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Mammalian Genome Analyses Find Elephants Have Large Number of Olfactory Receptor Genes

NEW YORK (GenomeWeb) – Using a phylogenetic-based approach to study the genomes of more than a dozen mammals, University of Tokyo researchers found that African elephants have the largest number of characterized olfactory receptor genes.

African elephants, they reported in Genome Research today, have some 2,000 functional OR genes. By contrast, mice have about 1,200 OR genes and humans have around 400 OR genes

"The functions of these genes are not well known, but they are likely important for the living environment of African elephants," said first author Yoshihito Niimura in a statement. "Apparently, an elephant's nose is not only long but also superior."

By drawing on the deep sequence coverage available for 13 placental mammalian genomes belonging to seven orders, Niimura and his colleagues identified the OR genes present in each animal, and then turned to a phylogeny-based method to identify orthologous gene groups present in those species, then characterize and compare them.

The researched identified more than 20,000 total OR genes, and noted that the number of OR genes varied widely by species. Pseudogenes, they added, also varied by species and did not seem to correlate with the number of functional genes.

They classified the more than 10,000 intact OR genes into 781 orthologous gene groups (OGGs) found in these species and suggested that the most recent common ancestor of placental mammals had about that many functional OR genes.

Most — 81.4 percent — of the OGGs could be classified as Class II OR genes, while the rest were Class I genes. The two classes vary by sequence and seem to also vary by whether they bind hydrophilic or hydrophobic compounds. Most OGGs, the researchers noted, contained a small number of OR genes — roughly a dozen, on average — though Class II OGGs tend to contain more genes than Class I OGGs.

By calculating the extent of purifying selection using a maximum likelihood-based approach, Niimura and his colleagues found that the evolution of Class II genes seems to have been more dynamic than that of Class I genes. This led them to suspect that gene lineages with more duplications were under weaker evolutionary constraints.

Some OGGs, they noted, were quite large, indicating that a few ancestral OR genes had more than 100 descendent genes in the 13 modern species. OGG2-1, for instance, has 159 intact OR genes found in dogs, cows, rabbits, and orangutans, though some expansions occurred separately in each lineage. The second largest OGG was OGG2-2, which has 84 intact elephant OR genes.

After calculating the expansion rate for both OGGs and specific species, the researchers noted that OGG2-22 had the largest expansion rate, followed by OGG2-2, the one with many elephant OR genes.

Elephants, Niimura and his colleagues reported, had 1,948 intact OR genes. This, they added, could reflect elephants' use of smell for foraging, communication, and reproduction. Asian elephants, they noted, are one of the few mammalian species with a chemically identified sex pheromone.

By comparing the elephant OGGs to those found in mouse, which has some 1,113 intact OR genes, the researchers found that the elephant genome contains many more large-sized OR gene clusters than mice. Elephants have 148 clusters containing five or more OR genes, while mice have 34 such clusters.

Many of these clusters, though, could be found in other species, indicating that species-specific clusters were rare.

Overall, though, the elephant and mouse genomes contained a similar number of OR gene clusters, even though elephants had more OR genes and clusters that typically contained more OR genes.

OR genes have been added and lost in each taxonomic lineage, the researchers said, such that species with similar numbers of OR genes may have different OR gene repertoires. For instance, both dog and guinea pigs have about the same number of OR genes, but they share only about half of their genes.

For each taxonomic branch, Niimura and his colleagues calculated the rate of gene birth and gene death, finding the values to be higher that previously reported values for genomic turnover.

They also found using a dataset of OR-odorant pairs for humans and mice that the number of ligands per OR was positively correlated with OGG size, suggesting that generalist ORs have expanded more during the course of evolution than specialist ORs. They cautioned, though, that this analysis was based on a limited amount of data.

"This study clearly illustrates that analyses of evolutionary dynamics of genes can provide insights into gene function," Niimura and his colleagues wrote. "Nevertheless, more ORs should be deorphanized and more OR gene repertoires should be analyzed from many organisms to further elucidate the differences in the evolutionary fates of genes."