundings. The site is mentioned in chroniclers’ entries referring to the stronghold Cherven’ (Tale of Bygone Years, first mention under the year 981) and the so-called Cherven’ Towns. Given the scarcity of written records regarding the history of today’s Eastern Poland, Ukraine, and Belarus in the 10th and 11th centuries, recent archaeological research, supported by geoenvironmental analyses and absolute dating, brought a significant qualitative change. In 2014 and 2015, the remains of the oldest rampart of the stronghold were uncovered for the first time. A series of radiocarbon datings allows us to refer the erection of the stronghold to the second half/late 10th century. The results of several years’ interdisciplinary research (2012-2020) introduce qualitatively new data to the issue of the Cherven’ Towns, which both change current considerations and confirm the extraordinary research potential in the archeology of the discussed region.

A Well-Ordered Thing

2018 ◽  
Author(s):  
Michael D. Gordin
Keyword(s):  
Nineteenth Century ◽  
History Of Science ◽  
Periodic Table ◽  
The Arctic ◽  
Classic Work ◽  
Hot Air ◽  
History Of ◽  
First Time

Dmitrii Mendeleev (1834–1907) is a name we recognize, but perhaps only as the creator of the periodic table of elements. Generally, little else has been known about him. This book is an authoritative biography of Mendeleev that draws a multifaceted portrait of his life for the first time. As the book reveals, Mendeleev was not only a luminary in the history of science, he was also an astonishingly wide-ranging political and cultural figure. From his attack on Spiritualism to his failed voyage to the Arctic and his near-mythical hot-air balloon trip, this is the story of an extraordinary maverick. The ideals that shaped his work outside science also led Mendeleev to order the elements and, eventually, to engineer one of the most fascinating scientific developments of the nineteenth century. This book is a classic work that tells the story of one of the world's most important minds.

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