Duplication Mechanism Research Articles

Decrease in purifying selection pressures on wheat homoeologous genes: tetraploidization versus hexaploidization.

A series of polyploidizations in higher-order polyploids is the main event affecting gene content in a genome. Each polyploidization event can lead to massive functional divergence because of the subsequent decrease in selection pressure on duplicated genes; however, the causal relationship between multiple rounds of polyploidization and the functional divergence of duplicated genes is poorly understood. We focused on the Triticum-Aegilops complex lineage and compared selection pressure before and after tetraploidization and hexaploidization events. Although both events led to decreased selection pressure on homoeologous gene pairs (compared with diploids and tetraploids), the initial tetraploidization had a greater impact on selection pressure on homoeologous gene pairs than did subsequent hexaploidization. Consistent with this, selection pressure on expression patterns for the initial event relaxed more than those for the subsequent event. Surprisingly, the decreased selection pressure on these homoeologous genes was independent of the existence of in-paralogs within the same subgenome. Wheat homoeologous pairs had different evolutionary consequences compared with orthologs related to other mechanisms (ancient allopolyploidization, ancient autopolyploidization, and small-scale duplication). Furthermore, tetraploidization and hexaploidization also seemed to have different evolutionary consequences. This suggests that homoeologous genes retain unique functions, including functions that are unlikely to be preserved in genes generated by the other duplication mechanisms. We found that their unique functions differed between tetraploidization and hexaploidization (e.g., reproductive and chromosome segregation processes). These findings imply that the substantial number of gene pairs resulting from multiple allopolyploidization events, especially initial tetraploidization, may have been a unique source of functional divergence.

Genomic Analysis and Expression Dynamics of GH3 Genes Under Abiotic Stresses in Brassica rapa

ABSTRACTIn silico characterization of the Gretchen Hagen3 (GH3) gene family is required for understanding phytohormone regulation and stress responses in Brassica rapa to develop the improved stress‐tolerant cultivars. The main objective of this research was to identify the key BrGH3 genes under different abiotic stresses. Using bioinformatics tools, a total of 27 BrGH3 genes were identified in B. rapa for which phylogenetic relationship, syntenic pairing, conserved motifs, miRNA regulation, and cis‐regulatory elements of BrGH3s were also studied. BrGH3 gene expression has been examined in numerous tissues and under various abiotic and phytohormone stressors. Phylogenetic studies separated BrGH3 genes into three major classes and nine subclasses based on gene functional evolution. Collinearity analysis demonstrated that all BrGH3 genes had syntenic linkage with AtGH3, BnaGH3, and BolGH3, indicating that genome duplication mechanisms were crucial to BrGH3 gene evolution. The expression dynamics of BrGH3 under diverse phytohormonal stresses methyl jasmonate (MeJA), auxin (IAA), abscisic acid (ABA), gibberellic acid (GA), and salicylic acid (SA) at different time intervals suggest that BrGH3‐5.1 has a consistently greater expression than other BrGH3 genes. Under salt, drought, and low temperature stress, BrGH3‐1 and BrGH3‐4 genes expressed comparatively higher. The findings suggest that five genes (BrGH3‐5.1, BrGH3‐5.2, BrGH3‐15, BrGH3‐17.2, and BrGH3‐19) have a key role in inducing broad stress resilience. These results can be beneficial in developing stress‐tolerant varieties of Chinese cabbage.

Genome-Wide Analysis of MYB Gene Family in Chrysanthemum ×morifolium Provides Insights into Flower Color Regulation.

MYBs constitute the second largest transcription factor (TF) superfamily in flowering plants with substantial structural and functional diversity, which have been brought into focus because they affect flower colors by regulating anthocyanin biosynthesis. Up to now, the genomic data of several Chrysanthemum species have been released, which provides us with abundant genomic resources for revealing the evolution of the MYB gene family in Chrysanthemum species. In the present study, comparative analyses of the MYB gene family in six representative species, including C. lavandulifolium, C. seticuspe, C. ×morifolium, Helianthus annuus, Lactuca sativa, and Arabidopsis thaliana, were performed. A total of 1104 MYBs, which were classified into four subfamilies and 35 lineages, were identified in the three Chrysanthemum species (C. lavandulifolium, C. seticuspe, and C. ×morifolium). We found that whole-genome duplication and tandem duplication are the main duplication mechanisms that drove the occurrence of duplicates in CmMYBs (particularly in the R2R3-MYB subfamily) during the evolution of the cultivated chrysanthemums. Sequence structure and selective pressure analyses of the MYB gene family revealed that some of R2R3-MYBs were subjected to positive selection, which are mostly located on the distal telomere segments of the chromosomes and contain motifs 7 and 8. In addition, the gene expression analysis of CmMYBs in different organs and at various capitulum developmental stages of C. ×morifolium indicated that CmMYBS2, CmMYB96, and CmMYB109 might be the negative regulators for anthocyanin biosynthesis. Our results provide the phylogenetic context for research on the genetic and functional evolution of the MYB gene family in Chrysanthemum species and deepen our understanding of the regulatory mechanism of MYB TFs on the flower color of C. ×morifolium.

Duplicate Gene Expression and Possible Mechanisms of Paralog Retention During Bacterial Genome Expansion.

Gene duplication contributes to the evolution of expression and the origin of new genes, but the relative importance of different patterns of duplicate gene expression and mechanisms of retention remains debated and particularly poorly understood in bacteria. Here, we investigated gene expression patterns for two lab strains of the cyanobacterium Acaryochloris marina with expanding genomes that contain about 10-fold more gene duplicates compared with most bacteria. Strikingly, we observed a generally stoichiometric pattern of greater combined duplicate transcript dosage with increased gene copy number, in contrast to the prevalence of expression reduction reported for many eukaryotes. We conclude that increased transcript dosage is likely an important mechanism of initial duplicate retention in these bacteria and may persist over long periods of evolutionary time. However, we also observed that paralog expression can diverge rapidly, including possible functional partitioning, for which different copies were respectively more highly expressed in at least one condition. Divergence may be promoted by the physical separation of most Acaryochloris duplicates on different genetic elements. In addition, expression pattern for ancestrally shared duplicates could differ between strains, emphasizing that duplicate expression fate need not be deterministic. We further observed evidence for context-dependent transcript dosage, where the aggregate expression of duplicates was either greater or lower than their single-copy homolog depending on physiological state. Finally, we illustrate how these different expression patterns of duplicated genes impact Acaryochloris biology for the innovation of a novel light-harvesting apparatus and for the regulation of recA paralogs in response to environmental change.

Deduplication using Cloud Computing

There has been decreased reliance on the deployment and maintenance of local storages as the cloud infrastructure has been consistently getting improved over time. The paradigm shift in the data storage department from local storages to cloud solutions has been aggressive. This is due to the fact that the cloud solution allows for a much convenient and hassle free experience that can allow for a much better handling and perseverance of data. There are a large number of organizations that utilize these services of which large number of employees access a singular file that leads to a lot of duplicates. The duplicates can take up unnecessary space which can be problematic with limited space and expensive online storage options. Therefore, there is a need for a de duplication mechanism where the duplicates on a shared cloud storage can be eliminated to improve experience and reduce storage consumption. The proposed approach utilizes the Amazon RDS approach which achieves highly satisfactory results. Keywords: Data Deduplication; Cloud Storage, Amazon RDS. Cloud computing, cloud solution, reliability, load balancing, encryption, secure de-duplication, data integrity.

ApproxDup: Developing an Approximate Instruction Duplication Mechanism for Efficient SDC Detection in GPGPUs

ApproxDup: Developing an Approximate Instruction Duplication Mechanism for Efficient SDC Detection in GPGPUs

Characterizing PALB2 intragenic duplication breakpoints in a triple-negative breast cancer case using long-read sequencing.

Accurate identification and characterization of Large Genomic Rearrangements (LGR), especially duplications, are crucial for precise diagnosis and risk assessment. In this report, we characterized an intragenic duplication breakpoint of PALB2 to determine its pathogenicity significance. A 52-year-old female with triple-negative breast cancer was diagnosed with a novel PALB2 LGR. An efficient and accurate methodology was applied, combining long-read sequencing and transcript analysis for the rapid characterization of the duplication. Duplication of exons 5 and 6 of PALB2 was validated by transcript analysis. Long-read sequencing enabled the localization of breakpoints within Alu elements, providing insights into the mechanism of duplication via non-allelic homologous recombination. Using our combined methodology, we reclassified the PALB2 duplication as a pathogenic variant. This reclassification suggests a possible causative link between this specific genetic alteration and the aggressive phenotype of the patient.

Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints.

Gene duplication is recognized as a critical process in genome evolution; however, many questions about this process remain unanswered. Although gene duplicability has been observed to differ by duplication mechanism and evolutionary rate, there is so far no broad characterization of its determinants. Many features correlate with this difference in duplicability; however, our ability to exploit these observations to advance our understanding of the role of duplication in evolution is hampered by limitations within existing work. In particular, the existence of methodological differences across studies impedes meaningful comparison. Here, we use consistent definitions of duplicability in the human lineage to explore these associations, allow resolution of the impact of confounding factors, and define the overall relevance of individual features. Using a classifier approach and controlling for the confounding effect of duplicate longevity, we find a subset of gene features important in differentiating genes duplicable by small-scale duplication from those duplicable by whole-genome duplication, revealing critical roles for gene dosage and expression costs in duplicability. We further delve into patterns of functional enrichment and find a lack of constraint on duplicate retention in any context for genes duplicable by small-scale duplication.

Consolidating Industrial Small Files Using Robust Graph Clustering

Small file management is widely encountered in industrial areas. Consolidating small files can benefit the performance of the data management system. Many existing consolidation solutions fail to realize the importance of a proper consolidation schema. Therefore, they use very primitive and ineffective schemas. In this paper, we focus on proposing an effective and robust consolidation schema. Unlike most of the existing solutions that only focus on the historical workload, we consider the workload uncertainty issue and propose a graph-clustering-based solution that is more robust to workload uncertainty in the future. To do this, we introduce robust optimization, a mathematical model that provides theoretical support for solving uncertainty issues. Then, we demonstrate that the robustness of the consolidation schema can be achieved using a graph clustering algorithm with a duplication mechanism. Since duplication leads to data redundancy, we propose a parameter to control the redundancy and the robustness of the schema. We also propose two algorithms to estimate the parameter automatically. Experimental results on both the synthetic and real-life data sets show the effectiveness of our algorithm.

Reliability, Rental-Cost and Energy-Aware Multi-Workflow Scheduling on Multi-Cloud Systems

Computationally intensive applications with a wide range of requirements are advancing to cloud computing platforms. However, with the growing demands from users, cloud providers are not always able to provide all the prerequisites of the application. Hence, flexible computation and storage systems, such as multi-cloud systems, emerged as a suitable solution. Different charging mechanisms, vast resource configuration, different energy consumption, and reliability are the key issues for multi-cloud systems. To address these issues, we propose a multi-workflow scheduling framework for multi-cloud systems, intending to lower the monetary cost and energy consumption while enhancing the reliability of application execution. Our proposed platform presents different methods (utilizing resource gaps, the DVFS utilized method, and a task duplication mechanism) to ensure each application's requirement. The Weibull distribution is used to model task reliability at different resource fault rates and fault behavior. Various synthetic workflow applications are used to perform simulation experiments. The results of the performance evaluation demonstrated that our proposed algorithms outperform (in the terms of resource rental cost, efficient energy consumption, and improved reliability) state-of-the-art algorithms for multi-cloud systems.

Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat.

Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.

Diversification processes of teleost intron-less opsin genes

Opsins are universal photosensitive proteins in animals. Vertebrates have a variety of opsin genes for visual and non-visual photoreceptions. Analysis of the gene structures shows that most opsin genes have introns in their coding regions. However, teleosts exceptionally have several intron-less opsin genes that are presumed to have been duplicated by an RNA-based gene duplication mechanism, retroduplication. Among these retrogenes, we focused on the Opn4 (melanopsin) gene responsible for non-image-forming photoreception. Many teleosts have five Opn4 genes including one intron-less gene, which is speculated to have been formed from a parental intron-containing gene in the Actinopterygii. In this study, to reveal the evolutionary history of Opn4 genes, we analyzed them in teleost (zebrafish and medaka) and non-teleost (bichir, sturgeon, and gar) fishes. Our synteny analysis suggests that the intron-less Opn4 gene emerged by retroduplication after the branching of the bichir lineage. In addition, our biochemical and histochemical analyses showed that, in the teleost lineage, the newly acquired intron-less Opn4 gene became abundantly used without substantial changes in the molecular properties of the Opn4 protein. This stepwise evolutionary model of Opn4 genes is quite similar to that of rhodopsin genes in the Actinopterygii. The unique acquisition of rhodopsin and Opn4 retrogenes would have contributed to the diversification of the opsin gene repertoires in the Actinopterygii and the adaptation of teleosts to various aquatic environments.

Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

BackgroundIn the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.ResultsOur research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations.ConclusionsThis study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.

Promoter evolution of mammalian gene duplicates

BackgroundGene duplication is thought to be a central process in evolution to gain new functions. The factors that dictate gene retention following duplication as well paralog gene divergence in sequence, expression and function have been extensively studied. However, relatively little is known about the evolution of promoter regions of gene duplicates and how they influence gene duplicate divergence. Here, we focus on promoters of paralog genes, comparing their similarity in sequence, in the sets of transcription factors (TFs) that bind them, and in their overall promoter architecture.ResultsWe observe that promoters of recent duplications display higher sequence similarity between them and that sequence similarity rapidly declines between promoters of more ancient paralogs. In contrast, similarity in cis-regulation, as measured by the set of TFs that bind promoters of both paralogs, does not simply decrease with time from duplication and is instead related to promoter architecture—paralogs with CpG Islands (CGIs) in their promoters share a greater fraction of TFs, while CGI-less paralogs are more divergent in their TF binding set.Focusing on recent duplication events and partitioning them by their duplication mechanism enables us to uncover promoter properties associated with gene retention, as well as to characterize the evolution of promoters of newly born genes: In recent retrotransposition-mediated duplications, we observe asymmetry in cis-regulation of paralog pairs: Retrocopy genes are lowly expressed and their promoters are bound by fewer TFs and are depleted of CGIs, in comparison with the original gene copy. Furthermore, looking at recent segmental duplication regions in primates enable us to compare successful retentions versus loss of duplicates, showing that duplicate retention is associated with fewer TFs and with CGI-less promoter architecture.ConclusionsIn this work, we profiled promoters of gene duplicates and their inter-paralog divergence. We also studied how their characteristics are associated with duplication time and duplication mechanism, as well as with the fate of these duplicates. These results underline the importance of cis-regulatory mechanisms in shaping the evolution of new genes and their fate following duplication.

Multi-Connectivity-Based Adaptive Fractional Packet Duplication in Cellular Networks

Mobile networks of the fifth generation have stringent requirements for data throughput, latency and reliability. Dual or multi-connectivity is implemented to meet the mobility requirements for certain essential 5G use cases, and this ensures the user’s connection to one or more radio links. Packet duplication (PD) over multi-connectivity is a method of compensating for lost packets by reducing re-transmissions on the same erroneous wireless channel. Utilizing two or more uncorrelated links, a high degree of availability can be attained with this strategy. However, complete packet duplication is inefficient and frequently unnecessary. The wireless channel conditions can change frequently and not allow for a PD. We provide a novel adaptive fractional packet duplication (A-FPD) mechanism for enabling and disabling packet duplication based on a variety of parameters. The signal-to-interference-plus-noise ratio (SINR) and fade duration outage probability (FDOP) are important performance indicators for wireless networks and are used to evaluate and contrast several packet duplication scenarios. Using ns-3 and MATLAB, we present our simulation results for the multi-connectivity and proposed A-FPD schemes. Our technique merely duplicates enough packets across multiple connections to meet the outage criteria.

Ras protein abundance correlates with Ras isoform mutation patterns in cancer

Activating mutations of Ras genes are often observed in cancer. The protein products of the three Ras genes are almost identical. However, for reasons that remain unclear, KRAS is far more frequently mutated than the other Ras isoforms in cancer and RASopathies. We have quantified HRAS, NRAS, KRAS4A and KRAS4B protein abundance across a large panel of cell lines and healthy tissues. We observe consistent patterns of KRAS > NRAS»HRAS protein expression in cells that correlate with the rank order of Ras mutation frequencies in cancer. Our data provide support for the model of a sweet-spot of Ras dosage mediating isoform-specific contributions to cancer and development. We suggest that in most cases, being the most abundant Ras isoform correlates with occupying the sweet-spot and that HRAS and NRAS expression is usually insufficient to promote oncogenesis when mutated. However, our results challenge the notion that rare codons mechanistically underpin the predominance of KRAS mutant cancers. Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage.

Spiking neural P systems without duplication

Spiking neural P systems (SN P systems, 2006) provide an abstraction of the structure and function of nervous systems and neurons. Many variants of such systems have interesting computational properties, usually assuming that their basic elements, spikes, are propagated from one neuron to other neuron(s) in a broadcast way, sending copies to all postsynaptic neurons at the same time. By removing such a mechanism of duplication, we propose a new class of these systems: SN P systems without duplication (SNP-WOD systems), in which only one of the postsynaptic neurons can get the spikes produced when the origin neuron fires. To keep the necessary number of spikes present in the system during computation, the amplification of pulses during the firing of spiking rules is allowed, to produce a number exceeding that consumed. To control the flow direction of spikes, channel labels are introduced to mark different synapses. SNP-WOD systems are proved to be universal in the generation of numbers. A small universal SNP-WOD system is built using 25 neurons for computing functions.

A recent burst of gene duplications in Triticeae

Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement. The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years, but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated. Here, we found that a recent burst of gene duplications (hereafter abbreviated as the RBGD) has probably occurred in all sequenced Triticeae species. Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element (TE) activity may have been involved in generating the RBGD. We also characterized the duplication timing, retention pattern, diversification, and expression of the duplicates following the evolution of Triticeae. Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat. Moreover, several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat. Our results provide insights into a unique source of gene duplicates in Triticeae species, which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.

Mitogenomes of Accipitriformes and Cathartiformes Were Subjected to Ancestral and Recent Duplications Followed by Gradual Degeneration.

The rearrangement of 37 genes with one control region, firstly identified in Gallus gallus mitogenome, is believed to be ancestral for all Aves. However, mitogenomic sequences obtained in recent years revealed that many avian mitogenomes contain duplicated regions that were omitted in previous genomic versions. Their evolution and mechanism of duplication are still poorly understood. The order of Accipitriformes is especially interesting in this context because its representatives contain a duplicated control region in various stages of degeneration. Therefore, we applied an appropriate PCR strategy to look for duplications within the mitogenomes of the early diverged species Sagittarius serpentarius and Cathartiformes, which is a sister order to Accipitriformes. The analyses revealed the same duplicated gene order in all examined taxa and the common ancestor of these groups. The duplicated regions were subjected to gradual degeneration and homogenization during concerted evolution. The latter process occurred recently in the species of Cathartiformes as well as in the early diverged lineages of Accipitriformes, that is, Sagittarius serpentarius and Pandion haliaetus. However, in other lineages, that is, Pernis ptilorhynchus, as well as representatives of Aegypiinae, Aquilinae, and five related subfamilies of Accipitriformes (Accipitrinae, Circinae, Buteoninae, Haliaeetinae, and Milvinae), the duplications were evolving independently for at least 14–47 Myr. Different portions of control regions in Cathartiformes showed conflicting phylogenetic signals indicating that some sections of these regions were homogenized at a frequency higher than the rate of speciation, whereas others have still evolved separately.

Comparative and evolutionary analyses reveal conservation and divergence of the notch pathway in lophotrochozoa

Lophotrochozoan species exhibit wide morphological diversity; however, the molecular basis underlying this diversity remains unclear. Here, we explored the evolution of Notch pathway genes across 37 metazoan species via phylogenetic and molecular evolutionary studies with emphasis on the lophotrochozoans. We displayed the components of Notch pathway in metazoans and found that Delta and Hes/Hey-related genes, as well as their functional domains, are duplicated in lophotrochozoans. Comparative transcriptomics analyses allow us to pinpoint sequence divergence of multigene families in the Notch signalling pathway. We identified the duplication mechanism of a mollusc-specific gene, Delta2, and found it displayed complementary expression throughout development. Furthermore, we found the functional diversification not only in expanded genes in the Notch pathway (Delta and Hes/Hey-related genes), but also in evolutionary conservative genes (Notch, Presenilin, and Su(H)). Together, this comprehensive study demonstrates conservation and divergence within the Notch pathway, reveals evolutionary relationships among metazoans, and provides evidence for the occurrence of developmental diversity in lophotrochozoans, as well as a basis for future gene function studies.