A comparison of the human and chimpanzee olfactory receptor gene repertoires

Gilad, Yoav; Man, Orna; Glusman, Gustavo

doi:10.1101/gr.2846405

Cited by 125 publications

(87 citation statements)

References 34 publications

(56 reference statements)

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“…We further performed biological ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional enrichment analyses for the human genes with the highest and lowest GDI values (18)(19)(20). We found that the list of genes with the highest GDI values was strongly enriched in sensory perception genes (P = 1.00 × 10 −23 ), including, in particular, the genes of the olfactory receptor superfamily (∼400 protein-coding genes), which has been shown to be under positive selection constraints in the human lineage (21,22). The list of genes with the lowest GDI values was enriched in ribosome, chemokine signaling, proteasome, and spliceosome genes, all of which are highly conserved in species lineages predating the emergence of vertebrates (23-26) (Dataset S1, Tab S2 and Figs.…”

Section: Genes Found To Be Highly Mutated In Patients With Monogenicmentioning

confidence: 96%

The human gene damage index as a gene-level approach to prioritizing exome variants

Itan

Shang

Boisson

et al. 2015

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

214

238

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The protein-coding exome of a patient with a monogenic disease contains about 20,000 variants, only one or two of which are disease causing. We found that 58% of rare variants in the protein-coding exome of the general population are located in only 2% of the genes. Prompted by this observation, we aimed to develop a gene-level approach for predicting whether a given human protein-coding gene is likely to harbor disease-causing mutations. To this end, we derived the gene damage index (GDI): a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population. We found that the GDI was correlated with selective evolutionary pressure, protein complexity, coding sequence length, and the number of paralogs. We compared GDI with the leading gene-level approaches, genic intolerance, and de novo excess, and demonstrated that GDI performed best for the detection of false positives (i.e., removing exome variants in genes irrelevant to disease), whereas genic intolerance and de novo excess performed better for the detection of true positives (i.e., assessing de novo mutations in genes likely to be disease causing). The GDI server, data, and software are freely available to noncommercial users from lab.rockefeller.edu/casanova/GDI.

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Section: Genes Found To Be Highly Mutated In Patients With Monogenicmentioning

confidence: 96%

The human gene damage index as a gene-level approach to prioritizing exome variants

Itan

Shang

Boisson

et al. 2015

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

214

238

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“…Humans also appear to be losing Ors more quickly than their closest relatives (24). And although there has been no comprehensive comparison of Ka/Ks between the human and chimpanzee lineages, at least a few genes have elevated ratios in humans (25). The spatial distribution of replacement substitutions along human Ors with high Ka/Ks, however, does not appear to be heterogeneous (26), and most studies find that human Or evolution is consistent with relaxed selective constraint in a species that no longer relies heavily on its sense of smell (but see refs.…”

Section: Discussionmentioning

confidence: 99%

Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia

McBride

2007

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

212

252

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Our understanding of the genetic basis of host specialization in insects is limited to basic information on the number and location of genetic factors underlying changes in conspicuous phenotypes. We know nothing about general patterns of molecular evolution that may accompany host specialization but are not traceable to a single prominent phenotypic change. Here, I describe changes in the entire repertoire of 136 olfactory receptor (Or) and gustatory receptor (Gr) genes of the recently specialized vinegar fly Drosophila sechellia. I find that D. sechellia is losing Or and Gr genes nearly 10 times faster than its generalist sibling Drosophila simulans. Moreover, those D. sechellia receptors that remain intact have fixed amino acid replacement mutations at a higher rate relative to silent mutations than have their D. simulans orthologs. Comparison of these patterns with those observed in a random sample of genes indicates that the changes at Or and Gr loci are likely to reflect positive selection and/or relaxed constraint associated with the altered ecological niche of this fly.comparative genomics ͉ gustatory receptor ͉ host adaptation ͉ lineage-specific ͉ olfactory receptor H ost specialization and host shifts in insects that feed on plants provide excellent opportunities to study the genetic basis of ecological adaptation. Until now, however, this endeavor has been limited to attempts to map factors responsible for conspicuous phenotypic changes that accompany the ecological shifts (e.g., refs. 1-5). We know nothing about genetic changes whose individual effects are subtle, but whose combined presence may leave a striking signature on the genomes of specializing or host-shifting insects.For example, insects evaluate their environment largely by smell and taste, and we might therefore expect their chemical sensory systems to evolve during host specialization or shifts. The acquisition of a novel host may drive the adaptive divergence of sensory systems by positive selection, and the abandonment of an ancestral host may result in the deterioration of older sensory adaptations by genetic drift (or positive selection). Despite their potentially subtle phenotypic effects, such changes are likely to be pervasive (particularly because new host plants challenge insects with the task of recognizing and responding not only to a new food but often also to novel toxins, bacteria, fungi, predators, parasitoids, pupation sites, and mating environments) and are best detected by examining entire genomes or large groups of genes simultaneously.The olfactory receptor (Or) and gustatory receptor (Gr) gene families encode a diverse group of transmembrane proteins that bind volatile and soluble chemicals from the environment and trigger nerve impulses to the brain (6). Individual receptor genes in insects are highly divergent (paralogous genes from a single species often sharing Ͻ20% of their amino acids), are expressed in narrow subsets of olfactory and gustatory neurons from well defined regions of smell and taste organs, and la...

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“…However, it was surprising to note that human and chimpanzee are placed in two separate clades. Although, human and chimpanzee are genetically close to each other [28], gross differences at several genes have also been observed [29]. Included in these genes is a gene responsible for malaria susceptibility in humans and chimpanzee [30].…”

confidence: 99%

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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A comparison of the human and chimpanzee olfactory receptor gene repertoires

Cited by 125 publications

References 34 publications

The human gene damage index as a gene-level approach to prioritizing exome variants

The human gene damage index as a gene-level approach to prioritizing exome variants

Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia

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

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