scholarly journals Conserved gene clusters in the scrambled plastomes of IRLC legumes (Fabaceae: Trifolieae and Fabeae).

2016 ◽  
Author(s):  
Saemundur Sveinsson ◽  
Quentin Cronk
Keyword(s):  
Inverted Repeat ◽  
High Frequency ◽  
Plastid Genome ◽  
Gene Clusters ◽  
Functional Constraint ◽  
Legume Species ◽  
Data Set ◽  
Plastid Genomes ◽  
Conserved Gene ◽  
Internal Rearrangement

The plastid genome retains several features from its cyanobacterial-like ancestor, one being the co-transcriptional organization of genes into operon-like structures. Some plastid operons have been identified but undoubtedly many more remain undiscovered. Here we utilize the highly variable plastome structure that exists within certain legumes of the inverted repeat lost clade (IRLC) to find conserved gene clusters. These plastomes exhibit an unusually high frequency of translocations and inversions. We analysed the plastomes of 23 legume species and identified 32 locally collinear blocks (LCBs), which are regions within the plastid genomes that occur in different orientation and/or order among the plastid genomes but are themselves free from internal rearrangements. Several represent gene clusters that have previously been recognized as plastid operons. It appears that the number of LCBs has reached saturation in our data set, suggesting that these LCBs are not random, but likely represent legume plastid operons protected from internal rearrangement by functional constraint. Some of the LCBs we identify, such as psbD/C/Z, are previously known plastid operons. Others, such as rpl32-ndhF-psbA-matK-rbcL-atpB-atpE, may represent novel polycistronic operons in legumes.

scholarly journals PACVr: Plastome Assembly Coverage Visualization in R

2019 ◽  
Author(s):  
Michael Gruenstaeudl ◽  
Nils Jenke
Keyword(s):  
Genome Assembly ◽  
Inverted Repeat ◽  
Plastid Genome ◽  
Genome Structure ◽  
Software Tools ◽  
Coverage Depth ◽  
Assembly Quality ◽  
Gene Synteny ◽  
Plastid Genomes ◽  
A Genome

ABSTRACTBackgroundThe circular, quadripartite structure of plastid genomes which includes two inverted repeat regions renders the automatic assembly of plastid genomes challenging. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on plastid genome structure and evolution. Plastome-based phylogenetic or population genetic investigations, for example, require the precise identification of DNA sequence and length to determine the location of nucleotide polymorphisms. The average coverage depth of a genome assembly is often used as an indicator for assembly quality. Visualizing coverage depth across a draft genome allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Based on such visualizations, users can conduct a local re-assembly or other forms of targeted error correction. Few, if any, contemporary software tools can visualize the coverage depth of a plastid genome assembly while taking its quadripartite structure into account, despite the interplay between genome structure and assembly quality. A software tool is needed that visualizes the coverage depth of a plastid genome assembly on a circular, quadripartite map of the plastid genome.ResultsWe introduce ‘PACVr’, an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as to the individual plastome genes. The tool allows visualizations on different scales using a variable window approach and also visualizes the equality of gene synteny in the inverted repeat regions of the plastid genome, thus providing an additional measure of assembly quality. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be directly invoked from a Unix shell, thus facilitating its use in automated quality control. We illustrate the application of PACVr on two empirical datasets and compare the resulting visualizations with alternative software tools for displaying plastome sequencing coverage.ConclusionsPACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) the equality of gene synteny in the inverted repeat regions. It, thus, contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences, especially in light of incongruence among the visualization results of alternative software tools. The software, example datasets, technical documentation, and a tutorial are available with the package at https://github.com/michaelgruenstaeudl/PACVr.

scholarly journals Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Can Yuan ◽  
Xiufen Sha ◽  
Miao Xiong ◽  
Wenjuan Zhong ◽  
Yu Wei ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Species Discrimination ◽  
Chloroplast Genomes ◽  
Genomic Arrangement ◽  
Phylogenetic Implications ◽  
Solid Foundation ◽  
Conserved Gene ◽  
Fine Resolution ◽  
Genome Scale ◽  
First Time

AbstractLigusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

scholarly journals Statistical analysis of Stromboli VLP tremor in the band [0.1–0.5] Hz: some consequences for vibrating structures

2006 ◽  
Vol 13 (4) ◽  
pp. 393-400 ◽  
Author(s):  
E. De Lauro ◽  
S. De Martino ◽  
M. Falanga ◽  
M. Palo
Keyword(s):  
Frequency Band ◽  
High Frequency ◽  
Noise Source ◽  
Volcanic Tremor ◽  
Large Data ◽  
Musical Instruments ◽  
Data Set ◽  
Long Period ◽  
Vibrating Structures ◽  
Analyze Time Series

Abstract. We analyze time series of Strombolian volcanic tremor, focusing our attention on the frequency band [0.1–0.5] Hz (very long period (VLP) tremor). Although this frequency band is largely affected by noise, we evidence two significant components by using Independent Component Analysis with the frequencies, respectively, of ~0.2 and ~0.4 Hz. We show that these components display wavefield features similar to those of the high frequency Strombolian signals (>0.5 Hz). In fact, they are radially polarised and located within the crater area. This characterization is lost when an enhancement of energy appears. In this case, the presence of microseismic noise becomes relevant. Investigating the entire large data set available, we determine how microseismic noise influences the signals. We ascribe the microseismic noise source to Scirocco wind. Moreover, our analysis allows one to evidence that the Strombolian conduit vibrates like the asymmetric cavity associated with musical instruments generating self-sustained tones.

scholarly journals Conserved Gene Clusters in Bacterial Genomes Provide Further Support for the Primacy of RNA

1997 ◽  
Vol 45 (5) ◽  
pp. 467-472 ◽  
Author(s):  
Janet L. Siefert ◽  
Kirt A. Martin ◽  
Fadi Abdi ◽  
William R. Widger ◽  
George E. Fox
Keyword(s):  
Gene Clusters ◽  
Bacterial Genomes ◽  
Conserved Gene

Source dynamics of the 1979 Imperial Valley earthquake from near-source observations (of ground acceleration and velocity)

1982 ◽  
Vol 72 (6A) ◽  
pp. 1957-1968
Author(s):  
Mansour Niazi
Keyword(s):  
Particle Acceleration ◽  
Particle Velocity ◽  
High Frequency ◽  
Observation Point ◽  
P Wave ◽  
Imperial Valley ◽  
Ground Acceleration ◽  
Data Set ◽  
Ground Shaking ◽  
Fault Surface

abstract Two sets of observations obtained during the 15 October 1979 Imperial Valley earthquake, MS 6.9, are presented. The data suggest different dynamic characteristics of the source when viewed in different frequency bands. The first data set consists of the observed residuals of the horizontal peak ground accelerations and particle velocity from predicted values within 50 km of the fault surface. The residuals are calculated from a nonlinear regression analysis of the data (Campbell, 1981) to the following empirical relationships, PGA = A 1 ( R + C 1 ) − d 1 , PGV = A 2 ( R + C 2 ) − d 2 in which R is the closest distance to the plane of rupture. The so-calculated residuals are correlated with a positive scalar factor signifying the focusing potential at each observation point. The focusing potential is determined on the basis of the geometrical relation of the station relative to the rupture front on the fault plane. The second data set consists of the acceleration directions derived from the windowed-time histories of the horizontal ground acceleration across the El Centro Differential Array (ECDA). The horizontal peak velocity residuals and the low-pass particle acceleration directions across ECDA require the fault rupture to propagate northwestward. The horizontal peak ground acceleration residuals and the high-frequency particle acceleration directions, however, are either inconclusive or suggest an opposite direction for rupture propagation. The inconsistency can best be explained to have resulted from the incoherence of the high-frequency radiation which contributes most effectively to the registration of PGA. A test for the sensitivity of the correlation procedure to the souce location is conducted by ascribing the observed strong ground shaking to a single asperity located 12 km northwest of the hypocenter. The resulting inconsistency between the peak acceleration and velocity observations in relation to the focusing potential is accentuated. The particle velocity of Delta Station, Mexico, in either case appears abnormally high and disagrees with other observations near the southeastern end of the fault trace. From the observation of a nearly continuous counterclockwise rotation of the plane of P-wave particle motion at ECDA, the average rupture velocity during the first several seconds of source activation is estimated to be 2.0 to 3.0 km/sec. A 3 km upper bound estimate of barrier dimensions is tentatively made on the basis of the observed quasiperiodic variation of the polarization angles.

scholarly journals Intergeneric Relationships within the Early-Diverging Angiosperm Family Nymphaeaceae Based on Chloroplast Phylogenomics

2018 ◽  
Vol 19 (12) ◽  
pp. 3780 ◽  
Author(s):  
Dingxuan He ◽  
Andrew Gichira ◽  
Zhizhong Li ◽  
John Nzei ◽  
Youhao Guo ◽  
...  
Keyword(s):  
Genome Structure ◽  
Morphological Data ◽  
Basal Angiosperm ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Gene Data ◽  
High Degree

The order Nymphaeales, consisting of three families with a record of eight genera, has gained significant interest from botanists, probably due to its position as a basal angiosperm. The phylogenetic relationships within the order have been well studied; however, a few controversial nodes still remain in the Nymphaeaceae. The position of the Nuphar genus and the monophyly of the Nymphaeaceae family remain uncertain. This study adds to the increasing number of the completely sequenced plastid genomes of the Nymphaeales and applies a large chloroplast gene data set in reconstructing the intergeneric relationships within the Nymphaeaceae. Five complete chloroplast genomes were newly generated, including a first for the monotypic Euryale genus. Using a set of 66 protein-coding genes from the chloroplast genomes of 17 taxa, the phylogenetic position of Nuphar was determined and a monophyletic Nymphaeaceae family was obtained with convincing statistical support from both partitioned and unpartitioned data schemes. Although genomic comparative analyses revealed a high degree of synteny among the chloroplast genomes of the ancient angiosperms, key minor variations were evident, particularly in the contraction/expansion of the inverted-repeat regions and in RNA-editing events. Genome structure, and gene content and arrangement were highly conserved among the chloroplast genomes. The intergeneric relationships defined in this study are congruent with those inferred using morphological data.

scholarly journals ‘Where’ Questions and Their Responses in Duna (Papua New Guinea)

2016 ◽  
Vol 2 (1) ◽  
Author(s):  
Lila San Roque
Keyword(s):  
Papua New Guinea ◽  
High Frequency ◽  
New Guinea ◽  
Direct Reference ◽  
Space And Place ◽  
Frequency Function ◽  
Data Set ◽  
Functional Flexibility ◽  
Information Gap ◽  
Question Formation

AbstractDespite their central role in question formation, content interrogatives in spontaneous conversation remain relatively under-explored cross-linguistically. This paper outlines the structure of ‘where’ expressions in Duna, a language spoken in Papua New Guinea, and examines where-questions in a small Duna data set in terms of their frequency, function, and the responses they elicit. Questions that ask ‘where?’ have been identified as a useful tool in studying the language of space and place, and, in the Duna case and elsewhere, show high frequency and functional flexibility. Although where-questions formulate place as an information gap, they are not always answered through direct reference to canonical places. While some question types may be especially “socially costly” (Levinson 2012), asking ‘where’ perhaps provides a relatively innocuous way of bringing a particular event or situation into focus.

scholarly journals Estimates of European emissions of methyl chloroform using a Bayesian inversion method

2014 ◽  
Vol 14 (18) ◽  
pp. 9755-9770 ◽  
Author(s):  
M. Maione ◽  
F. Graziosi ◽  
J. Arduini ◽  
F. Furlani ◽  
U. Giostra ◽  
...  
Keyword(s):  
Point Source ◽  
High Frequency ◽  
Stratospheric Ozone ◽  
Montreal Protocol ◽  
Source Analysis ◽  
Bayesian Inversion ◽  
Inversion Method ◽  
Data Set ◽  
Methyl Chloroform

Abstract. Methyl chloroform (MCF) is a man-made chlorinated solvent contributing to the destruction of stratospheric ozone and is controlled under the "Montreal Protocol on Substances that Deplete the Ozone Layer" and its amendments, which called for its phase-out in 1996 in developed countries and 2015 in developing countries. Long-term, high-frequency observations of MCF carried out at three European sites show a constant decline in the background mixing ratios of MCF. However, we observe persistent non-negligible mixing ratio enhancements of MCF in pollution episodes, suggesting unexpectedly high ongoing emissions in Europe. In order to identify the source regions and to give an estimate of the magnitude of such emissions, we have used a Bayesian inversion method and a point source analysis, based on high-frequency long-term observations at the three European sites. The inversion identified southeastern France (SEF) as a region with enhanced MCF emissions. This estimate was confirmed by the point source analysis. We performed this analysis using an 11-year data set, from January 2002 to December 2012. Overall, emissions estimated for the European study domain decreased nearly exponentially from 1.1 Gg yr−1 in 2002 to 0.32 Gg yr−1 in 2012, of which the estimated emissions from the SEF region accounted for 0.49 Gg yr−1 in 2002 and 0.20 Gg yr−1 in 2012. The European estimates are a significant fraction of the total semi-hemisphere (30–90° N) emissions, contributing a minimum of 9.8% in 2004 and a maximum of 33.7% in 2011, of which on average 50% are from the SEF region. On the global scale, the SEF region is thus responsible for a minimum of 2.6% (in 2003) and a maximum of 10.3% (in 2009) of the global MCF emissions.

scholarly journals Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7500 ◽  
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Plant Species ◽  
Mutation Rate ◽  
Plastid Genome ◽  
Gene Content ◽  
High Mutation Rate ◽  
Base Pairs ◽  
Plastid Genomes ◽  
The Family

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

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