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 Extensive Shifts from Cis- to Trans-splicing of Gymnosperm Mitochondrial Introns

2020 ◽  
Vol 37 (6) ◽  
pp. 1615-1620
Author(s):  
Wenhu Guo ◽  
Andan Zhu ◽  
Weishu Fan ◽  
Robert P Adams ◽  
Jeffrey P Mower
Keyword(s):  
Common Ancestor ◽  
Vascular Plant ◽  
Plant Mitochondria ◽  
Intron Loss ◽  
Seed Plants ◽  
Diverse Species ◽  
Rnaseq Data ◽  
Trans Splicing ◽  
The Common ◽  
Mitochondrial Introns

Abstract Hundreds of plant mitogenomes have been sequenced from angiosperms, but relatively few mitogenomes are available from its sister lineage, gymnosperms. To examine mitogenomic diversity among extant gymnosperms, we generated draft mitogenomes from 11 diverse species and compared them with four previously published mitogenomes. Examined mitogenomes from Pinaceae and cycads retained all 41 protein genes and 26 introns present in the common ancestor of seed plants, whereas gnetophyte and cupressophyte mitogenomes experienced extensive gene and intron loss. In Pinaceae and cupressophyte mitogenomes, an unprecedented number of exons are distantly dispersed, requiring trans-splicing of 50–70% of mitochondrial introns to generate mature transcripts. RNAseq data confirm trans-splicing of these dispersed exons in Pinus. The prevalence of trans-splicing in vascular plant lineages with recombinogenic mitogenomes suggests that genomic rearrangement is the primary cause of shifts from cis- to trans-splicing in plant mitochondria.

A Study of Contemporary System Performance Testing Framework

2018 ◽  
pp. 7563-7576
Author(s):  
Alex Ng ◽  
Shiping Chen
Keyword(s):  
System Performance ◽  
Large Scale ◽  
Performance Test ◽  
Performance Testing ◽  
General Purpose ◽  
Testing Framework ◽  
The Core ◽  
Application Logic ◽  
The Common ◽  
Whole Life Cycle

Performance testing is one of the vital activities spanning the whole life cycle of software engineering. As a result, there are a considerable number of performance testing products and open source tools available. It has been observed that most of the existing performance testing products and tools are either too expensive and complicated for small projects, or too specific and simple for diverse performance tests. In this chapter, we will present an overview of existing performance test products/tools, provide a summary of some of the contemporary system performance testing frameworks, and capture the key requirements for a general-purpose performance testing framework. Based on our previous works, we propose a system performance testing framework which is suitable for both simple and small, as well as complicated and large-scale performance testing projects. The core of our framework contains an abstraction to facilitate performance testing by separating the application logic from the common performance testing functionality, and a set of general-purpose data model.

scholarly journals Floral homeotic genes were recruited from homologous MADS-box genes preexisting in the common ancestor of ferns and seed plants

1997 ◽  
Vol 94 (6) ◽  
pp. 2415-2420 ◽  
Author(s):  
T. Munster ◽  
J. Pahnke ◽  
A. Di Rosa ◽  
J. T. Kim ◽  
W. Martin ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Seed Plants ◽  
Homeotic Genes ◽  
Mads Box ◽  
Mads Box Genes ◽  
Floral Homeotic Genes ◽  
The Common ◽  
Floral Homeotic

scholarly journals Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases

2001 ◽  
Vol 183 (2) ◽  
pp. 680-686 ◽  
Author(s):  
Kathryn A. Buss ◽  
David R. Cooper ◽  
Cheryl Ingram-Smith ◽  
James G. Ferry ◽  
David Avram Sanders ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Acetate Kinase ◽  
Active Site Residues ◽  
Methanosarcina Thermophila ◽  
The Core ◽  
Binding Domains ◽  
The Common ◽  
Actin Superfamily

ABSTRACT Acetate kinase, an enzyme widely distributed in theBacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina thermophila acetate kinase bound to ADP through crystallography. As we previously predicted, acetate kinase contains a core fold that is topologically identical to that of the ADP-binding domains of glycerol kinase, hexokinase, the 70-kDa heat shock cognate (Hsc70), and actin. Numerous charged active-site residues are conserved within acetate kinases, but few are conserved within the phosphotransferase superfamily. The identity of the points of insertion of polypeptide segments into the core fold of the superfamily members indicates that the insertions existed in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that directly precedes a conserved glycine residue (Gly-331 in acetate kinase) that binds the α-phosphate of ADP. Structural, biochemical, and geochemical considerations indicate that an acetate kinase may be the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.

scholarly journals Phylogenetic Analysis and Karyotype Evolution in Two Species of Core Gruiformes: Aramides cajaneus and Psophia viridis

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 307 ◽  
Author(s):  
Ivanete de Oliveira Furo ◽  
Rafael Kretschmer ◽  
Patrícia C. M. O’Brien ◽  
Jorge C. Pereira ◽  
Malcolm A. Ferguson-Smith ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Common Ancestor ◽  
Karyotype Evolution ◽  
Molecular Cytogenetics ◽  
Ancestral Karyotype ◽  
The Core ◽  
Fulica Atra ◽  
The Common ◽  
Different Origins

Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by conventional staining or molecular cytogenetics. Due to this, this study aimed to analyze the karyotype of two species (Aramides cajaneus and Psophia viridis) belonging to families Rallidae and Psopiidae, respectively, by comparative chromosome painting. The results show that some chromosome rearrangements in this group have different origins, such as the association of GGA5/GGA7 in A. cajaneus, as well as the fission of GGA4p and association GGA6/GGA7, which place P. viridis close to Fulica atra and Gallinula chloropus. In addition, we conclude that the common ancestor of the core Gruiformes maintained the original syntenic groups found in the putative avian ancestral karyotype.

scholarly journals Molecular Evolution of Auxin-Mediated Root Initiation in Plants

2020 ◽  
Vol 37 (5) ◽  
pp. 1387-1393 ◽  
Author(s):  
Jie Yu ◽  
Yuyun Zhang ◽  
Wu Liu ◽  
Hua Wang ◽  
Shaoting Wen ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Common Ancestor ◽  
Seed Plants ◽  
Root Initiation ◽  
Ceratopteris Richardii ◽  
Molecular Pathway ◽  
Wox Genes ◽  
The Common ◽  
Evolutionary Route ◽  
Root Types

Abstract The root originated independently in euphyllophytes (ferns and seed plants) and lycophytes; however, the molecular evolutionary route of root initiation remains elusive. By analyses of the fern Ceratopteris richardii and seed plants, here we show that the molecular pathway involving auxin, intermediate-clade WUSCHEL-RELATED HOMEOBOX (IC-WOX) genes, and WUSCHEL-clade WOX (WC-WOX) genes could be conserved in root initiation. We propose that the “auxin>IC-WOX>WC-WOX” module in root initiation might have arisen in the common ancestor of euphyllophytes during the second origin of roots, and that this module has further developed during the evolution of different root types in ferns and seed plants.

scholarly journals Expansion of phycobilisome linker gene families in mesophilic red algae

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
JunMo Lee ◽  
Dongseok Kim ◽  
Debashish Bhattacharya ◽  
Hwan Su Yoon
Keyword(s):  
Red Algae ◽  
Common Ancestor ◽  
Nuclear Gene ◽  
Gene Families ◽  
Red Alga ◽  
Gene Duplications ◽  
Porphyridium Purpureum ◽  
The Core ◽  
Photosynthetic Machinery ◽  
The Common

Abstract The common ancestor of red algae (Rhodophyta) has undergone massive genome reduction, whereby 25% of the gene inventory has been lost, followed by its split into the species-poor extremophilic Cyanidiophytina and the broadly distributed mesophilic red algae. Success of the mesophile radiation is surprising given their highly reduced gene inventory. To address this latter issue, we combine an improved genome assembly from the unicellular red alga Porphyridium purpureum with a diverse collection of other algal genomes to reconstruct ancient endosymbiotic gene transfers (EGTs) and gene duplications. We find EGTs associated with the core photosynthetic machinery that may have played important roles in plastid establishment. More significant are the extensive duplications and diversification of nuclear gene families encoding phycobilisome linker proteins that stabilize light-harvesting functions. We speculate that the origin of these complex families in mesophilic red algae may have contributed to their adaptation to a diversity of light environments.

A Study of Contemporary System Performance Testing Framework

2019 ◽  
pp. 1546-1561 ◽  
Author(s):  
Alex Ng ◽  
Shiping Chen
Keyword(s):  
System Performance ◽  
Large Scale ◽  
Performance Test ◽  
Performance Testing ◽  
General Purpose ◽  
Testing Framework ◽  
The Core ◽  
Application Logic ◽  
The Common ◽  
Whole Life Cycle

Performance testing is one of the vital activities spanning the whole life cycle of software engineering. As a result, there are a considerable number of performance testing products and open source tools available. It has been observed that most of the existing performance testing products and tools are either too expensive and complicated for small projects or too specific and simple for diverse performance tests. In this chapter, the authors present an overview of existing performance test products/tools, provide a summary of some of the contemporary system performance testing frameworks, and capture the key requirements for a general-purpose performance testing framework. Based on previous works, the authors propose a system performance testing framework that is suitable for both simple and small as well as complicated and large-scale performance testing projects. The core of the framework contains an abstraction to facilitate performance testing by separating the application logic from the common performance testing functionality and a general-purpose data model.

scholarly journals Adult, intensively socialized wolves show features of attachment behaviour to their handler

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rita Lenkei ◽  
Dóra Újváry ◽  
Viktória Bakos ◽  
Tamás Faragó
Keyword(s):  
Cognitive Abilities ◽  
Common Ancestor ◽  
Social Bonds ◽  
Social Bond ◽  
Secure Base ◽  
The Core ◽  
The Common ◽  
Attachment Behaviour

Abstract Dogs’ attachment towards humans might be the core of their social skillset, yet the origins of their ability to build such a bond are still unclear. Here we show that adult, hand-reared wolves, similarly to dogs, form individualized relationship with their handler. During separation from their handler, wolves, much like family dogs, showed signs of higher-level stress and contact seeking behaviour, compared to when an unfamiliar person left them. They also used their handler as a secure base, suggesting that the ability to form interspecific social bonds could have been present already in the common ancestor of dogs and wolves. We propose that their capacity to form at least some features of attachment with humans may stem from the ability to form social bond with pack members. This might have been then re-directed to humans during early domestication, providing the basis for the evolution of other socio-cognitive abilities in dogs.

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.

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