Manyuan Long
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View article: Sex-biased duplicates are rapidly generated during <i>Drosophila</i> tRNA repertoire evolution
Sex-biased duplicates are rapidly generated during <i>Drosophila</i> tRNA repertoire evolution Open
Eukaryotic genomes encode hundreds of transfer RNA genes ostensibly to ensure efficient translation. How these seemingly redundant tRNA copies arise and are naturally selected in metazoan genomes and populations remains largely unexplored,…
View article: Gadolinium Pollution—A Future Forward Perspective on Human and Environmental Impact
Gadolinium Pollution—A Future Forward Perspective on Human and Environmental Impact Open
The widespread use of gadolinium‐based contrast agents (GBCAs) in magnetic resonance imaging (MRI) has been instrumental in enhancing diagnostic capabilities. However, the potential environmental and human health impacts of gadolinium poll…
View article: Bryophytes hold a larger gene family space than vascular plants
Bryophytes hold a larger gene family space than vascular plants Open
View article: Genetic composition and heterozygosity of gibberellin-induced 2n gametes evaluated by SSR markers in Populus
Genetic composition and heterozygosity of gibberellin-induced 2n gametes evaluated by SSR markers in Populus Open
Not applicable.
View article: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection Open
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. However, their phenotypic impacts and evolutionary patterns over time remain elusive in humans owing to the technical and ethical complexities of functional s…
View article: Subcellular Enrichment Patterns of New Genes in <i>Drosophila</i> Evolution
Subcellular Enrichment Patterns of New Genes in <i>Drosophila</i> Evolution Open
The evolutionary patterns of proteins within subcellular compartments underlie the innovation and diversification foundation of the living eukaryotic organism. The location of proteins in subcellular compartments promotes the formation of …
View article: Applications of Artificial Intelligence in Ophthalmic Diseases
Applications of Artificial Intelligence in Ophthalmic Diseases Open
View article: The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence
The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence Open
Previous evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment by distally duplicated genes is an efficient mechanism for modulati…
View article: Genetic variations in morphology, chromosome number, and physiology of backcross progeny of the triploid hybrid clone ‘Beilinxiongzhu 1#’
Genetic variations in morphology, chromosome number, and physiology of backcross progeny of the triploid hybrid clone ‘Beilinxiongzhu 1#’ Open
This study provides new genetic material with different chromosome compositions, which will contribute to analyzing chromosomal function and integrate the variations in chromosomal dosage into Populus breeding programs.
View article: The Rapid Evolution of De Novo Proteins in Structure and Complex
The Rapid Evolution of De Novo Proteins in Structure and Complex Open
Recent studies in the rice genome-wide have established that de novo genes, evolving from noncoding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their evolution in protein structure over…
View article: High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the <i>Drosophila virilis</i> Subgroup
High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the <i>Drosophila virilis</i> Subgroup Open
High-quality genome assemblies across a range of nontraditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly stu…
View article: One million years of solitude: the rapid evolution of de novo protein structure and complex
One million years of solitude: the rapid evolution of de novo protein structure and complex Open
Recent studies have established that de novo genes, evolving from non-coding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their structural evolution over time remain unclear. Here, we ad…
View article: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. Open
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. However, their phenotypic impacts and evolutionary patterns over time remain elusive in humans due to the technical and ethical complexities of functional stu…
View article: High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the<i>Drosophila virilis</i>sub-group
High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the<i>Drosophila virilis</i>sub-group Open
High-quality genome assemblies across a range of non-traditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly st…
View article: Human Gene Age Dating Reveals an Early and Rapid Evolutionary Construction of the Adaptive Immune System
Human Gene Age Dating Reveals an Early and Rapid Evolutionary Construction of the Adaptive Immune System Open
T cells are a type of white blood cell that play a critical role in the immune response against foreign pathogens through a process called T cell adaptive immunity (TCAI). However, the evolution of the genes and nucleotide sequences involv…
View article: New gene evolution with subcellular expression patterns detected in PacBio-sequenced genomes of<i>Drosophila</i>genus
New gene evolution with subcellular expression patterns detected in PacBio-sequenced genomes of<i>Drosophila</i>genus Open
Previous studies described gene age distributions in the focal species of Drosophila melanogaster . Using third-generation PacBio technology to sequence Drosophila species we investigated gene age distribution in the two subgenera of Droso…
View article: The 3-Dimensional Genome Drives the Evolution of Asymmetric Gene Duplicates via Enhancer Capture-Divergence
The 3-Dimensional Genome Drives the Evolution of Asymmetric Gene Duplicates via Enhancer Capture-Divergence Open
Previous evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment of distally duplicated genes (enhancer capture) is an efficient mec…
View article: Evolution and maintenance of phenotypic plasticity
Evolution and maintenance of phenotypic plasticity Open
We introduce a novel framework for exploring the evolutionary consequences of phenotypic plasticity (adaptive and non-adaptive) integrating both genic and epigenetic effects on phenotype via stochastic differential equations and in-silico …
View article: Evolutionary New Genes in a Growing Paradigm
Evolutionary New Genes in a Growing Paradigm Open
How new genes evolve has become an interesting problem in biology, particularly in evolutionary biology [...]
View article: Gene fusion as an important mechanism to generate new genes in the genus Oryza
Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Background Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. Results We conduct genome-wide interrogations of four Oryza genomes by desi…
View article: Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes
Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes Open
Genes that originate during evolution are an important source of novel biological functions. Retrogenes are functional copies of genes produced by retroduplication and as such are located in different genomic positions. To investigate retr…
View article: Additional file 10 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 10 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 10. Gene structure re-annotation of species-specific fusion gene in four focus species.
View article: Additional file 8 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 8 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 8. The generation patterns of fusion genes.
View article: Additional file 4 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 4 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 4. FPKM of fusion gene and short copy homologs in O. sativa v.g. japonica, O. barthii, O. glaberrima, O. punctate, O. branchyantha and Leersia.
View article: Additional file 7 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 7 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 7. Correlation between the maximum FPKM value of long-homologous copies and the short-homologous copies in four Oryza species.
View article: Additional file 6 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 6 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 6. Correlation of O. japonica fusion gene and its short copies FPKM value in different tissues.
View article: Additional file 2 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 2 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 2. Candidate fusion gene presented in four focus species.
View article: Additional file 9 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 9 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 9. Transposable element retrieved from O. sativa v.g. japonica fusion genes.
View article: Additional file 3 of Gene fusion as an important mechanism to generate new genes in the genus Oryza
Additional file 3 of Gene fusion as an important mechanism to generate new genes in the genus Oryza Open
Additional file 3. Fixation frequency of species-specific fusion gene included in four focus species.
View article: Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in Drosophila
Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in Drosophila Open
Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. Previous work identified a young regulatory duplicate gene in D…