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104 results for “gene duplications”
Data from: De novo gene birth, horizontal gene transfer and gene duplication as sources of new gene families associated with the origin of a symbiosis in Amanita
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Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.
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Exploring whole-genome duplicate gene retention with complex genetic interaction analysis
<p>Whole-genome duplication<b> </b>has played a central role in genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated and factors that influence the retention of persisting duplicates remain poorly understood. Here, we describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping digenic interactions for a deletion mutant of each paralog and trigenic interactions for the double mutant provides insight into their roles and a quantitative measure of their functional redundancy. Trigenic interaction analysis distinguishes two classes of paralogs, a more functionally divergent subset and another that retained more functional overlap. Gene feature analysis and modeling suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and structural entanglement factors.</p>
Data from: Invasive invertebrates associated with highly duplicated gene content
Invasions of alien species have led to serious problems, including the destruction of native ecosystems. In general, invasive species adapt to novel various environments rapidly, suggesting that they have high genetic diversity that could directly influences environmental adaptability. However, we do not yet know how genomic architecture generates genetic diversity that leads to invasive species. Recent studies showed that the proportion of duplicated genes (PD) in whole animal genomes correlated with environmental variability within habitat. Here, we show that PD and propagule size significantly explain the differences in species categories (invasive species, non-invasive species and parasites). PD correlated negatively with propagule size, and then, based on the residual values of regression of propagule size on PD, invasive species had higher PD values and larger propagule size than non-invasive species whereas parasites had lower PD values and smaller propagule size than others. There were no correlations between invasive species and other genomic factors including genome size, number of genes, and certain gene families. Our results suggest that PD values of a genome might be potential genomic sources producing genetic variations for adaptation to diverse environments. The results also showed that the invasive status of species can be fairly predicted by the residual values of the regression of propagule size on PD. Our innovative approach gives us a measure that can be used to estimate the environmental adaptability of organisms based on genomic data.
Data from: Gene duplication and the evolution of phenotypic diversity in insect societies
Gene duplication is an important evolutionary process thought to facilitate the evolution of phenotypic diversity. We investigated if gene duplication was associated with the evolution of phenotypic differences in a highly social insect, the honeybee Apis mellifera. We hypothesized that the genetic redundancy provided by gene duplication could promote the evolution of social and sexual phenotypes associated with advanced societies. We found a positive correlation between sociality and rate of gene duplications across the Apoidea, indicating that gene duplication may be associated with sociality. We also discovered that genes showing biased expression between A. mellifera alternative phenotypes tended to be found more frequently than expected among duplicated genes than singletons. Moreover, duplicated genes had higher levels of caste-, sex-, behavior-, and tissue-biased expression compared to singletons, as expected if gene duplication facilitated phenotypic differentiation. We also found that duplicated genes were maintained in the A. mellifera genome through the processes of conservation, neofunctionalization, and specialization, but not subfunctionalization. Overall, we conclude that gene duplication may have facilitated the evolution of social and sexual phenotypes, as well as tissue differentiation. Thus this study further supports the idea that gene duplication allows species to evolve an increased range of phenotypic diversity.
Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana
Gene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. Using RNA-seq we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in alpha whole genome duplicates, and 33% of AS events in tandem duplicates, are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this divergence. Conserved events had different frequencies, as only 31% of shared AS events in alpha whole genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative divergence. Analysis of published RNA-seq data from nonsense mediated decay (NMD) mutants indicated that 85% of alpha whole genome duplicates and 89% of tandem duplicates have diverged in their AS-induced NMD. Our results indicate that alternative splicing shows a high degree of divergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative divergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level divergence.
Data from: Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates
Gene duplications can have a major role in adaptation, and gene families underlying chemosensation are particularly interesting due to their essential role in chemical recognition of mates, predators and food resources. Social insects add yet another dimension to the study of chemosensory genomics, as the key components of their social life rely on chemical communication. Still, chemosensory gene families are little studied in social insects. Here we annotated chemosensory protein (CSP) genes from seven ant genomes and studied their evolution. The number of functional CSP genes ranges from 11 to 21 depending on species, and the estimated rates of gene birth and death indicate high turnover of genes. Ant CSP genes include seven conservative orthologous groups present in all the ants, and a group of genes that has expanded independently in different ant lineages. Interestingly, the expanded group of genes has a differing mode of evolution from the orthologous groups. The expanded group shows rapid evolution as indicated by a high dN/dS (nonsynonymous to synonymous changes) ratio, several sites under positive selection and many pseudogenes, whereas the genes in the seven orthologous groups evolve slowly under purifying selection and include only one pseudogene. These results show that adaptive changes have played a role in ant CSP evolution. The expanded group of ant-specific genes is phylogenetically close to a conservative orthologous group CSP7, which includes genes known to be involved in ant nestmate recognition, raising an interesting possibility that the expanded CSPs function in ant chemical communication.
Data from: Gene duplication and co-evolution of G1/S transcription factors specificity in fungi are essential for optimizing cell fitness
Transcriptional regulatory networks play a central role in optimizing cell survival. How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear. Here we experimentally explore how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes. Over 300 G1/S genes are regulated by either one of the two TF complexes, SBF and MBF, which bind to specific DNA binding sequences, SCB and MCB, respectively. Our data suggests that whilst SBF is the likely ancestral regulatory complex, the ancestral DNA binding element is more MCB-like. G1/S network expansion took place by both cis- and trans- co-evolutionary changes in closely related but distinct regulatory sequences. Replacement of the endogenous SBF DNA-binding domain (DBD) with that from more distantly related fungi leads to a contraction of the G1/S network in budding yeast, which also correlates with increased defects in cell growth, cell size, and proliferation. This indicates that expansion of the G1/S network in budding yeast may represent an evolutionary product of selection for cell cycle fitness.
Data from: Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species
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Data from: Gene duplication and co-evolution of G1/S transcription factors specificity in fungi are essential for optimizing cell fitness
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Data from: Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates
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Data from: Gene duplication in an African cichlid adaptive radiation
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Data from: Domain loss facilitates accelerated evolution and neofunctionalization of duplicate snake venom metalloproteinase toxin genes
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Data from: The limited contribution of reciprocal gene loss to increased speciation rates following whole-genome duplication
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Data from: Na+/K+‐ATPase gene duplications in clitellate annelids are associated with freshwater colonization
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Data from: Gene duplication and the evolution of phenotypic diversity in insect societies
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Data from: Origin, evolution, and population genetics of the selfish Segregation distorter gene duplication in European and African populations of Drosophila melanogaster
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Exploring whole-genome duplicate gene retention with complex genetic interaction analysis
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Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana
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Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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