@ChenxinLi2 In general, plus they lead to higher rates of genetic diversity. https://t.co/NV3UcEPOBT And this is different between primary and specialized metabolism. https://t.co/7u5CvIeNlE There are similar papers in Maize, Pine, etc. Usually just a se
“In the absence of functional biochemical evidence, it is difficult to classify gene expression changes between tandem duplicates as true sub-functionalization versus neo-functionalization coupled with intraspecific gene expression variation." https://t.co
“In primary metabolic pathways where variation may be detrimental, this may actually select against the presence of duplicated genes and variable expression patterns." https://t.co/o8Qye3Vj32
“In secondary metabolic pathways where variation is required, duplicates will be maintained and evolve diverse expression patterns.“ https://t.co/o8Qye3Vj32
“I suggest a model in which gene duplication provides raw material for evolution but, at least in metabolic pathways, the biology of the pathway determines the likelihood that duplicated genes are maintained and evolve altered functionality." https://t.co/
“This work shows that the availability of gene duplications and the function of biochemical pathways interact to influence gene expression variation across a diverse array of biological and genetic factors." https://t.co/o8Qye3Vj32
“A potential explanation for increased genetic diversity in the aliphatic glucosinolate biosynthetic pathway may be that gene expression diversity enables response to fluctuations in natural insect populations between different generations." https://t.co/o
Elevated gene expression variation, “suggesting that variation in this pathway may be selected to generate structural diversity." https://t.co/o8Qye3Vj32
“Gene expression variation across the different accessions was distributed such that the enzymatic steps responsible for determining the final chemical structure had elevated gene expression variation.” https://t.co/o8Qye3Vj32
“Pathway level transcript variation for the aliphatic glucosinolate biosynthetic pathway was a dramatic outlier in both accession datasets." https://t.co/o8Qye3Vj32
Duplicated enzymes. “However, biochemical analysis of these gene families shows that they have already undergone neo-functionalization, creating new biosynthetic activities in the duplicate enzymes." https://t.co/o8Qye3Vj32
Duplicated enzymes. “This tempts the conclusion that these gene families are undergoing genetic sub-functionalization.” https://t.co/o8Qye3Vj32
“Within the aliphatic glucosinolate biosynthetic pathway, increased transcript variation across naturally variable Arabidopsis accessions is associated with tandemly duplicated enzymes.” https://t.co/o8Qye3Vj32
“As such, the influence of gene duplication on intraspecific gene expression variation partly depends upon the biological function of the gene involved." https://t.co/o8Qye3Vj32
“A major secondary metabolite pathway in Arabidopsis showed a significantly increased level of gene duplication and intraspecific gene expression variation, suggesting that this pathway may be structured to cope with fluctuating selection in the wild.“ htt
“This suggests that these primary metabolism pathways are genetically constrained." https://t.co/o8Qye3Vj32
“Gene participation in specific metabolic pathways predicted the level of intraspecific variation in gene expression, with major energy and amino acid pathways having relatively lower levels of gene expression variation.” https://t.co/o8Qye3Vj32
“Gene expression variation of segmental and tandem duplicated genes was controlled by a greater number of genetic loci, and these loci had larger effects on gene expression variation for tandem duplicated genes." https://t.co/o8Qye3Vj32
“In contrast, a major herbivory defense pathway showed significantly elevated intraspecific variation suggesting that it may be under pressure to maintain and/or generate diversity in response to fluctuating insect herbivory pressures." https://t.co/o8Qye3
“The major energy metabolism and biosynthetic pathways showed decreased variation, suggesting that they are constrained in their ability to accumulate gene expression variation." https://t.co/o8Qye3Vj32
“The specific biological function of the gene as defined by metabolic pathway also modulated the level of intraspecific gene expression variation.“ https://t.co/o8Qye3Vj32
“Surprisingly, the older segmental duplicates also showed evidence of elevated intraspecific gene expression variation albeit typically lower than for the tandem duplicates." https://t.co/o8Qye3Vj32
“In all instances, the younger tandem duplicated genes showed higher intraspecific gene expression variation than the average Arabidopsis gene." https://t.co/o8Qye3Vj32
Calvin cycle and photosynthesis pathways. “These pathways showed significant genetic constraint but no statistical support for developmental constraints most likely due to the difference in photosynthetic capacity between roots and shoots." https://t.co/o8
"The two exceptions to the observation that major energy metabolic pathways are constrained are the calvin cycle and photosynthesis pathways.“ https://t.co/o8Qye3Vj32
Essential metabolic pathways. “This constraint agrees with the essentiality of these pathways, e.g. aerobic respiration and the TCA cycle, to an individual cells survival." https://t.co/o8Qye3Vj32
Essential metabolic pathways. “This suggests that gene expression for these pathways is constrained across a range of external, internal and genetic stimuli.“ https://t.co/o8Qye3Vj32
"Essential metabolic pathways required for the production and movement of energy within the plant showed significantly lower levels of gene expression variation across development, abiotic stress and natural genetic variation.” https://t.co/o8Qye3Vj32
“This suggests that duplicated genes are involved in less constrained pathways than unique genes." https://t.co/o8Qye3Vj32
“The function of segmental duplicated genes is more likely to have been fixed than the tandem genes." https://t.co/o8Qye3Vj32
“Tandem duplications are likely younger than segmentally duplicated chromosome regions, which were probably generated during whole genome duplication events approximately 20–40 million years ago." https://t.co/o8Qye3Vj32
“Tandem duplicated genes in Arabidopsis thaliana show increased levels of intraspecific gene expression in all tested datasets." https://t.co/o8Qye3Vj32
“This study explores how gene duplication and metabolic function interact to control intraspecific variation in gene expression.“ https://t.co/o8Qye3Vj32
“I estimated the impact of gene duplication and metabolic function upon intraspecific gene expression variation of segmental and tandem duplicated genes within Arabidopsis thaliana." https://t.co/o8Qye3Vj32
“This analysis includes 21,460 genes for which there are both microarray data and assigned duplication status. 12,676 genes are classified as unique." https://t.co/o8Qye3Vj32
“To understand the role that gene duplication and gene expression diversity may play in controlling metabolic pathways, I analyzed transcript accumulation for the complete genome.” https://t.co/o8Qye3Vj32
“We hypothesize that such secondary metabolite pathways may have higher levels of gene duplication and greater gene expression diversity than primary metabolite enzymes." https://t.co/o8Qye3Vj32
“The evolution of this diversity is predicted to be driven by gene duplication and consequent neo-functionalization of enzymes." https://t.co/o8Qye3Vj32
“In contrast to primary metabolism, genes involved in secondary metabolite pathways are marked by a high level of inter and intraspecific variation.” https://t.co/o8Qye3Vj32
“The critical function of the genes in these primary metabolic pathways may be constrained in the range of gene expression values that the pathways transcripts can occupy.” https://t.co/o8Qye3Vj32
“These databases provide specific metabolic roles for genes acting as a highly refined function prediction." https://t.co/o8Qye3Vj32
“A rich source for testing the relationship between biological function, gene duplication and intraspecific genetic variation are databases describing the metabolic pathways known and predicted within a host of organisms.” https://t.co/o8Qye3Vj32
“It is commonly held that some essential biological processes, such as primary energy metabolism, may be constrained in their ability to vary." https://t.co/o8Qye3Vj32
“Another factor controlling the divergence and maintenance of gene duplicates is the biological function of the gene.” https://t.co/o8Qye3Vj32
Segmentally duplicated genes acting as unique genes. “As such, it would be expected that increases in intraspecific variation may only be detected among younger tandem duplicated genes." https://t.co/o8Qye3Vj32
“Given that segmental duplications are typically older than speciation events, it is likely that segmentally duplicated genes have fixed different functions and are in essence acting as unique genes.” https://t.co/o8Qye3Vj32
“Gene duplication is thought to provide much of the genetic material allowing plants to generate a vast diversity of metabolites." https://t.co/o8Qye3Vj32
“This process is contingent upon genetic neo-functionalization and would suggest that duplicated genes should show higher levels of intraspecific variation in gene expression than “unique” genes." https://t.co/o8Qye3Vj32
“Gene duplication may also allow partitioning of function among genotypes within a species, leading to genetic differentiation/intraspecific variation.” https://t.co/o8Qye3Vj32
“Gene duplication has been associated with enabling neo- and sub-functionalization whereby duplicate genes may diverge." https://t.co/o8Qye3Vj32
“In a number of species, recent work has associated gene duplication with divergent gene expression patterns in response to developmental or abiotic stress cues." https://t.co/o8Qye3Vj32
“Alternatively, one of the duplicates can obtain a novel function, a process known as neo-functionalization.“ https://t.co/o8Qye3Vj32
Gene duplication. “This divergence can occur via sub-functionalization such that the duplicate copies obtain differential expression patterns in terms of tissue specificity or stress response.” https://t.co/o8Qye3Vj32
“Alternatively, both duplicated genes can be maintained if the presence of both copies is advantageous. Over time, the function of these duplicated genes can diverge from the ancestral gene or from each other." https://t.co/o8Qye3Vj32
“Following either tandem or segmental duplication events, one of the duplicated genes can be rendered non-functional via the accumulation of deleterious mutations.” https://t.co/o8Qye3Vj32
“Gene duplicates may also undergo partitioning of function among different genotypes of a species leading to genetic differentiation. Finally, the ability of gene duplicates to diverge may be limited by their biological function." https://t.co/o8Qye3Vj32
“In addition to whole genome events, small local events can generate tandem duplicated genes which are often considered younger than segmental duplicated genes obtained from a whole genome duplication." https://t.co/o8Qye3Vj32
“Recent studies have shown that the function of these duplicated genes can diverge from the ancestral gene via neo- or sub-functionalization within single genotypes." https://t.co/o8Qye3Vj32
“Most eukaryotic genomes have undergone whole genome duplications during their evolutionary history.” https://t.co/o8Qye3Vj32