Accelerated Rates of Intron Gain/Loss and Protein Evolution in Duplicate Genes in Human and Mouse Malaria Parasites

Castillo-Davis, Cristian I.; Bedford, Trevor; Hartl, Daniel L.

doi:10.1093/molbev/msh143

Cited by 40 publications

(34 citation statements)

References 35 publications

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“…This finding refutes the notion that genes with fast evolving coding sequences show a higher turnover of introns than sequences with a slower rate of evolution (Castillo-Davis et al 2004).…”

Section: ‫01מ‬supporting

confidence: 87%

Evolutionarily conserved genes preferentially accumulate introns

Carmel¹,

Rogozin²,

Wolf³

et al. 2007

Genome Res.

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Introns that interrupt eukaryotic protein-coding sequences are generally thought to be nonfunctional. However, for reasons still poorly understood, positions of many introns are highly conserved in evolution. Previous reconstructions of intron gain and loss events during eukaryotic evolution used a variety of simplified evolutionary models that yielded contradicting conclusions and are not suited to reveal some of the key underlying processes. We combine a comprehensive probabilistic model and an extended data set, including 391 conserved genes from 19 eukaryotes, to uncover previously unnoticed aspects of intron evolution-in particular, to assign intron gain and loss rates to individual genes. The rates of intron gain and loss in a gene show moderate positive correlation. A gene's intron gain rate shows a highly significant negative correlation with the coding-sequence evolution rate; intron loss rate also significantly, but positively, correlates with the sequence evolution rate. Correlations of the opposite signs, albeit less significant ones, are observed between intron gain and loss rates and gene expression level. It is proposed that intron evolution includes a neutral component, which is manifest in the positive correlation between the gain and loss rates and a selection-driven component as reflected in the links between intron gain and loss and sequence evolution. The increased intron gain and decreased intron loss in evolutionarily conserved genes indicate that intron insertion often might be adaptive, whereas some of the intron losses might be deleterious. This apparent functional importance of introns is likely to be due, at least in part, to their multiple effects on gene expression.

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Section: ‫01מ‬supporting

confidence: 87%

Evolutionarily conserved genes preferentially accumulate introns

Carmel¹,

Rogozin²,

Wolf³

et al. 2007

Genome Res.

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“…In contrast to the characters of orthologous genes, no clear pattern was observed for the paralogous genes. This observation fits to the findings in the malaria parasite, Plasmodium falciparum and P. yoelli yoelii, where duplicate genes or paralogous genes in both the species exhibit a dramatic acceleration of intron gain/loss and protein evolution in comparison with orthologous genes, suggesting increased directional and/or relaxed selection in duplicate genes [25]. In contrast, the unique genes are mostly intron-less and might be evolving at a faster rate loosing the non-coding portions; hence homologs of these genes are no more recognizable [26].…”

confidence: 89%

Fine-scale evolutionary genetic insights into Anopheles gambiae X-chromosome

Srivastava¹,

Dixit²,

Dash³

et al. 2009

JBiSE

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Understanding the genetic architecture of individual taxa of medical importance is the first step for designing disease preventive strategies. To understand the genetic details and evolutionary perspective of the model malaria vector, Anopheles gambiae and to use the information in other species of local importance, we scanned the published X-chromosome sequence for detail characterization and obtain evolutionary status of different genes. The telocentric X-chromosome contains 106 genes of known functions and 982 novel genes. Majorities of both the known and novel genes are with introns. The known genes are strictly biased towards less number of introns; about half of the total known genes have only one or two introns. The extreme sized (either long or short) genes were found to be most prevalent (58% short and 23% large). Statistically significant positive correlations between gene length and intron length as well as with intron number and intron length were obtained signifying the role of introns in contributing to the overall size of the known genes of X-chromosome in An. gambiae. We compared each individual gene of An. gambiae with 33 other taxa having whole genome sequence information. In general, the mosquito Aedes aegypti was found to be genetically closest and the yeast Saccharomyces cerevisiae as most distant taxa to An. gambiae. Further, only about a quarter of the known genes of X-chromosome were unique to An. gambiae and majorities have orthologs in different taxa. A phylogenetic tree was constructed based on a single gene found to be highly orthologous across all the 34 taxa. Evolutionary relationships among 13 different taxa were inferred which corroborate the previous and present findings on genetic relationships across various taxa.

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“…Significant numbers of E. histolytica genes are in multiple copies or are members of highly homologous gene family members. Duplicate genes have higher rates of intron gain or loss in comparison to orthologues and are under accelerated evolutionary pressures either through decreased functional constraints or via positive selection (8,16,28,38,74). E. histolytica contains a number of episomally maintained DNA circles, which in other systems contribute to genome plasticity due to intramolecular homologous recombination between direct tandem repeats (20,24).…”

Section: Discussionmentioning

confidence: 99%

Comparative Genomic Hybridizations ofEntamoebaStrains Reveal Unique Genetic Fingerprints That Correlate with Virulence

et al. 2005

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Variable phenotypes have been identified for Entamoeba species. Entamoeba histolytica is invasive and causes colitis and liver abscesses but only in ϳ10% of infected individuals; 90% remain asymptomatically colonized. Entamoeba dispar, a closely related species, is avirulent. To determine the extent of genetic diversity among Entamoeba isolates and potential genotype-phenotype correlations, we have developed an E. histolytica genomic DNA microarray and used it to genotype strains of E. histolytica and E. dispar. On the basis of the identification of divergent genetic loci, all strains had unique genetic fingerprints. Comparison of divergent genetic regions allowed us to distinguish between E. histolytica and E. dispar, identify novel genetic regions usable for strain and species typing, and identify a number of genes restricted to virulent strains. Among the four E. histolytica strains, a strain with attenuated virulence was the most divergent and phylogenetically distinct strain, raising the intriguing possibility that genetic subtypes of E. histolytica may be partially responsible for the observed variability in clinical outcomes. This microarray-based genotyping assay can readily be applied to the study of E. histolytica clinical isolates to determine genetic diversity and potential genotypic-phenotypic associations.Entamoeba histolytica causes amebic colitis and liver abscesses. Worldwide, 50 million people have invasive E. histolytica, and 100,000 die each year, making it the second most common cause of parasitic death in humans (71). In Dhaka, Bangladesh, where diarrheal diseases are the leading cause of death in children less than 6 years old, ϳ50% of children have serological evidence of exposure to E. histolytica by age 5 (34, 35). Infected children suffer from significant morbidity with malnourishment and growth delays. A number of interesting epidemiologic trends have been identified for amebic disease. The data, although limited, indicate that a minority (ϳ10%) of individuals who become infected with E. histolytica progress to clinically overt disease; others remain asymptomatically colonized (29). In individuals with invasive disease, occurrence of amebic liver abscess (ALA) is 5 to 50 times less common than diarrhea (65). Geographically variable disease predilections have been observed, and invasive disease predominantly affects men (1, 2, 11, 61).The extent of genetic diversity among E. histolytica clinical isolates is unclear. Studies have analyzed a small number of highly repetitive and polymorphic genetic loci by techniques, such as randomly amplified polymorphic DNA (RAPD), RNA arbitrarily primed PCR, and restriction fragment length polymorphism (RFLP), to conclude that there is significant genetic diversity (7,18,23,31,33,64,72,73). Contradictory data were obtained by two studies; in one study, the lectin gene was sequenced, and in the other study, the intergenic region between the superoxide dismutase gene and the actin 3 gene was analyzed (9, 30). These studies found minimal genetic diversi...

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Accelerated Rates of Intron Gain/Loss and Protein Evolution in Duplicate Genes in Human and Mouse Malaria Parasites

Cited by 40 publications

References 35 publications

Evolutionarily conserved genes preferentially accumulate introns

Evolutionarily conserved genes preferentially accumulate introns

Fine-scale evolutionary genetic insights into Anopheles gambiae X-chromosome

Comparative Genomic Hybridizations ofEntamoebaStrains Reveal Unique Genetic Fingerprints That Correlate with Virulence

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