scholarly journals Introns structure patterns of variation in nucleotide composition in Arabidopsis thaliana and rice protein-coding genes

2014 ◽  
Author(s):  
Adrienne Ressayre ◽  
Sylvain Glemin ◽  
Pierre Montalent ◽  
Laurana Serres-Giardi ◽  
Christine Dillmann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Nucleotide Composition ◽  
Coding Region ◽  
Protein Coding ◽  
Plant Genomes ◽  
A Genome ◽  
Wide Range ◽  
Intron Number ◽  
Species Specific ◽  
Range Of Variation

Plant genomes are large, intron-rich and present a wide range of variation in coding region G+C content. Concerning coding regions, a sort of syndrome can be described in plants: the increase in G+C content is associated with both the increase in heterogeneity among genes within a genome and the increase in variation across genes. Taking advantage of the large number of genes composing plant genomes and the wide range of variation in gene intron number, we performed a comprehensive survey of the patterns of variation in G+C content at different scales from the nucleotide level to the genome scale in two species Arabidopsis thaliana and Oryza sativa, comparing the patterns in genes with different intron numbers. In both species, we observed a pervasive effect of gene intron number and location along genes on G+C content, codon and amino acid frequencies suggesting that in both species, introns have a barrier effect structuring G+C content along genes. In external gene regions (located upstream first or downstream last intron), species-specific factors are shaping G+C content while in internal gene regions (surrounded by introns), G+C content is constrained to remain within a range common to both species. In rice, introns appear as a major determinant of gene G+C content while in A. thaliana introns have a weaker but significant effect. The structuring effect of introns in both species is susceptible to explain the G+C content syndrome observed in plants.

Differential Induction of Glutathione Transferases and Glucosyltransferases in Wheat, Maize and Arabidopsis thaliana by Herbicide Safeners

2005 ◽  
Vol 60 (3-4) ◽  
pp. 307-316 ◽  
Author(s):  
Robert Edwards ◽  
Daniele Del Buono ◽  
Michael Fordham ◽  
Mark Skipsey ◽  
Melissa Brazier ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Crop Protection ◽  
Detoxification Enzymes ◽  
Glutathione Transferases ◽  
Wide Range ◽  
Breeding Programmes ◽  
Model Plant Arabidopsis Thaliana ◽  
Herbicide Safeners ◽  
Species Specific ◽  
The Right

Abstract By learning lessons from weed science we have adopted three approaches to make plants more effective in phytoremediation: 1. The application of functional genomics to identify key components involved in the detoxification of, or tolerance to, xenobiotics for use in subsequent genetic engineering/breeding programmes. 2. The rational metabolic engineering of plants through the use of forced evolution of protective enzymes, or alternatively transgenesis of detoxification pathways. 3. The use of chemical treatments which protect plants from herbicide injury. In this paper we examine the regulation of the xenome by herbicide safeners, which are chemicals widely used in crop protection due to their ability to enhance herbicide selectivity in cereals. We demonstrate that these chemicals act to enhance two major groups of phase 2 detoxification enzymes, notably the glutathione transferases and glucosyltransferases, in both cereals and the model plant Arabidopsis thaliana, with the safeners acting in a chemical- and species-specific manner. Our results demonstrate that by choosing the right combination of safener and plant it should be possible to enhance the tolerance of diverse plants to a wide range of xenobiotics including pollutants.

Variability of Echiniscus tristis Gąsiorek & Kristensen, 2018—is morphology sufficient for taxonomic differentiation of Echiniscidae?

Zootaxa ◽  
2019 ◽  
Vol 4701 (1) ◽  
pp. 1-24 ◽  
Author(s):  
TOMASZ BARTYLAK ◽  
ADAM KULPA ◽  
DARIA GROBYS ◽  
MARTA KEPEL ◽  
ANDRZEJ KEPEL ◽  
...  
Keyword(s):  
Dna Sequences ◽  
28S Rrna ◽  
Life Stages ◽  
Significant Genetic Differentiation ◽  
Wide Range ◽  
Microscope Images ◽  
Different Types ◽  
Taxonomic Confusion ◽  
Species Specific ◽  
Range Of Variation

The majority of species in the genus Echiniscus (Heterotardigrada) have been described based on differences in the chaetotaxy or dorsal sculpture. Dorsal sculpture is, in general, considered to be species-specific and not very variable; however, many problems have arisen due to various interpretations of microscope images, which has led to taxonomic confusion in the genus Echiniscus. Conversely, chaetotaxy is generally much easier to interpret, even using low-quality microscope optics. In this study, we emended the description of Madagascan population of Echiniscus tristis Gąsiorek & Kristensen, 2018 that exhibits several different types of chaetotaxy and dorsal sculpture. The analysed specimens were characterised by two types of chaetotaxy, A-C-Dd-E and A-Dd-E, but we also found a wide range of variation in appendage number, shape and length. The observed differences are partly correlated with life stages. Additionally, we analysed DNA sequences of 28S rRNA, ITS-2 and COI of the two main morphotypes, and did not find significant genetic differentiation of the two morphotypes. This highlights the importance of analysing the morphology of both immature stages and adults, as well as of DNA markers in tardigrade species identification. 

scholarly journals The maternal environment interacts with genetic variation in regulating seed dormancy in Arabidopsis thaliana

2017 ◽  
Author(s):  
Envel Kerdaffrec ◽  
Magnus Nordborg
Keyword(s):  
Arabidopsis Thaliana ◽  
Association Study ◽  
Seed Dormancy ◽  
Genome Wide Association Study ◽  
Seed Maturation ◽  
Genome Wide Association ◽  
Maternal Environment ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

AbstractSeed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait. By performing a genome-wide association study (GWAS), we identified several candidate genes that could account for this plasticity, two of which are involved in the photoinduction of germination. Altogether, our results provide insight into both the molecular mechanisms and the evolution of dormancy plasticity, and can serve to improve our understanding of environmentally dependent life-history transitions.HighlightThe effect of low seed-maturation temperatures on seed dormancy is highly variable in Arabidopsis thaliana accessions from Sweden, denoting strong genotype-environment interactions, and a genome-wide association study identified compelling candidates that could account for this plasticity.

scholarly journals Evidence of Recombination among Enteroviruses

1999 ◽  
Vol 73 (10) ◽  
pp. 8741-8749 ◽  
Author(s):  
Juhana Santti ◽  
Timo Hyypiä ◽  
Leena Kinnunen ◽  
Mika Salminen
Keyword(s):  
Genetic Relationships ◽  
Detailed Comparison ◽  
Evolutionary Divergence ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Bootstrap Analysis ◽  
Protein Coding ◽  
Wide Range ◽  
Genetic Clusters ◽  
Genomic Regions

ABSTRACT Human enteroviruses consist of more than 60 serotypes, reflecting a wide range of evolutionary divergence. They have been genetically classified into four clusters on the basis of sequence homology in the coding region of the single-stranded RNA genome. To explore further the genetic relationships between human enteroviruses and to characterize the evolutionary mechanisms responsible for variation, previously sequenced genomes were subjected to detailed comparison. Bootstrap and genetic similarity analyses were used to systematically scan the alignments of complete genomic sequences. Bootstrap analysis provided evidence from an early recombination event at the junction of the 5′ noncoding and coding regions of the progenitors of the current clusters. Analysis within the genetic clusters indicated that enterovirus prototype strains include intraspecies recombinants. Recombination breakpoints were detected in all genomic regions except the capsid protein coding region. Our results suggest that recombination is a significant and relatively frequent mechanism in the evolution of enterovirus genomes.

scholarly journals Phylogenomics for Chagas Disease Vectors of the Rhodnius Genus (Hemiptera, Triatominae): What We Learn From Mito-Nuclear Conflicts and Recommendations

2022 ◽  
Vol 9 ◽  
Author(s):  
Jonathan Filée ◽  
Marie Merle ◽  
Héloïse Bastide ◽  
Florence Mougel ◽  
Jean-Michel Bérenger ◽  
...  
Keyword(s):  
Molecular Data ◽  
Mitochondrial Genes ◽  
Valid Species ◽  
Close Relative ◽  
Protein Coding ◽  
Genome Wide ◽  
A Genome ◽  
Chagas Disease Vectors ◽  
Tree Topologies ◽  
Species Specific

We provide in this study a very large DNA dataset on Rhodnius species including 36 samples representing 16 valid species of the three Rhodnius groups, pictipes, prolixus and pallescens. Samples were sequenced at low-depth with whole-genome shotgun sequencing (Illumina technology). Using phylogenomics including 15 mitochondrial genes (13.3 kb), partial nuclear rDNA (5.2 kb) and 51 nuclear protein-coding genes (36.3 kb), we resolve sticking points in the Rhodnius phylogeny. At the species level, we confirmed the species-specific status of R. montenegrensis and R. marabaensis and we agree with the synonymy of R. taquarussuensis with R. neglectus. We also invite to revisit the species-specific status of R. milesi that is more likely R. nasutus. We proposed to define a robustus species complex that comprises the four close relative species: R. marabaensis, R. montenegrensis, R. prolixus and R. robustus. As Psammolestes tertius was included in the Rhodnius clade, we strongly recommend reclassifying this species as R. tertius. At the Rhodnius group level, molecular data consistently supports the clustering of the pictipes and pallescens groups, more related to each other than they are to the prolixus group. Moreover, comparing mitochondrial and nuclear tree topologies, our results demonstrated that various introgression events occurred in all the three Rhodnius groups, in laboratory strains but also in wild specimens. We demonstrated that introgressions occurred frequently in the prolixus group, involving the related species of the robustus complex but also the pairwise R. nasutus and R. neglectus. A genome wide analysis highlighted an introgression event in the pictipes group between R. stali and R. brethesi and suggested a complex gene flow between the three species of the pallescens group, R. colombiensis, R. pallescens and R. ecuadoriensis. The molecular data supports also a sylvatic distribution of R. prolixus in Brazil (Pará state) and the monophyly of R. robustus. As we detected extensive introgression events and selective pressure on mitochondrial genes, we strongly recommend performing separate mitochondrial and nuclear phylogenies and to take advantages of mito-nuclear conflicts in order to have a comprehensive evolutionary vision of this genus.

scholarly journals Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

2017 ◽  
Author(s):  
Anuj Kumar ◽  
Aditi Chauhan ◽  
Mansi Sharma ◽  
Sai Kumar Kompelli ◽  
Vijay Gahlaut ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Full Length ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Mirna Genes ◽  
Genome Wide ◽  
Varying Length

AbstractSimple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

scholarly journals Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families

2019 ◽  
Vol 11 (11) ◽  
pp. 3309-3325 ◽  
Author(s):  
Wanxiangfu Tang ◽  
Ping Liang
Keyword(s):  
Comparative Genomics ◽  
Gene Function ◽  
Mobile Elements ◽  
Protein Coding ◽  
Dominant Class ◽  
Highly Active ◽  
Macaque Genome ◽  
A Genome ◽  
Orangutan Genome ◽  
Species Specific

Abstract Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution.

scholarly journals Evolutionary selection on synonymous codons in RNA G-quadruplex structural region

2021 ◽  
Author(s):  
Yuming Xu ◽  
Ting Qi ◽  
Zuhong Lu ◽  
Tong Zhou ◽  
Wanjun Gu
Keyword(s):  
Rna Structure ◽  
Nucleotide Composition ◽  
Sequence Information ◽  
Coding Region ◽  
Protein Coding ◽  
Translational Initiation ◽  
Evolutionary Selection ◽  
Synonymous Codons ◽  
G Quadruplex ◽  
Structural Region

ABSTRACTIn addition to the amino acid sequence information, synonymous codons can encode multiple regulatory and structural signals in protein coding region. In this study, we investigated how synonymous codons have been adapted to the formation of RNA G-quadruplex (rG4) structure. We found a universal selective pressure acting on synonymous codons to facilitate rG4 formation in five eukaryotic organisms. While G-rich codons are preferred in rG4 structural region, C-rich codons are selectively unpreferred for rG4 structures. Gene’s codon usage bias, nucleotide composition and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species. Moreover, rG4 structures in translational initiation region showed significantly higher selective pressures than those in translational elongation region. These results bring us another dimension of evolutionary selection on synonymous codons for proper RNA structure and function.

scholarly journals When Bigger Is Better: 3D RNA Profiling of the Developing Head in the Catshark Scyliorhinus canicula

2021 ◽  
Vol 9 ◽  
Author(s):  
Hélène Mayeur ◽  
Maxence Lanoizelet ◽  
Aurélie Quillien ◽  
Arnaud Menuet ◽  
Léo Michel ◽  
...  
Keyword(s):  
Neural Tube Closure ◽  
Digital Model ◽  
Model Organisms ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Rna Profiling ◽  
Scyliorhinus Canicula ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

We report the adaptation of RNA tomography, a technique allowing spatially resolved, genome-wide expression profiling, to a species occupying a key phylogenetic position in gnathostomes, the catshark Scyliorhinus canicula. We focused analysis on head explants at an embryonic stage, shortly following neural tube closure and of interest for a number of developmental processes, including early brain patterning, placode specification or the establishment of epithalamic asymmetry. As described in the zebrafish, we have sequenced RNAs extracted from serial sections along transverse, horizontal and sagittal planes, mapped the data onto a gene reference taking advantage of the high continuity genome recently released in the catshark, and projected read counts onto a digital model of the head obtained by confocal microscopy. This results in the generation of a genome-wide 3D atlas, containing expression data for most protein-coding genes in a digital model of the embryonic head. The digital profiles obtained for candidate forebrain regional markers along antero-posterior, dorso-ventral and left-right axes reproduce those obtained by in situ hybridization (ISH), with expected relative organizations. We also use spatial autocorrelation and correlation as measures to analyze these data and show that they provide adequate statistical tools to extract novel expression information from the model. These data and tools allow exhaustive searches of genes exhibiting any predefined expression characteristic, such a restriction to a territory of interest, thus providing a reference for comparative analyses across gnathostomes. This methodology appears best suited to species endowed with large embryo or organ sizes and opens novel perspectives to a wide range of evo-devo model organisms, traditionally counter-selected on size criterion.

scholarly journals Identification of Cellular Factors Required for SARS-CoV-2 Replication

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3159
Author(s):  
Aleksandra Synowiec ◽  
Malwina Jedrysik ◽  
Wojciech Branicki ◽  
Adrianna Klajmon ◽  
Jing Lei ◽  
...  
Keyword(s):  
Complex Analysis ◽  
Multiorgan Failure ◽  
Severe Disease ◽  
Antiviral Agents ◽  
Interaction Network ◽  
Knock Out ◽  
Interesting Insight ◽  
A Genome ◽  
Wide Range ◽  
Species Specific

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the recently emerged virus responsible for the COVID-19 pandemic. Clinical presentation can range from asymptomatic disease and mild respiratory tract infection to severe disease with lung injury, multiorgan failure, and death. SARS-CoV-2 is the third animal coronavirus to emerge in humans in the 21st century, and coronaviruses appear to possess a unique ability to cross borders between species and infect a wide range of organisms. This is somewhat surprising as, except for the requirement of host cell receptors, cell–pathogen interactions are usually species-specific. Insights into these host–virus interactions will provide a deeper understanding of the process of SARS-CoV-2 infection and provide a means for the design and development of antiviral agents. In this study, we describe a complex analysis of SARS-CoV-2 infection using a genome-wide CRISPR-Cas9 knock-out system in HeLa cells overexpressing entry receptor angiotensin-converting enzyme 2 (ACE2). This platform allows for the identification of factors required for viral replication. This study was designed to include a high number of replicates (48 replicates; 16 biological repeats with 3 technical replicates each) to prevent data instability, remove sources of bias, and allow multifactorial bioinformatic analyses in order to study the resulting interaction network. The results obtained provide an interesting insight into the replication mechanisms of SARS-CoV-2.

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