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"Mayer, F."
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Impact of transposable elements on genome structure and evolution in bread wheat
Background
Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes.
Results
The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.
Conclusions
Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.
Journal Article
The Roman Inquisition on the Stage of Italy, c. 1590-1640
From the moment of its founding in 1542, the Roman Inquisition acted as a political machine. Although inquisitors in earlier centuries had operated somewhat independently of papal authority, the gradual bureaucratization of the Roman Inquisition permitted the popes increasing license to establish and exercise direct control over local tribunals, though with varying degrees of success. In particular, Pope Urban VIII's aggressive drive to establish papal control through the agency of the Inquisition played out differently among the Italian states, whose local inquisitions varied in number and secular power. Rome's efforts to bring the Venetians to heel largely failed in spite of the interdict of 1606, and Venice maintained lay control of most religious matters. Although Florence and Naples resisted papal intrusions into their jurisdictions, on the other hand, they were eventually brought to answer directly to Rome-due in no small part to Urban VIII's subversions of the law.
Thomas F. Mayer provides a richly detailed account of the ways the Roman Inquisition operated to serve the papacy's long-standing political aims in Naples, Venice, and Florence. Drawing on the Inquisition's own records, diplomatic correspondence, local documents, newsletters, and other sources, Mayer sheds new light on papal interdicts and high-profile court cases that signaled significant shifts in inquisitorial authority for each Italian state. Alongside his earlier volume,The Roman Inquisition: A Papal Bureaucracy and Its Laws in the Age of Galileo, this masterful study extends and develops our understanding of the Inquisition as a political and legal institution.
eBook
The Culling Trials
\"A teenage girl torn from her family must survive a series of deadly trials to earn her place in a dangerous school of magic\"-- Provided by publisher.
Book
TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
Journal Article
Mass-spectrometry-based draft of the Arabidopsis proteome
Plants are essential for life and are extremely diverse organisms with unique molecular capabilities
1
. Here we present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant
Arabidopsis thaliana
. Our analysis provides initial answers to how many genes exist as proteins (more than 18,000), where they are expressed, in which approximate quantities (a dynamic range of more than six orders of magnitude) and to what extent they are phosphorylated (over 43,000 sites). We present examples of how the data may be used, such as to discover proteins that are translated from short open-reading frames, to uncover sequence motifs that are involved in the regulation of protein production, and to identify tissue-specific protein complexes or phosphorylation-mediated signalling events. Interactive access to this resource for the plant community is provided by the ProteomicsDB and ATHENA databases, which include powerful bioinformatics tools to explore and characterize
Arabidopsis
proteins, their modifications and interactions.
A quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant
Arabidopsis thaliana
provides a valuable resource for plant research.
Journal Article
Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat
Fine mapping and sequencing revealed 28 genes in the non-recombining haplotype containing Fhb1 . Of these, only a GDSL lipase gene shows a pathogen-dependent expression pattern. Fhb1 is a prominent Fusarium head blight resistance locus of wheat, which has been successfully introgressed in adapted breeding material, where it confers a significant increase in overall resistance to the causal pathogen Fusarium graminearum and the fungal virulence factor and mycotoxin deoxynivalenol. The Fhb1 region has been resolved for the susceptible wheat reference genotype Chinese Spring, yet the causal gene itself has not been identified in resistant cultivars. Here, we report the establishment of a 1 Mb contig embracing Fhb1 in the donor line CM-82036. Sequencing revealed that the region of Fhb1 deviates from the Chinese Spring reference in DNA size and gene content, which explains the repressed recombination at the locus in the performed fine mapping. Differences in genes expression between near-isogenic lines segregating for Fhb1 challenged with F. graminearum or treated with mock were investigated in a time-course experiment by RNA sequencing. Several candidate genes were identified, including a pathogen-responsive GDSL lipase absent in susceptible lines. The sequence of the Fhb1 region, the resulting list of candidate genes, and near-diagnostic KASP markers for Fhb1 constitute a valuable resource for breeding and further studies aiming to identify the gene(s) responsible for F. graminearum and deoxynivalenol resistance.
Journal Article
Analysis of the bread wheat genome using whole-genome shotgun sequencing
Bread wheat (
Triticum aestivum
) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.
Sequencing of the hexaploid bread wheat genome shows that it is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments.
The bread — and barley — of life
Two groups in this issue report the compilation and analysis of the genome sequences of major cereal crops — bread wheat and barley — providing important resources for future crop improvement. Bread wheat accounts for one-fifth of the calories consumed by humankind. It has a very large and complex hexaploid genome of 17 Gigabases. Michael Bevan and colleagues have analysed the genome using 454 pyrosequencing and compared it with diploid ancestral and progenitor genomes. The authors discovered significant loss of gene family members upon polyploidization and domestication, and expansion of gene classes that may be associated with crop productivity.
Barley is one of the earliest domesticated plant crops. Although diploid, it has a very large genome of 5.1 Gigabases. Nils Stein and colleagues describe a physical map anchored to a high-resolution genetic map, on top of which they have overlaid a deep whole-genome shotgun assembly, cDNA and RNA-seq data to provide the first in-depth genome-wide survey of the barley genome.
Journal Article
The Use of a 3D Simulator Software and 3D Printed Biomodels to Aid Autologous Breast Reconstruction
Aesthetically pleasing and symmetrical breasts are the goal of reconstructive breast surgery. However, multiple procedures are sometimes needed to improve a reconstructed breast’s symmetry and appearance. Since all breasts vary in terms of volume, height, width, projection, orientation, and shape, the lack of attention to these details at the moment of flap shaping in autologous reconstruction can lead to poor results. Recent advances in 3-dimensional (3D) surface imaging and printing technologies have allowed for improvement in autologous breast reconstruction symmetry. While 3D printing technology is becoming faster, more accurate, and less expensive, the technology required to obtain proper 3D breast images remains expensive, including laser scanners or 3D photogrammetric cameras. In this study, we present a novel use of an aesthetic surgery simulator software as an affordable alternative to obtaining 3D breast images and creating 3D printed biomodels to aid in the precise shaping of the flap. This approach aims to optimize aesthetic results in autologous breast reconstruction avoiding surgical revisions and reducing surgical times.Level of Evidence IVThis journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.
Journal Article