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15 papers · ranked by Valyu relevance

01
PPubMed9 Nov 2019
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements
Benjamin R Karin, Tony Gamble, Todd R Jackman, Nicolas Vidal
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors.…
93relevance
02
BbioRxiv15 Jun 2019
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements
Benjamin R. Karin, Tony Gamble, Todd R. Jackman
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors.…
86relevance
03
PPubMed6 Feb 2007
Splicing and the Evolution of Proteins in Mammals Splicing and the Evolution of Proteins
Joanna L Parmley, Araxi O Urrutia, Lukasz Potrzebowski, Henrik Kaessmann + 2 more
It is often supposed that a protein's rate of evolution and its amino acid content are determined by the function and anatomy of the protein. Here we examine an alternative possibility, namely that the requirement to specify in the unprocessed RNA, in the vicinity of intron-exon boundaries, information necessary for…
82relevance
04
BbioRxiv5 Apr 2022
Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor
Satoshi Fukuchi, Tamotsu Noguchi, Hiroto Anbo, Keiichi Homma
Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, while the typical eukaryotic protein is comprised of multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has…
79relevance
05
PPubMed19 Dec 2022
Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor
Satoshi Fukuchi, Tamotsu Noguchi, Hiroto Anbo, Keiichi Homma + 1 more
'Jun Gojobori'] Title: Abstract Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, whereas the typical eukaryotic protein comprises multiple SDs and IDRs. How eukaryotic proteins evolved to differ…
77relevance
06
PPubMed25 Jan 2010
Mobile DNA and evolution in the 21st century
James A Shapiro
Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome…
76relevance
07
PPubMed6 Dec 2017
Living Organisms Author Their Read-Write Genomes in Evolution
James A. Shapiro, Andrés Moya
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii)…
72relevance
08
PPubMed20 Oct 2008
Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences Origin of Split Gene Structure
Rahul Regulapati, Ashwini Bhasi, Chandan Kumar Singh, Periannan Senapathy + 1 more
'Periannan Senapathy' 'Dawn Field'] The mechanism by which protein-coding portions of eukaryotic genes came to be separated by long non-coding stretches of DNA, and the purpose for this perplexing arrangement, have remained unresolved fundamental biological problems for three decades. We report here a plausible…
70relevance
09
AarXiv2 Jul 2024
Reassessing the exon–foldon correspondence using frustration analysis
Ezequiel A. Galpern, Hana Jaafari, Carlos Bueno, Peter G. Wolynes + 1 more
'Diego U. Ferreiro'] Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron organization and extensive protein sequence data, we explore exon…
65relevance
10
AarXiv2016
Simplification, innateness, and the absorption of meaning from context: how novelty arises from gradual network evolution
Adi Livnat
The theory of interaction-based evolution argues that, at the most basic level of analysis, there is a third alternative for how adaptive evolution works besides a) accidental mutation and natural selection and b) Lamarckism, namely, c) information provided by natural selection on the fit between the organism and its…
62relevance
11
BbioRxiv1 Mar 2016
Core Genes Evolve Rapidly in the Long-term Evolution Experiment with *Escherichia coli*
Rohan Maddamsetti, Philip J. Hatcher, Barry L. Williams, Richard E. Lenski
Conserved genes evolve slowly in nature, by definition, but we find that some conserved genes are among the fastest-evolving genes in the long-term evolution experiment with Escherichia coli (LTEE). We identified the set of almost 2000 core genes shared among sixty clinical, environmental, and laboratory strains of E.…
61relevance
12
BbioRxiv18 Mar 2018
Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya
Irma Lozada-Chávez, Peter F. Stadler, Sonja J. Prohaska
The impact of spliceosomal introns on genome and organismal evolution remains puzzling. Here, we investigated the correlative associations among genome-wide features of introns from protein-coding genes (e.g., size, density, genome-content, repeats), genome size and multicellular complexity on 461 eukaryotes. Thus, we…
61relevance
13
AarXiv2022
Transcriptome Complexities Across Eukaryotes
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
59relevance
14
AarXiv2021
Chromosomal rearrangements as a source of local adaptation in island Drosophila
Brandon A. Turner, Theresa R. Miorin, Nicholas B. Stewart, Robert W. Reid + 2 more
The genetic response to shifting selective pressures remains one of the most fundamental questions in evolutionary theory. How does genetic variation appear and contribute to phenotypic changes during sudden or extreme shifts in habitat [1]? Among the potential genetic responders to selection, SNPs have received ready…
58relevance
15
BbioRxiv29 Jun 2020
Functional and structural basis of extreme non-coding conservation in vertebrate mRNA 5’ untranslated regions
Gun Woo Byeon, Elif Sarinay Cenik, Lihua Jiang, Hua Tang + 2 more
The lack of RNA-level knowledge about extreme conservation in the genome remains a major gap in our understanding of the evolution of gene regulation. While previous findings have mainly focused on the role of extreme conservation in transcriptional regulation, its implications for RNA biology remains largely…
55relevance

Results for rapidly evolving long exons

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Splicing and the Evolution of Proteins in Mammals Splicing and the Evolution of Proteins

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Mobile DNA and evolution in the 21st century

Living Organisms Author Their Read-Write Genomes in Evolution

Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences Origin of Split Gene Structure

Reassessing the exon–foldon correspondence using frustration analysis

Simplification, innateness, and the absorption of meaning from context: how novelty arises from gradual network evolution

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

Transcriptome Complexities Across Eukaryotes

Chromosomal rearrangements as a source of local adaptation in island Drosophila

Functional and structural basis of extreme non-coding conservation in vertebrate mRNA 5’ untranslated regions

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Splicing and the Evolution of Proteins in Mammals Splicing and the Evolution of Proteins

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Mobile DNA and evolution in the 21st century

Living Organisms Author Their Read-Write Genomes in Evolution

Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences Origin of Split Gene Structure

Reassessing the exon–foldon correspondence using frustration analysis

Simplification, innateness, and the absorption of meaning from context: how novelty arises from gradual network evolution

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

Transcriptome Complexities Across Eukaryotes

Chromosomal rearrangements as a source of local adaptation in island Drosophila

Functional and structural basis of extreme non-coding conservation in vertebrate mRNA 5’ untranslated regions

Results for rapidly evolving long exons

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Splicing and the Evolution of Proteins in Mammals Splicing and the Evolution of Proteins

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Mobile DNA and evolution in the 21st century

Living Organisms Author Their Read-Write Genomes in Evolution

Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences Origin of Split Gene Structure

Reassessing the exon–foldon correspondence using frustration analysis

Simplification, innateness, and the absorption of meaning from context: how novelty arises from gradual network evolution

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with *Escherichia coli*

Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

Transcriptome Complexities Across Eukaryotes

Chromosomal rearrangements as a source of local adaptation in island Drosophila

Functional and structural basis of extreme non-coding conservation in vertebrate mRNA 5’ untranslated regions

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Splicing and the Evolution of Proteins in Mammals Splicing and the Evolution of Proteins

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

Mobile DNA and evolution in the 21st century

Living Organisms Author Their Read-Write Genomes in Evolution

Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences Origin of Split Gene Structure

Reassessing the exon–foldon correspondence using frustration analysis

Simplification, innateness, and the absorption of meaning from context: how novelty arises from gradual network evolution

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with *Escherichia coli*

Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

Transcriptome Complexities Across Eukaryotes

Chromosomal rearrangements as a source of local adaptation in island Drosophila

Functional and structural basis of extreme non-coding conservation in vertebrate mRNA 5’ untranslated regions

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli