Positive Darwinian selection in the singularly large taste receptor gene family of an ‘ancient-fish, Latimeria chalumnae

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• 作者：Adnan S Syed ; Sigrun I Korsching
• 关键词：Coelacanth ; Bitter taste ; Pheromone ; Phylogeny ; Sarcopterygian ; Evolution
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：3,103 KB
• 参考文献：1. Mombaerts, P (2004) Genes and ligands for odorant, vomeronasal and taste receptors. Nat Rev Neurosci 5: pp. 263-278 CrossRef
  2. Mueller, KL, Hoon, MA, Erlenbach, I, Chandrashekar, J, Zuker, CS, Ryba, NJ (2005) The receptors and coding logic for bitter taste. Nature 434: pp. 225-229 CrossRef
  3. Mori, K, Sakano, H (2011) How is the olfactory map formed and interpreted in the mammalian brain?. Annu Rev Neurosci 34: pp. 467-499 CrossRef
  4. Kapsimali, M, Barlow, LA (2013) Developing a sense of taste. Semin Cell Dev Biol 24: pp. 200-209 CrossRef
  5. Baier, H, Korsching, S (1994) Olfactory glomeruli in the zebrafish form an invariant pattern and are identifiable across animals. J Neurosci 14: pp. 219-230
  6. Friedrich, RW, Korsching, SI (1998) Chemotopic, combinatorial, and noncombinatorial odorant representations in the olfactory bulb revealed using a voltage-sensitive axon tracer. J Neurosci 18: pp. 9977-9988
  7. Friedrich, RW, Korsching, SI (1997) Combinatorial and chemotopic odorant coding in the zebrafish olfactory bulb visualized by optical imaging. Neuron 18: pp. 737-752 CrossRef
  8. Nei, M, Niimura, Y, Nozawa, M (2008) The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 9: pp. 951-963 CrossRef
  9. Grus, WE, Shi, P, Zhang, J (2007) Largest vertebrate vomeronasal type 1 receptor gene repertoire in the semiaquatic platypus. Mol Biol Evol 24: pp. 2153-2157 CrossRef
  10. Saraiva, LR, Korsching, SI (2007) A novel olfactory receptor gene family in teleost fish. Genome Res 17: pp. 1448-1457 CrossRef
  11. Dong, D, Jones, G, Zhang, S (2009) Dynamic evolution of bitter taste receptor genes in vertebrates. BMC Evol Biol 9: pp. 12 CrossRef
  12. Hussain, A, Saraiva, LR, Korsching, SI (2009) Positive Darwinian selection and the birth of an olfactory receptor clade in teleosts. Proc Natl Acad Sci U S A 106: pp. 4313-4318 CrossRef
  13. Young, JM, Massa, HF, Hsu, L, Trask, BJ (2010) Extreme variability among mammalian V1R gene families. Genome Res 20: pp. 10-18 CrossRef
  14. Ishimaru, Y, Okada, S, Naito, H, Nagai, T, Yasuoka, A, Matsumoto, I, Abe, K (2005) Two families of candidate taste receptors in fishes. Mech Dev 122: pp. 1310-1321 CrossRef
  15. Li, D, Zhang, J (2014) Diet shapes the evolution of the vertebrate bitter taste receptor gene repertoire. Mol Biol Evol 31: pp. 303-309 CrossRef
  16. Dulac, C, Torello, AT (2003) Molecular detection of pheromone signals in mammals: from genes to behaviour. Nat Rev Neurosci 4: pp. 551-562 CrossRef
  17. Zardoya, R, Meyer, A (1996) Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene. Proc Natl Acad Sci U S A 93: pp. 5449-5454 CrossRef
  18. Amemiya, CT, Alfoldi, J, Lee, AP, Fan, S, Philippe, H, Maccallum, I, Braasch, I, Manousaki, T, Schneider, I, Rohner, N, Organ, C, Chalopin, D, Smith, JJ, Robinson, M, Dorrington, RA, Gerdol, M, Aken, B, Biscotti, MA, Barucca, M, Baurain, D, Berlin, AM, Blatch, GL, Buonocore, F, Burmester, T, Campbell, MS, Canapa, A, Cannon, JP, Christoffels, A, De Moro, G, Edkins, AL (2013) The African coelacanth genome provides
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Chemical senses are one of the foremost means by which organisms make sense of their environment, among them the olfactory and gustatory sense of vertebrates and arthropods. Both senses use large repertoires of receptors to achieve perception of complex chemosensory stimuli. High evolutionary dynamics of some olfactory and gustatory receptor gene families result in considerable variance of chemosensory perception between species. Interestingly, both ora/v1r genes and the closely related t2r genes constitute small and rather conserved families in teleost fish, but show rapid evolution and large species differences in tetrapods. To understand this transition, chemosensory gene repertoires of earlier diverging members of the tetrapod lineage, i.e. lobe-finned fish such as Latimeria would be of high interest. Results We report here the complete T2R repertoire of Latimeria chalumnae, using thorough data mining and extensive phylogenetic analysis. Eighty t2r genes were identified, by far the largest family reported for any species so far. The genomic neighborhood of t2r genes is enriched in repeat elements, which may have facilitated the extensive gene duplication events resulting in such a large family. Examination of non-synonymous vs. synonymous substitution rates (dN/dS) suggests pronounced positive Darwinian selection in Latimeria T2Rs, conceivably ensuring efficient neo-functionalization of newly born t2r genes. Notably, both traits, positive selection and enrichment of repeat elements in the genomic neighborhood, are absent in the twenty v1r genes of Latimeria. Sequence divergence in Latimeria T2Rs and V1Rs is high, reminescent of the corresponding teleost families. Some conserved sequence motifs of Latimeria T2Rs and V1Rs are shared with the respective teleost but not tetrapod genes, consistent with a potential role of such motifs in detection of aquatic chemosensory stimuli. Conclusions The singularly large T2R repertoire of Latimeria may have been generated by facilitating local gene duplication via increased density of repeat elements, and efficient neofunctionalization via positive Darwinian selection. The high evolutionary dynamics of tetrapod t2r gene families precedes the emergence of tetrapods, i.e. the water-to-land transition, and thus constitutes a basal feature of the lobe-finned lineage of vertebrates.