scholarly journals Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region

2021 ◽  
Vol 12 ◽  
Author(s):  
Neng Wei ◽  
Oscar A. Pérez-Escobar ◽  
Paul M. Musili ◽  
Wei-Chang Huang ◽  
Jun-Bo Yang ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Large Scale ◽  
Structural Variations ◽  
Inverted Repeat Region ◽  
Sister Relationship ◽  
Comparative Analyses ◽  
Coding Regions ◽  
Plastome Evolution ◽  
First Time ◽  
Range Of Variation

With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.

scholarly journals The evolution of chloroplast genome structure in ferns

Genome ◽  
2010 ◽  
Vol 53 (9) ◽  
pp. 731-738 ◽  
Author(s):  
Paul G. Wolf ◽  
Jessie M. Roper ◽  
Aaron M. Duffy
Keyword(s):  
Large Scale ◽  
Common Ancestor ◽  
Genome Structure ◽  
Intron Loss ◽  
Seed Plants ◽  
Plant Structure ◽  
The Core ◽  
Plastome Evolution ◽  
The Common ◽  
First Time

The plastid genome (plastome) is a rich source of phylogenetic and other comparative data in plants. Most land plants possess a plastome of similar structure. However, in a major group of plants, the ferns, a unique plastome structure has evolved. The gene order in ferns has been explained by a series of genomic inversions relative to the plastome organization of seed plants. Here, we examine for the first time the structure of the plastome across fern phylogeny. We used a PCR-based strategy to map and partially sequence plastomes. We found that a pair of partially overlapping inversions in the region of the inverted repeat occurred in the common ancestor of most ferns. However, the ancestral (seed plant) structure is still found in early diverging branches leading to the osmundoid and filmy fern lineages. We found that a second pair of overlapping inversions occurred on a branch leading to the core leptosporangiates. We also found that the unique placement of the gene matK in ferns (lacking a flanking intron) is not a result of a large-scale inversion, as previously thought. This is because the intron loss maps to an earlier point on the phylogeny than the nearby inversion. We speculate on why inversions may occur in pairs and what this may mean for the dynamics of plastome evolution.

scholarly journals A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes

2020 ◽  
Vol 12 (10) ◽  
pp. 1841-1857
Author(s):  
Luiz Augusto Cauz-Santos ◽  
Zirlane Portugal da Costa ◽  
Caroline Callot ◽  
Stéphane Cauet ◽  
Maria Imaculada Zucchi ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Inverted Repeat ◽  
Evolutionary History ◽  
Rare Event ◽  
Repeat Region ◽  
Inverted Repeat Region ◽  
Chloroplast Genomes ◽  
The Family ◽  
First Time ◽  
Phylogenomic Study

Abstract Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with ∼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in Passiflora capsularis and Passiflora costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.

scholarly journals Plastome analysis unveils Inverted Repeat (IR) expansion and positive selection in Sea Lavenders (Limonium, Plumbaginaceae, Limonioideae, Limonieae)

PhytoKeys ◽  
2021 ◽  
Vol 175 ◽  
pp. 121-139
Author(s):  
Ashwini M. Darshetkar ◽  
Satish Maurya ◽  
Changyoung Lee ◽  
Badamtsetseg Bazarragchaa ◽  
Gantuya Batdelger ◽  
...  
Keyword(s):  
Positive Selection ◽  
Inverted Repeat ◽  
Nucleotide Diversity ◽  
Gene Content ◽  
Structural Variations ◽  
The Family ◽  
Time Expansion ◽  
First Time

The genus Limonium, commonly known as Sea Lavenders, is one of the most species-rich genera of the family Plumbaginaceae. In this study, two new plastomes for the genus Limonium, viz. L. tetragonum and L. bicolor, were sequenced and compared to available Limonium plastomes, viz. L. aureum and L. tenellum, to understand the gene content and structural variations within the family. The loss of the rpl16 intron and pseudogenisation of rpl23 was observed. This study reports, for the first time, expansion of the IRs to include the ycf1 gene in Limonium plastomes, incongruent with previous studies. Two positively selected genes, viz. ndhF and ycf2, were identified. Furthermore, putative barcodes are proposed for the genus, based on the nucleotide diversity of four Limonium plastomes.

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.

scholarly journals Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

2021 ◽  
Vol 7 (3) ◽  
pp. 47
Author(s):  
Marios Lange ◽  
Rodiola Begolli ◽  
Antonis Giakountis
Keyword(s):  
Disease Onset ◽  
Cancer Genome ◽  
Driver Mutations ◽  
Nucleotide Polymorphisms ◽  
Structural Variations ◽  
Coding Regions ◽  
Functional Variants ◽  
Coding Variants ◽  
Clinical Potential

The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.

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 3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

2020 ◽  
Vol 49 (D1) ◽  
pp. D38-D46
Author(s):  
Kyukwang Kim ◽  
Insu Jang ◽  
Mooyoung Kim ◽  
Jinhyuk Choi ◽  
Min-Seo Kim ◽  
...  
Keyword(s):  
Cell Line ◽  
Large Scale ◽  
Three Dimensional ◽  
Cancer Cell Line ◽  
Cancer Genome ◽  
Structural Variations ◽  
3D Genome ◽  
Tightly Coupled ◽  
Regulatory Effects ◽  
The Impact

Abstract Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene expression. However, unraveling the pathogenicity of the 3D cancer genome remains a challenge since closer examinations have been greatly limited due to the lack of appropriate tools specialized for disorganized higher-order chromatin structure. Here, we updated a 3D-genome Interaction Viewer and database named 3DIV by uniformly processing ∼230 billion raw Hi-C reads to expand our contents to the 3D cancer genome. The updates of 3DIV are listed as follows: (i) the collection of 401 samples including 220 cancer cell line/tumor Hi-C data, 153 normal cell line/tissue Hi-C data, and 28 promoter capture Hi-C data, (ii) the live interactive manipulation of the 3D cancer genome to simulate the impact of structural variations and (iii) the reconstruction of Hi-C contact maps by user-defined chromosome order to investigate the 3D genome of the complex genomic rearrangement. In summary, the updated 3DIV will be the most comprehensive resource to explore the gene regulatory effects of both the normal and cancer 3D genome. ‘3DIV’ is freely available at http://3div.kr.

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