Evolution of protein-coding genes in Drosophila

Larracuente, Amanda M.; Sackton, Timothy B.; Greenberg, Anthony J.; Wong, Alex; Singh, Nadia D.; Sturgill, David; Zhang, Yu; Oliver, Brian; Clark, Andrew G.

doi:10.1016/j.tig.2007.12.001

Cited by 256 publications

(385 citation statements)

References 70 publications

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“…To distinguish possible positive selection from relaxed constraint, we tested explicitly for genes that have a subset of codons with signatures of positive selection, using codon-based likelihood models of molecular evolution, implemented in PAML 78,79 (Supplementary Information section 11.1). Although this test is typically regarded as a conservative test for positive selection, it may be confounded by selection at synonymous sites.…”

Section: Articlesmentioning

confidence: 99%

“…Previous analyses have suggested that although the level of gene expression consistently seems to be a major determinant of variation in rates of evolution among proteins 86,87 , other factors probably play a significant, if perhaps minor, part [88][89][90][91] . In Drosophila, although highly expressed genes do evolve more slowly, breadth of expression across tissues, gene essentiality and intron number all also independently correlate with rates of protein evolution, suggesting that the additional complexities of multicellular organisms are important factors in modulating rates of protein evolution 78 . The presence of repetitive amino acid sequences has a role as well: nonrepeat regions in proteins containing repeats evolve faster and show more evidence for positive selection than genes lacking repeats 92 .…”

Section: Articlesmentioning

confidence: 99%

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Evolution of genes and genomes on the Drosophila phylogeny

Clark¹,

Eisen²,

Smith³

et al. 2007

Nature

1,795

1,021

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Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

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Section: Articlesmentioning

confidence: 99%

Section: Articlesmentioning

confidence: 99%

Evolution of genes and genomes on the Drosophila phylogeny

Clark¹,

Eisen²,

Smith³

et al. 2007

Nature

1,795

1,021

View full text Add to dashboard Cite

show abstract

“…Recombination is a major determinant in genome evolution (Gaut et al, 2007;Larracuente et al, 2008). Regions that lack recombination tend to lose functional genes and accumulate junk DNA because the evolutionary fates of mutations in non-recombining regions are not independent and natural selection cannot effectively eliminate deleterious and fix advantageous mutations (Hill and Robertson, 1966;Felsenstein, 1974).…”

Section: Introductionmentioning

confidence: 99%

DNA polymorphism in recombining and non-recombing mating-type-specific loci of the smut fungus Microbotryum

Votintseva

Filatov

2010

Heredity

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The population-genetic processes leading to the genetic degeneration of non-recombining regions have mainly been studied in animal and plant sex chromosomes. Here, we report population genetic analysis of the processes in the non-recombining mating-type-specific regions of the smut fungus Microbotryum violaceum. M. violaceum has A1 and A2 mating types, determined by mating-type-specific 'sex chromosomes' that contain 1-2 Mb long non-recombining regions. If genetic degeneration were occurring, then one would expect reduced DNA polymorphism in the non-recombining regions of this fungus. The analysis of DNA diversity among 19 M. violaceum strains, collected across Europe from Silene latifolia flowers, revealed that (i) DNA polymorphism is relatively low in all 20 studied loci (pB0.15%), (ii) it is not significantly different between the two mating-type-specific chromosomes nor between the non-recombining and recombining regions, (iii) there is substantial population structure in M. violaceum populations, which resembles that of its host species, S. latifolia, and (iv) there is significant linkage disequilibrium, suggesting that widespread selfing in this species results in a reduction of the effective recombination rate across the genome. We hypothesise that selfing-related reduction of recombination across the M. violaceum genome negates the difference in the level of DNA polymorphism between the recombining and non-recombining regions, and may possibly lead to similar levels of genetic degeneration in the mating-type-specific regions of the non-recombining 'sex chromosomes' and elsewhere in the genome.

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“…gene dispensability, number of interacting proteins, and local recombination rate, influence the rate of molecular evolution (1)(2)(3)(4)(5)(6)(7). Among them, gene expression level and ubiquity (or specificity) are of particular interest, because both are general characters and easily measurable.…”

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confidence: 99%

Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs

Shen

Huang

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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There exists an inverse relationship between the rate of molecular evolution and the level of gene expression. Among the many explanations, the "toxic-error" hypothesis is a most general one, which posits that processing errors may often be toxic to the cells. However, toxic errors that constrain the evolution of highly expressed genes are often difficult to measure. In this study, we test the toxic-error hypothesis by using microRNA (miRNA) genes because their processing errors can be directly measured by deep sequencing. A miRNA gene consists of a small mature product (≈22 nt long) and a "backbone." Our analysis shows that (i) like the mature miRNA, the backbone is highly conserved; (ii) the rate of sequence evolution in the backbone is negatively correlated with expression; and (iii) although conserved between distantly related species, the error rate in miRNA processing is also negatively correlated with the expression level. The observations suggest that, as a miRNA gene becomes more highly (or more ubiquitously) expressed, its sequence evolves toward a structure that minimizes processing errors.evolutionary rate | microRNA biogenesis | microRNA evolution

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Evolution of protein-coding genes in Drosophila

Cited by 256 publications

References 70 publications

Evolution of genes and genomes on the Drosophila phylogeny

Evolution of genes and genomes on the Drosophila phylogeny

DNA polymorphism in recombining and non-recombing mating-type-specific loci of the smut fungus Microbotryum

Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs

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