Massive Losses of Taste Receptor Genes in Toothed and Baleen Whales

Genome Biology and Evolution - Tập 6 Số 6 - Trang 1254-1265 - 2014
Ping Feng1, Jinsong Zheng2, Stephen J. Rossiter3, Ding Wang2, Huabin Zhao1
1Department of Zoology, College of Life Sciences, Wuhan University, China
2Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
3School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom

Tóm tắt

Từ khóa


Tài liệu tham khảo

Adler, 2000, A novel family of mammalian taste receptors, Cell, 100, 693, 10.1016/S0092-8674(00)80705-9

Altschul, 1990, Basic local alignment search tool, J Mol Biol., 215, 403, 10.1016/S0022-2836(05)80360-2

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389

Arvy, 1970, The tongue of Platanista gangetica and remarks on the cetacean tongue, Investigations on Cetacea, 75

Bachmanov, 2007, Taste receptor genes, Annu Rev Nutr., 27, 389, 10.1146/annurev.nutr.26.061505.111329

Behrens, 2011, Gustatory and extragustatory functions of mammalian taste receptors, Physiol Behav., 105, 4, 10.1016/j.physbeh.2011.02.010

Birney, 2004, GeneWise and Genomewise, Genome Res., 14, 988, 10.1101/gr.1865504

Canessa, 1994, Amiloride-sensitive epithelial Na+ channel is made of three homologous subunits, Nature, 367, 463, 10.1038/367463a0

Chandrashekar, 2000, T2Rs function as bitter taste receptors, Cell, 100, 703, 10.1016/S0092-8674(00)80706-0

Chang, 1996, Mutations in subunits of the epithelial sodium channel cause salt wasting with hyperkalaemic acidosis, pseudohypoaldosteronism type 1, Nat Genet., 12, 248, 10.1038/ng0396-248

Damak, 2006, Trpm5 null mice respond to bitter, sweet, and umami compounds, Chem Senses., 31, 253, 10.1093/chemse/bjj027

Darriba, 2012, jModelTest 2: more models, new heuristics and parallel computing, Nat Methods., 9, 772, 10.1038/nmeth.2109

Firsov, 1998, The heterotetrameric architecture of the epithelial sodium channel (ENaC), EMBO J., 17, 344, 10.1093/emboj/17.2.344

Friedl, 1990, Taste reception in the Pacific bottlenose dolphin (Tursiops truncatus gilli) and the California sea lion (Zalophus californianus), Sensory abilities of cetaceans, 447, 10.1007/978-1-4899-0858-2_31

Glendinning, 1994, Is the bitter rejection response always adaptive?, Physiol Behav, 56, 1217, 10.1016/0031-9384(94)90369-7

Guindon, 2010, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol., 59, 307, 10.1093/sysbio/syq010

Hall, 1999, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/WT, Nucleic Acids Symp Ser., 41, 95

Hasegawa, 2003, Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution, Genes Genet Syst., 78, 267, 10.1266/ggs.78.267

Heck, 1984, Salt taste transduction occurs through an aniloride-sensitive sodium transport pathway, Science, 223, 403, 10.1126/science.6691151

Hedges, 2004, A molecular timescale of eukaryote evolution and the rise of complex multicellular life, BMC Evol Biol., 4, 2, 10.1186/1471-2148-4-2

Huang, 2006, The cells and logic for mammalian sour taste detection, Nature, 442, 934, 10.1038/nature05084

Huelsenbeck, 2001, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754

Ikeda, 1909, New seasonings, J Chem Soc Tokyo., 30, 820

Ishimaru, 2006, Transient receptor potential family members PKD1L3 and PKD2L1 form a candidate sour taste receptor, Proc Natl Acad Sci U S A., 103, 12569, 10.1073/pnas.0602702103

Jiang, 2012, Major taste loss in carnivorous mammals, Proc Natl Acad Sci U S A., 109, 4956, 10.1073/pnas.1118360109

Kerem, 1999, Pulmonary epithelial sodium-channel dysfunction and excess airway liquid in pseudohypoaldosteronism, N Engl J Med., 341, 156, 10.1056/NEJM199907153410304

Komata, 1990, Umami taste of seafoods, Food Rev Int., 6, 457, 10.1080/87559129009540887

Kuznetsov, 1974, A method of studying chemoreception in the Black Sea bottlenose (Tursiops truncatus), Morfologiia, fiziologiya I akustika morskikh mlekopitayushchikh, 27

Kuznetzov, 1990, Chemical sense of dolphins: quasi-olfaction, Sensory abilities of cetaceans, 481, 10.1007/978-1-4899-0858-2_34

Li, 2014, Diet shapes the evolution of the vertebrate bitter taste receptor gene repertoire, Mol Biol Evol., 31, 303, 10.1093/molbev/mst219

Li, 2002, Human receptors for sweet and umami taste, Proc Natl Acad Sci U S A., 99, 4692, 10.1073/pnas.072090199

Li, 2005, Pseudogenization of a sweet-receptor gene accounts for cats' indifference toward sugar, PLoS Genet., 1, 27, 10.1371/journal.pgen.0010003

Lin, 2014, Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia), BMC Genomics, 15, 32, 10.1186/1471-2164-15-32

McGowen, 2012, Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown, Proc Biol Sci., 279, 3643, 10.1098/rspb.2012.0869

McGowen, 2009, Divergence date estimation and a comprehensive molecular tree of extant cetaceans, Mol Phylogenet Evol., 53, 891, 10.1016/j.ympev.2009.08.018

Nachtigall, 1984, Taste reception in the bottlenose dolphin, Acta Zool Fenn., 172, 147

Nei, 2008, The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity, Nat Rev Genet., 9, 951, 10.1038/nrg2480

Nelson, 2001, Mammalian sweet taste receptors, Cell, 106, 381, 10.1016/S0092-8674(01)00451-2

Nelson, 2002, An amino-acid taste receptor, Nature, 416, 199, 10.1038/nature726

Ottaviani, 2002, Amiloride-sensitive epithelial sodium channel subunits are expressed in human and mussel immunocytes, Dev Comp Immunol., 26, 395, 10.1016/S0145-305X(01)00097-0

Pfeiffer, 2001, Lingual ultrastructure of the long-finned pilot whale (Globicephala melas), Anat Histol Embryol., 30, 359, 10.1046/j.1439-0264.2001.00352.x

Sainz, 2001, Identification of a novel member of the T1R family of putative taste receptors, J Neurochem., 77, 896, 10.1046/j.1471-4159.2001.00292.x

Sato, 2012, Loss or major reduction of umami taste sensation in pinnipeds, Naturwissenschaften, 99, 655, 10.1007/s00114-012-0939-8

Schild, 1996, Identification of a PY motif in the epithelial Na channel subunits as a target sequence formutations causing channel activation found in Liddle syndrome, EMBO J., 15, 2381, 10.1002/j.1460-2075.1996.tb00594.x

Shi, 2006, Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes, Mol Biol Evol., 23, 292, 10.1093/molbev/msj028

Sonnhammer, 1998, A hidden Markov model for predicting transmembrane helices in protein sequences, Proc Int Conf Intell Syst Mol Biol., 6, 175

Tamura, 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol., 28, 2731, 10.1093/molbev/msr121

Taruno, 2013, CALHM1 ion channel mediates purinergic neurotransmission of sweet, bitter and umami tastes, Nature, 495, 223, 10.1038/nature11906

Thewissen, 2007, Whales originated from aquatic artiodactyls in the Eocene epoch of India, Nature, 450, 1190, 10.1038/nature06343

Thompson, 1997, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876

Wang, 2004, Relaxation of selective constraint and loss of function in the evolution of human bitter taste receptor genes, Hum Mol Genet., 13, 2671, 10.1093/hmg/ddh289

Xiao, 2013, Obligate mutualism within a host drives the extreme specialization of a fig wasp genome, Genome Biol., 14, R141, 10.1186/gb-2013-14-12-r141

Yamasaki, 1976, The tongue of the Franciscana La-Plata dolphin Pontoporia blainvillei, Okajimas Folia Anat Jpn., 53, 77, 10.2535/ofaj1936.53.2-3_77

Yang, 1995, A new method of inference of ancestral nucleotide and animo acid sequences, Genetics, 141, 1641, 10.1093/genetics/141.4.1641

Yang, 2007, PAML 4: phylogenetic analysis by maximum likelihood, Mol Biol Evol., 24, 1586, 10.1093/molbev/msm088

Yarmolinsky, 2009, Common sense about taste: from mammals to insects, Cell, 139, 234, 10.1016/j.cell.2009.10.001

Yim, 2014, Minke whale genome and aquatic adaptation in cetaceans, Nat Genet., 46, 88, 10.1038/ng.2835

Yoshimura, 1997, A comparative morphological study on the tongue and the lingual papillae of some marine mammals—particularly of four species of Odontoceti and Zalophus, Odontology, 85, 385

Zhang, 1998, Positive Darwinian selection after gene duplication in primate ribonuclease genes, Proc Natl Acad Sci U S A., 95, 3708, 10.1073/pnas.95.7.3708

Zhang, 2003, Coding of sweet, bitter, and umami tastes: different receptor cells sharing similar signaling pathways, Cell, 112, 293, 10.1016/S0092-8674(03)00071-0

Zhao, 2003, The receptors for mammalian sweet and umami taste, Cell, 115, 255, 10.1016/S0092-8674(03)00844-4

Zhao, 2012, Genomic and genetic evidence for the loss of umami taste in bats, Genome Biol Evol., 4, 73, 10.1093/gbe/evr126

Zhao, 2010, Pseudogenization of the umami taste receptor gene Tas1r1 in the giant panda coincided with its dietary switch to bamboo, Mol Biol Evol., 27, 2669, 10.1093/molbev/msq153

Zhao, 2012, Mismatches between feeding ecology and taste receptor evolution: an inconvenient truth, Proc Natl Acad Sci U S A., 109, E1464, 10.1073/pnas.1205205109

Zhao, 2010, Evolution of the sweet taste receptor gene Tas1r2 in bats, Mol Biol Evol., 27, 2642, 10.1093/molbev/msq152

Zhou, 2013, Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations, Nat Commun., 4, 2708, 10.1038/ncomms3708