Ancestral genome duplication in rice

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 610-614 ◽  
Author(s):  
Romain Guyot ◽  
Beat Keller
Keyword(s):  
Large Scale ◽  
Genome Duplication ◽  
Rice Genome ◽  
Block Size ◽  
Pairwise Comparisons ◽  
Comparative Genome Analysis ◽  
Important Species ◽  
Duplication Events ◽  
First Time ◽  
Grass Genomes

The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >1 Mb appears to be the rule and not the exception. Comparative mapping has shown high genetic colinearity among chromosomes of cereals, promoting rice as a model for studying grass genomes. Further comparative genome analysis should allow the study of the conservation and evolution of these duplication events in other important cereals such as rye, barley, and wheat.Key words: rice, genome duplication, genome evolution.

scholarly journals Evidence of multiple genome duplication events in Mytilus evolution

2021 ◽  
Author(s):  
Ana Corrochano-Fraile ◽  
Andrew Davie ◽  
Stefano Carboni ◽  
Michaël Bekaert
Keyword(s):  
Whole Genome Duplication ◽  
Evolutionary History ◽  
Reference Genome ◽  
Genome Duplication ◽  
Correct Identification ◽  
High Quality ◽  
Sequencing Technologies ◽  
Abiotic Stressors ◽  
Duplication Events ◽  
First Time

Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.

scholarly journals Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

2019 ◽  
Author(s):  
Grant T Godden ◽  
Taliesin J Kinser ◽  
Pamela S Soltis ◽  
Douglas E Soltis
Keyword(s):  
Gene Duplication ◽  
Large Scale ◽  
Plant Traits ◽  
Divergence Time ◽  
Evolutionary Process ◽  
Driver Gene ◽  
Important Species ◽  
Plant Groups ◽  
Duplication Events ◽  
Gene Duplicates

Abstract Ancient duplication events and retained gene duplicates have contributed to the evolution of many novel plant traits and, consequently, to the diversity and complexity within and across plant lineages. While mounting evidence highlights the importance of whole-genome duplication (WGD; polyploidy) and its key role as an evolutionary driver, gene duplication dynamics and mechanisms, both of which are fundamental to our understanding of evolutionary process and patterns of plant diversity, remain poorly characterized in many clades. We use newly available transcriptomic data and a robust phylogeny to investigate the prevalence, occurrence, and timing of gene duplications in Lamiaceae (mints), a species-rich and chemically diverse clade with many ecologically, economically, and culturally important species. We also infer putative WGDs—an extreme mechanism of gene duplication—using large-scale data sets from synonymous divergence (KS), phylotranscriptomic, and divergence time analyses. We find evidence for widespread but asymmetrical levels of gene duplication and ancient polyploidy in Lamiaceae that correlate with species richness, including pronounced levels of gene duplication and putative ancient WGDs (7–18 events) within the large subclade Nepetoideae and up to 10 additional WGD events in other subclades. Our results help disentangle WGD-derived gene duplicates from those produced by other mechanisms and illustrate the non-uniformity of duplication dynamics in mints, setting the stage for future investigations that explore their impacts on trait diversity and species diversification. Our results also provide a practical context for evaluating the benefits and limitations of transcriptome-based approaches to inferring WGD, and we offer recommendations for researchers interested in investigating ancient WGDs in other plant groups.

Scheming

2018 ◽  
Author(s):  
Seán Damer
Keyword(s):  
Social Class ◽  
Housing Policy ◽  
Large Scale ◽  
Class Structure ◽  
Local Council ◽  
Housing Scheme ◽  
Post War ◽  
First Time ◽  
The Voice ◽  
House Building

This book seeks to explain how the Corporation of Glasgow, in its large-scale council house-building programme in the inter- and post-war years, came to reproduce a hierarchical Victorian class structure. The three tiers of housing scheme which it constructed – Ordinary, Intermediate, and Slum-Clearance – effectively signified First, Second and Third Class. This came about because the Corporation uncritically reproduced the offensive and patriarchal attitudes of the Victorian bourgeoisie towards the working-class. The book shows how this worked out on the ground in Glasgow, and describes the attitudes of both authoritarian housing officials, and council tenants. This is the first time the voice of Glasgow’s council tenants has been heard. The conclusion is that local council housing policy was driven by unapologetic considerations of social class.

Superionic Lithium Intercalation through 2 nm x 2 nm Columns in the Crystallographic Shear Phase Nb18W8O69

2019 ◽  
Author(s):  
Kent Griffith ◽  
Clare Grey
Keyword(s):  
High Performance ◽  
Rate Capability ◽  
Block Size ◽  
Lithium Intercalation ◽  
Resonance Spectroscopy ◽  
Complex Metal Oxides ◽  
Battery Electrode ◽  
Crystallographic Shear ◽  
Battery Material ◽  
First Time

Nb18W8O69 (9Nb2O5×8WO3) is the tungsten-rich end-member of the Wadsley–Roth crystallographic shear (cs) structures within the Nb2O5–WO3 series. It has the largest block size of any known, stable Wadsley–Roth phase, comprising 5 ´ 5 units of corner-shared MO6 octahedra between the shear planes, giving rise to 2 nm ´ 2 nm blocks. Rapid lithium intercalation is observed in this new candidate battery material and 7Li pulsed field gradient nuclear magnetic resonance spectroscopy – measured in a battery electrode for the first time at room temperature – reveals superionic lithium conductivity. In addition to its promising rate capability, Nb18W8O69 adds a piece to the larger picture of our understanding of high-performance Wadsley–Roth complex metal oxides.

scholarly journals Shell-crossing in a ΛCDM Universe

2020 ◽  
Vol 501 (1) ◽  
pp. L71-L75
Author(s):  
Cornelius Rampf ◽  
Oliver Hahn
Keyword(s):  
Dark Matter ◽  
Perturbation Theory ◽  
Large Scale ◽  
Cold Dark Matter ◽  
Three Dimensional ◽  
Random Initial Data ◽  
Recursion Relations ◽  
Indispensable Tool ◽  
First Time ◽  
Very High

ABSTRACT Perturbation theory is an indispensable tool for studying the cosmic large-scale structure, and establishing its limits is therefore of utmost importance. One crucial limitation of perturbation theory is shell-crossing, which is the instance when cold-dark-matter trajectories intersect for the first time. We investigate Lagrangian perturbation theory (LPT) at very high orders in the vicinity of the first shell-crossing for random initial data in a realistic three-dimensional Universe. For this, we have numerically implemented the all-order recursion relations for the matter trajectories, from which the convergence of the LPT series at shell-crossing is established. Convergence studies performed at large orders reveal the nature of the convergence-limiting singularities. These singularities are not the well-known density singularities at shell-crossing but occur at later times when LPT already ceased to provide physically meaningful results.

3.17% efficient Cu2ZnSnS4–BiVO4 integrated tandem cell for standalone overall solar water splitting

2021 ◽  
Author(s):  
Dingwang Huang ◽  
Kang Wang ◽  
Lintao Li ◽  
Kuang Feng ◽  
Na An ◽  
...  
Keyword(s):  
Water Splitting ◽  
Large Scale ◽  
Tandem Cell ◽  
Solar Water ◽  
Solar Water Splitting ◽  
First Time

3.17% efficient Cu2ZnSnS4–BiVO4 integrated tandem cell and a large scale 5 × 5 cm integrated CZTS–BiVO4 tandem device for standalone overall solar water splitting was assembled for the first time.

scholarly journals Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amit Rai ◽  
Hideki Hirakawa ◽  
Ryo Nakabayashi ◽  
Shinji Kikuchi ◽  
Koki Hayashi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Whole Genome Duplication ◽  
Experimental Validation ◽  
Genome Duplication ◽  
Indole Alkaloids ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Plant Genomes ◽  
Genome Triplication ◽  
Chromosome Level

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

scholarly journals The SAMI Galaxy Survey: the third and final data release

2021 ◽  
Author(s):  
Scott M Croom ◽  
Matt S Owers ◽  
Nicholas Scott ◽  
Henry Poetrodjojo ◽  
Brent Groves ◽  
...  
Keyword(s):  
Large Scale ◽  
Resolving Power ◽  
Stellar Kinematics ◽  
New Era ◽  
Optical Wavelength ◽  
Astronomical Optics ◽  
Data Release ◽  
Gas Ionization ◽  
Release Data ◽  
First Time

Abstract We have entered a new era where integral-field spectroscopic surveys of galaxies are sufficiently large to adequately sample large-scale structure over a cosmologically significant volume. This was the primary design goal of the SAMI Galaxy Survey. Here, in Data Release 3 (DR3), we release data for the full sample of 3068 unique galaxies observed. This includes the SAMI cluster sample of 888 unique galaxies for the first time. For each galaxy, there are two primary spectral cubes covering the blue (370–570 nm) and red (630–740 nm) optical wavelength ranges at spectral resolving power of R = 1808 and 4304 respectively. For each primary cube, we also provide three spatially binned spectral cubes and a set of standardized aperture spectra. For each galaxy, we include complete 2D maps from parameterized fitting to the emission-line and absorption-line spectral data. These maps provide information on the gas ionization and kinematics, stellar kinematics and populations, and more. All data are available online through Australian Astronomical Optics (AAO) Data Central.

scholarly journals A Novel and Efficient High-Yield Method for Preparing Bacterial Ghosts

Toxins ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 420
Author(s):  
Yi Ma ◽  
Liu Cui ◽  
Meng Wang ◽  
Qiuli Sun ◽  
Kaisheng Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression System ◽  
High Yield ◽  
Wild Type ◽  
High Quality ◽  
Efficient Protection ◽  
Bacterial Ghosts ◽  
Cell Envelopes ◽  
Extracellular Structures ◽  
First Time

Bacterial ghosts (BGs) are empty cell envelopes possessing native extracellular structures without a cytoplasm and genetic materials. BGs are proposed to have significant prospects in biomedical research as vaccines or delivery carriers. The applications of BGs are often limited by inefficient bacterial lysis and a low yield. To solve these problems, we compared the lysis efficiency of the wild-type protein E (EW) from phage ΦX174 and the screened mutant protein E (EM) in the Escherichia coli BL21(DE3) strain. The results show that the lysis efficiency mediated by protein EM was improved. The implementation of the pLysS plasmid allowed nearly 100% lysis efficiency, with a high initial cell density as high as OD600 = 2.0, which was higher compared to the commonly used BG preparation method. The results of Western blot analysis and immunofluorescence indicate that the expression level of protein EM was significantly higher than that of the non-pLysS plasmid. High-quality BGs were observed by SEM and TEM. To verify the applicability of this method in other bacteria, the T7 RNA polymerase expression system was successfully constructed in Salmonella enterica (S. Enterica, SE). A pET vector containing EM and pLysS were introduced to obtain high-quality SE ghosts which could provide efficient protection for humans and animals. This paper describes a novel and commonly used method to produce high-quality BGs on a large scale for the first time.

Offshore Claims and Problems in the North Sea

1965 ◽  
Vol 59 (3) ◽  
pp. 505-522 ◽  
Author(s):  
Richard Young
Keyword(s):  
North Sea ◽  
Large Scale ◽  
Geneva Convention ◽  
Legal Principles ◽  
The North ◽  
Legal Problems ◽  
The North Sea ◽  
The Subject ◽  
First Time ◽  
Economic Considerations

The possible presence of very large petroleum and natural gas reserves in the area beneath the North Sea is currently the subject of intense investigation. If confirmed, as seems likely in at least some localities, this occurrence will raise legal problems of considerable interest and complexity. For the North Sea is not merely an oilfield covered by water: for centuries it has been one of the world's major fishery regions and the avenue to and from the world's busiest seaports. Thus all three of the present principal uses of the sea—fishing, navigation, and the exploitation of submarine resources—promise to meet for the first time on a large scale in an area where all are of major importance. The process of reconciling the various interests at stake will provide the first thoroughgoing test of the adequacy and acceptability of the general principles laid down in the 1958 Geneva Convention on the Continental Shelf and should add greatly to the practice and precedents available in this developing branch of the law. In the present article an attempt is made to review some of the geographical and economic considerations involved in the North Sea situation, to note some of the technical and legal developments that have already taken place, and to consider these elements in the light of the various interests and legal principles concerned.

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