Comparative genomics of the odorant-binding and chemosensory protein gene families across the arthropoda: Origin and evolutionary history of the chemosensory system

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 476-490

  Vieira, Filipe G ^a   Rozas, Julio ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Birth and death; CSP; Gene family evolution; OBP; Olfactory system

Indexed keywords

ANIMALIA; ARTHROPODA;

ANIMAL; ARTHROPOD; ARTICLE; COMPARATIVE STUDY; GENETICS; GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; OLFACTORY RECEPTOR; PHYLOGENY; PSEUDOGENE; SPECIES DIFFERENCE;

ANIMALS; ARTHROPODS; EVOLUTION, MOLECULAR; GENOME; MULTIGENE FAMILY; PHYLOGENY; PSEUDOGENES; RECEPTORS, ODORANT; SPECIES SPECIFICITY;

EID: 80055089239     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr033     Document Type: Article

References (94)

1. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
2. Andronopoulou E, et al. 2006. Specific interactions among odorant-binding proteins of the African malaria vector Anopheles gambiae. Insect Mol Biol. 15:797-811. (Pubitemid 44952714)
3. Angeli S, et al. 1999. Purification, structural characterization, cloning and immunocytochemical localization of chemoreception proteins from Schistocerca gregaria. Eur J Biochem. 262:745-754. (Pubitemid 29291032)
4. Asahina K, Pavlenkovich V, Vosshall LB. 2008. The survival advantage of olfaction in a competitive environment. Curr Biol. 18:1153-1155.
5. Benton R, Vannice KS, Gomez-Diaz C, Vosshall LB. 2009. Variant ionotropic glutamate receptors as chemosensory receptors in Drosophila. Cell. 136:149-162.
6. Berman HM, et al. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242. (Pubitemid 30047768)
7. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI. 2002. Large clusters of co-expressed genes in the Drosophila genome. Nature. 420:666-669. (Pubitemid 36764497)
8. Brigaud I, Montagne N, Monsempes C, Francois MC, Jacquin-Joly E. 2009. Identification of an atypical insect olfactory receptor subtype highly conserved within noctuids. FEBS J. 276:6537-6547.
9. Brody T, Cravchik A. 2000. Drosophila melanogaster G protein-coupled receptors. J Cell Biol. 150:F83-F88. (Pubitemid 30491351)
10. Croset V, et al. 2010. Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. PLoS Genet. 6: e1001064.
11. Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW. 2006. The evolution of mammalian gene families. PLoS One. 1:e85.
12. Drysdale R. 2008. FlyBase: a database for the Drosophila research community. Methods Mol Biol. 420:45-59.
13. Findlay GD, Yi X, Maccoss MJ, Swanson WJ. 2008. Proteomics reveals novel Drosophila seminal fluid proteins transferred at mating. PLoS Biol. 6:e178.
14. Finn RD, et al. 2006. Pfam: clans, web tools and services. Nucleic Acids Res. 34:D247-D251.
15. Flicek P, et al. 2008. Ensembl 2008. Nucleic Acids Res. 36:D707-D714. (Pubitemid 351149811)
16. Flower DR. 1996. The lipocalin protein family: structure and function. Biochem J. 318(Pt 1):1-14. (Pubitemid 26283618)
17. Foret S, Maleszka R. 2006. Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera). Genome Res. 16:1404-1413. (Pubitemid 44664683)
18. Foret S, Wanner KW, Maleszka R. 2007. Chemosensory proteins in the honey bee: insights from the annotated genome, comparative analyses and expressional profiling. Insect Biochem Mol Biol. 37:19-28. (Pubitemid 44908971)
19. Freitag J, Ludwig G, Andreini I, Rossler P, Breer H. 1998. Olfactory receptors in aquatic and terrestrial vertebrates. J Comp Physiol [A]. 183:635-650. (Pubitemid 28554073)
20. Gong DP, Zhang HJ, Zhao P, Xia QY, Xiang ZH. 2009. The odorant binding protein gene family from the genome of silkworm, Bombyx mori. BMC Genomics. 10:332.
21. Gong DP, et al. 2007. Identification and expression pattern of the chemosensory protein gene family in the silkworm, Bombyx mori. Insect Biochem Mol Biol. 37:266-277.
22. Graham LA, Brewer D, Lajoie G, Davies PL. 2003. Characterization of a subfamily of beetle odorant-binding proteins found in hemo-lymph. Mol Cell Proteomics. 2:541-549.
23. Grosse-Wilde E, Svatos A, Krieger J. 2006. A pheromone-binding protein mediates the bombykol-induced activation of a pheromone receptor in vitro. Chem Senses. 31:547-555. (Pubitemid 44303918)
24. Guo S, Kim J. 2007. Molecular evolution of Drosophila odorant receptor genes. Mol Biol Evol. 24:1198-1207. (Pubitemid 47343644)
25. Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. 2005. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15:1153-1160. (Pubitemid 41126871)
26. Hahn MW, Han MV, Han SG. 2007. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3:e197.
27. Hayden SM, et al. 2010. Ecological adaptation determines functional mammalian olfactory subgenomes. Genome Res. 20:1-9.
28. Hedges SB, Dudley J, Kumar S. 2006. TimeTree: a public knowledgebase of divergence times among organisms. Bioinformatics. 22: 2971-2972. (Pubitemid 44811578)
29. Hekmat-Scafe DS, Scafe CR, McKinney AJ, Tanouye MA. 2002. Genome-wide analysis of the odorant-binding protein gene family in Drosophila melanogaster. Genome Res. 12:1357-1369.
30. Hiller K, Grote A, Scheer M, Munch R, Jahn D. 2004. PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res. 32:W375-W379. (Pubitemid 38997362)
31. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
32. Kaissling KE. 2001. Olfactory perireceptor and receptor events in moths: a kinetic model. Chem Senses. 26:125-150.
33. Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518. (Pubitemid 40360980)
34. Kaupp UB. 2010. Olfactory signalling in vertebrates and insects: differences and commonalities. Nat Rev Neurosci. 11:188-200.
35. Kirkness EF, et al. 2010. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A. 107: 12168-12173.
36. Krieger J, Sandeman RE, Sandeman DC, Hansson BS, Harzsch S. 2010. Brain architecture of the largest living land arthropod, the Giant Robber Crab Birgus latro (Crustacea, Anomura, Coenobitidae): evidence for a prominent central olfactory pathway? Front Zool. 7:25.
37. Krieger MJ, Ross KG. 2002. Identification of a major gene regulating complex social behavior. Science. 295:328-332. (Pubitemid 34074363)
38. Labandeira CC. 2005. Invasion of the continents: cyanobacterial crusts to tree-inhabiting arthropods. Trends Ecol Evol. 20:253-262. (Pubitemid 40588910)
39. Larsson MC, et al. 2004. Or83b encodes a broadly expressed odorant receptor essential for Drosophila olfaction. Neuron. 43:703-714. (Pubitemid 39179729)
40. Lawson D, et al. 2007. VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res. 35:D503-D505. (Pubitemid 46056259)
41. Leal WS, et al. 2005. Kinetics and molecular properties of pheromone binding and release. Proc Natl Acad Sci U S A. 102:5386-5391. (Pubitemid 40530267)
42. Leal WS, Nikonova L, Peng G. 1999. Disulfide structure of the pheromone binding protein from the silkworm moth, Bombyx mori. FEBS Lett. 464:85-90. (Pubitemid 30009755)
43. Letunic I, Bork P. 2007. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 23: 127-128. (Pubitemid 46017867)
44. Ling X, He X, Xin D. 2009. Detecting gene clusters under evolutionary constraint in a large number of genomes. Bioinformatics. 25: 571-577.
45. Luc N, Risler JL, Bergeron A, Raffinot M. 2003. Gene teams: a new formalization of gene clusters for comparative genomics. Comput Biol Chem. 27:59-67.
46. Matsuo T, Sugaya S, Yasukawa J, Aigaki T, Fuyama Y. 2007. Odorant-binding proteins OBP57d and OBP57e affect taste perception and host-plant preference in Drosophila sechellia. PLoS Biol. 5:e118.
47. McGowen MR, Clark C, Gatesy J. 2008. The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods. Syst Biol. 57:574-590.
48. McGuffin LJ, Bryson K, Jones DT. 2000. The PSIPRED protein structure prediction server. Bioinformatics. 16:404-405. (Pubitemid 30417087)
49. Montfort WR, Weichsel A, Andersen JF. 2000. Nitrophorins and related antihemostatic lipocalins from Rhodnius prolixus and other bloodsucking arthropods. Biochim Biophys Acta. 1482:110-118.
50. Nei M. 2007. The new mutation theory of phenotypic evolution. Proc Natl Acad Sci U S A. 104:12235-12242. (Pubitemid 47206121)
51. Nei M, Niimura Y, Nozawa M. 2008. The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet. 9:951-963. (Pubitemid 50329069)
52. Nei M, Rooney AP. 2005. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet. 39:121-152. (Pubitemid 43011110)
53. Pelosi P, Calvello M, Ban L. 2005. Diversity of odorant-binding proteins and chemosensory proteins in insects. Chem Senses. 30(Suppl 1):i291-i292.
54. Pelosi P, Maida R. 1990. Odorant-binding proteins in vertebrates and insects: similarities and possible common function. Chem Senses. 15:205-215. (Pubitemid 20172839)
55. Pelosi P, Zhou JJ, Ban LP, Calvello M. 2006. Soluble proteins in insect chemical communication. Cell Mol Life Sci. 63:1658-1676. (Pubitemid 44252179)
56. Penalva-Arana DC, Lynch M, Robertson HM. 2009. The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors. BMC Evol Biol. 9:79.
57. Pertea M, Lin X, Salzberg SL. 2001. GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res. 29:1185-1190. (Pubitemid 32186204)
58. Pevzner P, Tesler G. 2003. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A. 100:7672-7677. (Pubitemid 36760028)
59. Pophof B. 2004. Pheromone-binding proteins contribute to the activation of olfactory receptor neurons in the silkmoths antheraea polyphemus and Bombyx mori. Chem Senses. 29:117-125. (Pubitemid 41288978)
60. Quijano C, et al. 2008. Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution. Genome Biol. 9:R176.
61. Robertson HM, Warr CG, Carlson JR. 2003. Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster. Proc Natl Acad Sci U S A. 100(Suppl 2):14537-14542. (Pubitemid 37499278)
62. Rutherford K, et al. 2000. Artemis: sequence visualization and annotation. Bioinformatics. 16:944-945.
63. Sanchez-Gracia A, Vieira FG, Almeida FC, Rozas J. 2011. Comparative genomics of the major chemosensory gene families in Arthropods. In: EncyclopediaofLife Sciences. Chichester (UK): JohnWiley&Sons, Ltd. doi:10.1002/9780470015902.a0022848.
64. Sanchez-Gracia A, Vieira FG, Rozas J. 2009. Molecular evolution of the major chemosensory gene families in insects. Heredity. 103:208-216.
65. Sanchez D, et al. 2000. Characterization of two novel lipocalins expressed in the Drosophila embryonic nervous system. Int J Dev Biol. 44:349-359. (Pubitemid 30624789)
66. Scaloni A, Monti M, Angeli S, Pelosi P. 1999. Structural analysis and disulfide-bridge pairing of two odorant-binding proteins from Bombyx mori. Biochem Biophys Res Commun. 266:386-391. (Pubitemid 30028678)
67. Slater GS, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 6:31.
68. Smadja C, Butlin RK. 2009. On the scent of speciation: the chemosensory system and its role in premating isolation. Heredity. 102:77-97. (Pubitemid 50239842)
69. Smadja C, Shi P, Butlin RK, Robertson HM. 2009. Large gene family expansions and adaptive evolution for odorant and gustatory receptors in the pea aphid, Acyrthosiphon pisum. Mol Biol Evol. 26:2073-2086.
70. Soding J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics. 21:951-960. (Pubitemid 40467915)
71. Stajich JE, et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12:1611-1618. (Pubitemid 35175100)
72. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylo-genetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688-2690. (Pubitemid 44642609)
73. Steinbrecht RA. 1998. Odorant-binding proteins: expression and function. Ann N Y Acad Sci. 855:323-332. (Pubitemid 29110003)
74. Stensmyr MC, et al. 2005. Insect-like olfactory adaptations in the terrestrial giant robber crab. Curr Biol. 15:116-121.
75. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 24:1596-1599. (Pubitemid 47236692)
76. Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol. 21:36-44. (Pubitemid 38233516)
77. Tegoni M, Campanacci V, Cambillau C. 2004. Structural aspects of sexual attraction and chemical communication in insects. Trends Biochem Sci. 29:257-264. (Pubitemid 38591320)
78. Valenzuela JG, et al. 2002. The D7 family of salivary proteins in blood sucking diptera. Insect Mol Biol. 11:149-155. (Pubitemid 34432240)
79. Vieira FG, Sanchez-Gracia A, Rozas J. 2007. Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution. Genome Biol. 8:R235.
80. Vogt RG, Riddiford LM. 1981. Pheromone binding and inactivation by moth antennae. Nature. 293:161-163. (Pubitemid 11009908)
81. von Grotthuss M, Ashburner M, Ranz JM. 2010. Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila. Genome Res. 20:1084-1096.
82. Wang J, et al. 2005. SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res. 33:D399-D402. (Pubitemid 40207903)
83. Wang L, Wang S, Li Y, Paradesi MSR, Brown SJ. 2007. BeetleBase: the model organism database for Tribolium castaneum. Nucl Acids Res. 35:D476-D479. (Pubitemid 46056254)
84. Wanner KW, et al. 2007. Female-biased expression of odourant receptor genes in the adult antennae of the silkworm, Bombyx mori. Insect Mol Biol. 16:107-119. (Pubitemid 46174969)
85. Wanner KW, Robertson HM. 2008. The gustatory receptor family in the silkworm moth Bombyx mori is characterized by a large expansion of a single lineage of putative bitter receptors. Insect Mol Biol. 17:621-629.
86. Ward P, Labandeira C, Laurin M, Berner RA. 2006. Confirmation of Romer's Gap as a low oxygen interval constraining the timing of initial arthropod and vertebrate terrestrialization. Proc Natl Acad Sci U S A. 103:16818-16822. (Pubitemid 44737336)
87. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699. (Pubitemid 32372940)
88. Whiteman NK, Pierce NE. 2008. Delicious poison: genetics of Drosophila host plant preference. Trends Ecol Evol. 23:473-478.
89. Xu P, Atkinson R, Jones DN, Smith DP. 2005. Drosophila OBP LUSH is required for activity of pheromone-sensitive neurons. Neuron. 45:193-200. (Pubitemid 40128114)
90. Xu PX, Zwiebel LJ, Smith DP. 2003. Identification of a distinct family of genes encoding atypical odorant-binding proteins in the malaria vector mosquito, Anopheles gambiae. Insect Mol Biol. 12: 549-560. (Pubitemid 37502461)
91. Ye Y, Godzik A. 2004. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 32:W582-W585. (Pubitemid 38997402)
92. Zhou JJ, He XL, Pickett JA, Field LM. 2008. Identification of odorant-binding proteins of the yellow fever mosquito Aedes aegypti: genome annotation and comparative analyses. Insect Mol Biol. 17:147-163. (Pubitemid 351392997)
93. Zhou JJ, Kan Y, Antoniw J, Pickett JA, Field LM. 2006. Genome and EST analyses and expression of a gene family with putative functions in insect chemoreception. Chem Senses. 31:453-465. (Pubitemid 43978556)
94. Zhou JJ, et al. 2010. Genome annotation and comparative analyses of the odorant-binding proteins and chemosensory proteins in the pea aphid Acyrthosiphon pisum. Insect Mol Biol. 19(Suppl 2):113-122.