Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  Larsson, Tomas A ^a   Olsson, Frida ^a   Sundstrom, Gorel ^a   Lundin, Lars Gustav ^a   Brenner, Sydney ^b   Venkatesh, Byrappa ^b   Larhammar, Dan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN BINDING PROTEIN; ADAM PROTEIN; ADAMTS14 PROTEIN; ADAMTS2 PROTEIN; ADAMTS3 PROTEIN; ANKYRIN; ANNEXIN; FIBROBLAST GROWTH FACTOR RECEPTOR; G PROTEIN COUPLED RECEPTOR; LIM PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; MITOGEN ACTIVATED PROTEIN KINASE PHOSPHATASE 1; NEUROPEPTIDE Y RECEPTOR; OXOGLUTARATE DEHYDROGENASE; RNA BINDING PROTEIN; SECRETED FRIZZLED RELATED PROTEIN 1; TACHYKININ RECEPTOR; TETRASPANIN; ZINC FINGER PROTEIN;

ARTICLE; CHROMOSOME 10; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 8; CHROMOSOME DUPLICATION; EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PHYLOGENY; PUFFER FISH; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICAL ANALYSIS; SYNTENY; TETRAODONTIFORMES; VERTEBRATE; ANIMAL; CHROMOSOME; GENE DUPLICATION; GENETICS; HUMAN; MOLECULAR EVOLUTION; MOUSE;

DANIO RERIO; GNATHOSTOMATA (VERTEBRATE); HOMO SAPIENS; MUS MUSCULUS; TAKIFUGU RUBRIPES; TELEOSTEI; TETRAODON NIGROVIRIDIS; VERTEBRATA;

ANIMALS; CHROMOSOMES; EVOLUTION, MOLECULAR; GENE DUPLICATION; HUMANS; MICE; MULTIGENE FAMILY; PHYLOGENY; RECEPTORS, NEUROPEPTIDE Y; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TAKIFUGU; TETRAODONTIFORMES; VERTEBRATES;

EID: 46949088293     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-184     Document Type: Article

References (119)

1. Evolution of the neuropeptide Y receptor family: gene and chromosome duplications deduced from the cloning and mapping of the five receptor subtype genes in pig. A Wraith A Tornsten P Chardon I Harbitz BP Chowdhary L Andersson LG Lundin D Larhammar, Genome research 2000 10 302 310 10720571 10.1101/gr.10.3.302
2. Phylogeny of NPY-family peptides and their receptors. D Larhammar R Fredriksson ET Larson E Salaneck, "Neuropeptide Y and Related Peptides", Handbook of Experimental Pharmacology Berlin-Heidelberg: Springer-Verlag, Michel MC, 2004 75 100
3. Multiplicity of neuropeptide Y receptors: cloning of a third distinct subtype in the zebrafish. M Ringvall MM Berglund D Larhammar, Biochem Biophys Res Commun 1997 241 749 755 10.1006/bbrc.1997.7886 9434780
4. Cloning and characterization of a novel neuropeptide Y receptor subtype in the zebrafish. I Lundell MM Berglund P Starback E Salaneck DR Gehlert D Larhammar, DNA Cell Biol 1997 16 1357 1363 9407007
5. Molecular evolution of NPY receptor subtypes. D Larhammar E Salaneck, Neuropeptides 2004 38 141 151 10.1016/j.npep.2004.06.002 15337367
6. S Ohno, Evolution by gene duplication Berlin: Springer Verlag 1970
7. Sequence analysis of the murine Hox-2.2, -2.3, and -2.4 homeo boxes: evolutionary and structural comparisons. CP Hart A Fainsod FH Ruddle, Genomics 1987 1 182 195 10.1016/0888-7543(87)90011-5 2891608
8. Gene homologies and the nerve system. L-G Lundin, Genetics of Neuropsychiatric Diseases. Wenner-Gren Internatl. Symp. Ser London: MacMillan Press, Wetterberg L, 1989 51 43 58
9. Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. LG Lundin, Genomics 1993 16 1 19 10.1006/geno.1993.1133 8486346
10. The human Hox-bearing chromosome regions did arise by block or chromosome (or even genome) duplications. D Larhammar LG Lundin F Hallbook, Genome research 2002 12 1910 1920 12466295 10.1101/gr.445702
11. Homeobox gene clusters and the human paralogy map. C Popovici M Leveugle D Birnbaum F Coulier, FEBS letters 2001 491 237 242 10.1016/S0014-5793(01)02187- 1 11240134
12. An insight into the phylogenetic history of HOX linked gene families in vertebrates. AA Abbasi KH Grzeschik, BMC Evol Biol 2007 7 239 18053128 10.1186/1471-2148-7-239
13. Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. MJ Pebusque F Coulier D Birnbaum P Pontarotti, Mol Biol Evol 1998 15 9 1145 1159 9729879
14. Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region. A Vienne J Rasmussen L Abi-Rached P Pontarotti A Gilles, Molecular biology and evolution 2003 20 1290 1298 10.1093/molbev/msg127
15. Coparalogy: physical and functional clusterings in the human genome. C Popovici M Leveugle D Birnbaum F Coulier, Biochem Biophys Res Commun 2001 288 362 370 10.1006/bbrc.2001.5794 11606051
16. The 2R hypothesis and the human genome sequence. K Hokamp A McLysaght KH Wolfe, J Struct Funct Genomics 2003 3 95 110 10.1023/A:1022661917301 12836689
17. Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates. LG Lundin D Larhammar F Hallbook, J Struct Funct Genomics 2003 3 53 63 10.1023/A:1022600813840 12836685
18. Evidence of en bloc duplication in vertebrate genomes. L Abi-Rached A Gilles T Shiina P Pontarotti H Inoko, Nature genetics 2002 31 100 105 10.1038/ng855 11967531
19. Two rounds of whole genome duplication in the ancestral vertebrate. P Dehal JL Boore, PLoS biology 2005 3 e314 16128622 10.1371/journal.pbio.0030314
20. Conserved synteny between the Ciona genome and human paralogons identifies large duplication events in the molecular evolution of the insulin-relaxin gene family. RP Olinski LG Lundin F Hallbook, Molecular biology and evolution 2006 23 10 22 10.1093/molbev/msj002
21. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Y Nakatani H Takeda Y Kohara S Morishita, Genome research 2007 17 1254 1265 17652425 10.1101/gr.6316407
22. MetaHox gene clusters. F Coulier C Popovici R Villet D Birnbaum, J Exp Zool 2000 288 345 351 10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0. CO;2-Y 11144283
23. Were vertebrates octoploid? RF Furlong PW Holland, Philos Trans R Soc Lond B Biol Sci 2002 357 531 544 12028790 10.1098/rstb.2001.1035
24. Uneven evolutionary rates of bradykinin B1 and B2 receptors in vertebrate lineages. T Bromee B Venkatesh S Brenner JH Postlethwait YL Yan D Larhammar, Gene 2006 373 100 108 10.1016/j.gene.2006.01.017 16530355
25. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. A Christoffels EG Koh JM Chia S Brenner S Aparicio B Venkatesh, Molecular biology and evolution 2004 21 1146 1151 10.1093/molbev/msh114
26. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. O Jaillon JM Aury F Brunet JL Petit N Stange-Thomann E Mauceli L Bouneau C Fischer C Ozouf-Costaz A Bernot S Nicaud D Jaffe S Fisher G Lutfalla C Dossat B Segurens C Dasilva M Salanoubat M Levy N Boudet S Castellano V Anthouard C Jubin V Castelli M Katinka B Vacherie C Biemont Z Skalli L Cattolico J Poulain, Nature 2004 431 946 957 10.1038/nature03025 15496914
27. The medaka draft genome and insights into vertebrate genome evolution. M Kasahara K Naruse S Sasaki Y Nakatani W Qu B Ahsan T Yamada Y Nagayasu K Doi Y Kasai T Jindo D Kobayashi A Shimada A Toyoda Y Kuroki A Fujiyama T Sasaki A Shimizu S Asakawa N Shimizu S Hashimoto J Yang Y Lee K Matsushima S Sugano M Sakaizumi T Narita K Ohishi S Haga F Ohta, Nature 2007 447 714 719 10.1038/nature05846 17554307
28. Zebrafish comparative genomics and the origins of vertebrate chromosomes. JH Postlethwait IG Woods P Ngo-Hazelett YL Yan PD Kelly F Chu H Huang A Hill-Force WS Talbot, Genome research 2000 10 1890 1902 10.1101/gr.164800 11116085
29. Tetraploid origin of the karyotype of catostomid fishes. T Uyeno GR Smith, Science 1972 175 644 646 10.1126/science.175.4022.644 5009763
30. Tetraploidy and the Evolution of Salmonid Fishes. FW Allendorf GH Thorgaard, The Evolutionary Genetics of Fishes Plenum Press, Turner BJ, 1984 1 53
31. Polyploid incidence and evolution. SP Otto J Whitton, Annu Rev Genet 2000 34 401 437 10.1146/annurev.genet.34.1.401 11092833
32. Polyploidy in fishes: patterns and processes. SC Le Comber C Smith, Biological Journal of the Linnean Society 2004 82 431 442 10.1111/j.1095-8312. 2004.00330.x
33. Asymmetric functional divergence of duplicate genes in yeast. A Wagner, Mol Biol Evol 2002 19 10 1760 1768 12270902
34. Asymmetric sequence divergence of duplicate genes. GC Conant A Wagner, Genome research 2003 13 2052 2058 12952876 10.1101/gr.1252603
35. Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail. R Aburomia O Khaner A Sidow, J Struct Funct Genomics 2003 3 45 52 10.1023/A:1022648729770 12836684
36. Ancient genome duplications did not structure the human Hox-bearing chromosomes. AL Hughes J da Silva R Friedman, Genome research 2001 11 771 780 11337473 10.1101/gr.GR-1600R
37. Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. JH Nadeau D Sankoff, Genetics 1997 147 1259 1266 9383068
38. Evidence in favour of ancient octaploidy in the vertebrate genome. TJ Gibson J Spring, Biochemical Society transactions 2000 28 259 264 10816139
39. Neuropeptide Y-family receptors Y6 and Y7 in chicken. Cloning, pharmacological characterization, tissue distribution and conserved synteny with human chromosome region. T Bromee P Sjodin R Fredriksson T Boswell TA Larsson E Salaneck R Zoorob N Mohell D Larhammar, Febs J 2006 273 2048 2063 10.1111/j.1742-4658.2006.05221.x 16640567
40. The hidden duplication past of Arabidopsis thaliana. C Simillion K Vandepoele MC Van Montagu M Zabeau Y Van de Peer, Proceedings of the National Academy of Sciences of the United States of America 2002 99 13627 13632 12374856 10.1073/pnas.212522399
41. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. K Vandepoele C Simillion Y Van de Peer, Trends Genet 2002 18 606 608 10.1016/S0168-9525(02)02796-8 12446138
42. Neuropeptide Y receptor subtype with unique properties cloned in the zebrafish: the zYa receptor. P Starback I Lundell R Fredriksson MM Berglund YL Yan A Wraith C Soderberg JH Postlethwait D Larhammar, Brain Res Mol Brain Res 1999 70 242 252 10.1016/S0169-328X(99)00152-7 10407172
43. Birth and death of neuropeptide Y receptor genes in relation to the teleost fish tetraploidization. E Salaneck TA Larsson ET Larson D Larhammar, Gene 2008 409 61 71 10.1016/j.gene.2007.11.011 18191918
44. The zebrafish genome in context: ohnologs gone missing. JH Postlethwait, Journal of experimental zoology Part B 2007 308 563 577 10.1002/jez.b.21137
45. The evolution of the vertebrate metzincins; insights from Ciona intestinalis and Danio rerio. J Huxley-Jones TK Clarke C Beck G Toubaris DL Robertson RP Boot-Handford, BMC Evol Biol 2007 7 63 17439641 10.1186/1471-2148-7-63
46. Molecular characterization of abLIM, a novel actin-binding and double zinc finger protein. DJ Roof A Hayes M Adamian AH Chishti T Li, The Journal of cell biology 1997 138 575 588 9245787 10.1083/jcb.138.3.575
47. Two novel members of the ABLIM protein family, ABLIM-2 and -3, associate with STARS and directly bind F-actin. T Barrientos D Frank K Kuwahara S Bezprozvannaya GC Pipes R Bassel-Duby JA Richardson HA Katus EN Olson N Frey, J Biol Chem 2007 282 8393 8403 10.1074/jbc.M607549200 17194709
48. UNC-115, a conserved protein with predicted LIM and actin-binding domains, mediates axon guidance in C. elegans. EA Lundquist RK Herman JE Shaw CI Bargmann, Neuron 1998 21 385 392 10.1016/S0896-6273(00)80547-4 9728919
49. Functional evolution of ADAMTS genes: evidence from analyses of phylogeny and gene organization. AC Nicholson SB Malik JM Logsdon Jr EG Van Meir, BMC Evol Biol 2005 5 11 15693998 10.1186/1471-2148-5-11
50. The annexins. SE Moss RO Morgan, Genome biology 2004 5 219 15059252 10.1186/gb-2004-5-4-219
51. Genetic analyses of adaptin function from yeast to mammals. M Boehm JS Bonifacino, Gene 2002 286 175 186 10.1016/S0378-1119(02)00422-5 11943473
52. The AP-3 complex: a coat of many colours. G Odorizzi CR Cowles SD Emr, Trends Cell Biol 1998 8 282 288 10.1016/S0962-8924(98)01295-1 9714600
53. Molecular cloning and characterization of a novel gene family of four ancient conserved domain proteins (ACDP). CY Wang JD Shi P Yang PG Kumar QZ Li QG Run YC Su HS Scott KJ Kao JX She, Gene 2003 306 37 44 10.1016/S0378-1119(02) 01210-6 12657465
54. Molecular cloning and characterization of the mouse Acdp gene family. CY Wang P Yang JD Shi S Purohit D Guo H An JG Gu J Ling Z Dong JX She, BMC genomics 2004 5 7 14723793 10.1186/1471-2164-5-7
55. MAP kinase phosphatases. A Theodosiou A Ashworth, Genome biology 2002 3 REVIEWS3009 12184814 10.1186/gb-2002-3-7-reviews3009
56. Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome. LD Hurst MJ Lercher, BMC Evol Biol 2005 5 62 16277660 10.1186/1471-2148-5-62
57. Of worms and men: an evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families. F Coulier P Pontarotti R Roubin H Hartung M Goldfarb D Birnbaum, Journal of molecular evolution 1997 44 43 56 10.1007/PL00006120 9010135
58. An evolutionary history of the FGF superfamily. C Popovici R Roubin F Coulier D Birnbaum, Bioessays 2005 27 849 857 10.1002/bies.20261 16015590
59. Evolution of the Fgf and Fgfr gene families. N Itoh DM Ornitz, Trends Genet 2004 20 563 569 10.1016/j.tig.2004.08.007 15475116
60. The human HNRPD locus maps to 4q21 and encodes a highly conserved protein. LA Dempsey MJ Li A DePace P Bray-Ward N Maizels, Genomics 1998 49 378 384 10.1006/geno.1998.5237 9615222
61. A novel gene, LGI1, from 10q24 is rearranged and downregulated in malignant brain tumors. OB Chernova RP Somerville JK Cowell, Oncogene 1998 17 2873 2881 10.1038/sj.onc.1202481 9879993
62. The LGI1 gene involved in lateral temporal lobe epilepsy belongs to a new subfamily of leucine-rich repeat proteins. W Gu A Wevers H Schroder KH Grzeschik C Derst E Brodtkorb R de Vos OK Steinlein, FEBS letters 2002 519 71 76 10.1016/S0014-5793(02)02713-8 12023020
63. ERK and p38 MAPK-activated protein kinases: a family of protein kinases with diverse biological functions. PP Roux J Blenis, Microbiol Mol Biol Rev 2004 68 320 344 15187187 10.1128/MMBR.68.2.320-344.2004
64. Functions of the MAPK family in vertebrate-development. SF Krens HP Spaink BE Snaar-Jagalska, FEBS letters 2006 580 4984 4990 10.1016/j.febslet. 2006.08.025 16949582
65. Mad3 and Mad4: novel Max-interacting transcriptional repressors that suppress c-myc dependent transformation and are expressed during neural and epidermal differentiation. PJ Hurlin C Queva PJ Koskinen E Steingrimsson DE Ayer NG Copeland NA Jenkins RN Eisenman, Embo J 1995 14 5646 5659 8521822
66. The MAX-interacting transcription factor network. PJ Hurlin J Huang, Semin Cancer Biol 2006 16 265 274 10.1016/j.semcancer.2006.07.009 16908182
67. Cellular integrity plus: organelle-related and protein-targeting functions of intermediate filaments. DM Toivola GZ Tao A Habtezion J Liao MB Omary, Trends Cell Biol 2005 15 608 617 10.1016/j.tcb.2005.09.004 16202602
68. Tachykinins and tachykinin receptors: a growing family. JN Pennefather A Lecci ML Candenas E Patak FM Pinto CA Maggi, Life Sci 2004 74 1445 1463 10.1016/j.lfs.2003.09.039 14729395
69. Cloning and nucleotide sequence of the cDNA encoding human 2-oxoglutarate dehydrogenase (lipoamide). K Koike Y Urata S Goto, Proceedings of the National Academy of Sciences of the United States of America 1992 89 1963 1967 1542694 10.1073/pnas.89.5.1963
70. Localization of the gene (OGDH) coding for the E1k component of the alpha-ketoglutarate dehydrogenase complex to chromosome 7p13-p11.2. P Szabo X Cai G Ali JP Blass, Genomics 1994 20 324 326 10.1006/geno.1994.1178 8020988
71. Identification and mRNA expression of Ogdh, QP-C, and two predicted genes in the postnatal mouse brain. T Sadakata T Furuichi, Neuroscience letters 2006 405 217 222 10.1016/j.neulet.2006.07.008 16901643
72. Insights into the Molecular Evolution of the PDZ/LIM Family and Identification of a Novel Conserved Protein Motif. AJ Te Velthuis T Isogai L Gerrits CP Bagowski, PLoS ONE 2007 2 e189 17285143 10.1371/journal.pone.0000189
73. PRELI (protein of relevant evolutionary and lymphoid interest) is located within an evolutionarily conserved gene cluster on chromosome 5q34-q35 and encodes a novel mitochondrial protein. EJ Fox SA Stubbs J Kyaw Tun JP Leek AF Markham SC Wright, The Biochemical journal 2004 378 817 825 14640972 10.1042/BJ20031504
74. Identification of a family of animal sphingomyelin synthases. K Huitema J van den Dikkenberg JF Brouwers JC Holthuis, Embo J 2004 23 33 44 14685263 10.1038/sj.emboj.7600034
75. SARPs: a family of secreted apoptosis-related proteins. HS Melkonyan WC Chang JP Shapiro M Mahadevappa PA Fitzpatrick MC Kiefer LD Tomei SR Umansky, Proceedings of the National Academy of Sciences of the United States of America 1997 94 13636 13641 9391078 10.1073/pnas.94.25.13636
76. Secreted Frizzled-related proteins: searching for relationships and patterns. SE Jones C Jomary, Bioessays 2002 24 811 820 10.1002/bies.10136 12210517
77. A family of secreted proteins contains homology to the cysteine-rich ligand-binding domain of frizzled receptors. A Rattner JC Hsieh PM Smallwood DJ Gilbert NG Copeland NA Jenkins J Nathans, Proceedings of the National Academy of Sciences of the United States of America 1997 94 2859 2863 9096311 10.1073/pnas.94.7.2859
78. Vinexin, CAP/ponsin, ArgBP2: a novel adaptor protein family regulating cytoskeletal organization and signal transduction. N Kioka K Ueda T Amachi, Cell Struct Funct 2002 27 1 7 10.1247/csf.27.1 11937713
79. Intron-exon organization and chromosomal localization of the human TIA-1 gene. A Kawakami Q Tian M Streuli M Poe S Edelhoff CM Disteche P Anderson, J Immunol 1994 152 4937 4945 8176212
80. Identification and functional characterization of a TIA-1-related nucleolysin. A Kawakami Q Tian X Duan M Streuli SF Schlossman P Anderson, Proceedings of the National Academy of Sciences of the United States of America 1992 89 8681 8685 1326761 10.1073/pnas.89.18.8681
81. The phylogenetic analysis of tetraspanins projects the evolution of cell-cell interactions from unicellular to multicellular organisms. S Huang S Yuan M Dong J Su C Yu Y Shen X Xie Y Yu X Yu S Chen, Genomics 2005 86 674 684 10.1016/j.ygeno.2005.08.004 16242907
82. The tetraspanin superfamily: molecular facilitators. HT Maecker SC Todd S Levy, Faseb J 1997 11 428 442 9194523
83. Vertebrate homologues of C. elegans UNC-5 are candidate netrin receptors. ED Leonardo L Hinck M Masu K Keino-Masu SL Ackerman M Tessier-Lavigne, Nature 1997 386 833 838 10.1038/386833a0 9126742
84. The Netrin family of guidance factors: emphasis on Netrin-1 signalling. MJ Barallobre M Pascual JA Del Rio E Soriano, Brain Res Brain Res Rev 2005 49 22 47 10.1016/j.brainresrev.2004.11.003 15960985
85. Zimp7 and Zimp10, two novel PIAS-like proteins, function as androgen receptor coregulators. J Beliakoff Z Sun, Nucl Recept Signal 2006 4 e017 16862223
86. hZimp7, a novel PIAS-like protein, enhances androgen receptor-mediated transcription and interacts with SWI/SNF-like BAF complexes. CY Huang J Beliakoff X Li J Lee X Li M Sharma B Lim Z Sun, Molecular endocrinology 2005 19 2915 2929 10.1210/me.2005-0097 16051670
87. hZimp10 is an androgen receptor co-activator and forms a complex with SUMO-1 at replication foci. M Sharma X Li Y Wang M Zarnegar CY Huang JJ Palvimo B Lim Z Sun, Embo J 2003 22 6101 6114 14609956 10.1093/emboj/cdg585
88. The novel PIAS-like protein hZimp10 enhances Smad transcriptional activity. X Li G Thyssen J Beliakoff Z Sun, J Biol Chem 2006 281 23748 23756 10.1074/jbc.M508365200 16777850
89. Origin of the prolactin-releasing hormone (PRLH) receptors: evidence of coevolution between PRLH and a redundant neuropeptide Y receptor during vertebrate evolution. MC Lagerstrom R Fredriksson TK Bjarnadottir D Fridmanis T Holmquist J Andersson YL Yan T Raudsepp R Zoorob JP Kukkonen LG Lundin J Klovins BP Chowdhary JH Postlethwait HB Schioth, Genomics 2005 85 688 703 10.1016/j.ygeno.2005.02.007 15885496
90. The melanocortin system in Fugu: determination of POMC/AGRP/MCR gene repertoire and synteny, as well as pharmacology and anatomical distribution of the MCRs. J Klovins T Haitina D Fridmanis Z Kilianova I Kapa R Fredriksson N Gallo-Payet HB Schioth, Molecular biology and evolution 2004 21 563 579 10.1093/molbev/msh050
91. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. S Aparicio J Chapman E Stupka N Putnam JM Chia P Dehal A Christoffels S Rash S Hoon A Smit MD Gelpke J Roach T Oh IY Ho M Wong C Detter F Verhoef P Predki A Tay S Lucas P Richardson SF Smith MS Clark YJ Edwards N Doggett A Zharkikh SV Tavtigian D Pruss M Barnstead C Evans, Science 2002 297 1301 1310 10.1126/science.1072104 12142439
92. Evolution of the neuropeptide Y family: New genes by chromosome duplications in early vertebrates and in teleost fishes. G Sundström TA Larsson S Brenner B Venkatesh D Larhammar, Gen Comp Endocrinol 2008 155 705 716 10.1016/j.ygcen.2007.08.016 17950734
93. Eukaryote genome duplication - where's the evidence? L Skrabanek KH Wolfe, Curr Opin Genet Dev 1998 8 694 700 10.1016/S0959-437X(98)80039-7 9914206
94. Computational approaches to unveiling ancient genome duplications. Y Van de Peer, Nat Rev Genet 2004 5 752 763 10.1038/nrg1449 15510166
95. Diagnosing duplications - can it be done? D Durand R Hoberman, Trends Genet 2006 22 156 164 10.1016/j.tig.2006.01.002 16442663
96. Recent developments in computational approaches for uncovering genomic homology. C Simillion K Vandepoele Y Van de Peer, Bioessays 2004 26 1225 1235 10.1002/bies.20127 15499578
97. Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event? N Martin EA Ruedi R Leduc FJ Sun G Caetano-Anolles, Biology direct 2007 2 23 17894859 10.1186/1745-6150-2-23
98. Identification of duplicated fourth alpha2-adrenergic receptor subtype by cloning and mapping of five receptor genes in zebrafish. JO Ruuskanen H Xhaard A Marjamaki E Salaneck T Salminen YL Yan JH Postlethwait MS Johnson D Larhammar M Scheinin, Molecular biology and evolution 2004 21 14 28 10.1093/molbev/msg224
99. The gain and loss of genes during 600 million years of vertebrate evolution. T Blomme K Vandepoele S De Bodt C Simillion S Maere Y Van de Peer, Genome biology 2006 7 R43 16723033 10.1186/gb-2006-7-5-r43
100. Hox clusters as models for vertebrate genome evolution. S Hoegg A Meyer, Trends Genet 2005 21 421 424 10.1016/j.tig.2005.06.004 15967537
101. The BioGRID. http://www.thebiogrid.org
102. BioGRID: a general repository for interaction datasets. C Stark BJ Breitkreutz T Reguly L Boucher A Breitkreutz M Tyers, Nucleic acids research 2006 34 D535 539 16381927 10.1093/nar/gkj109
103. Gene function, gene networks and the fate of duplicated genes. SM Shimeld, Semin Cell Dev Biol 1999 10 549 553 10.1006/scdb.1999.0336 10597639
104. Functional partitioning of yeast co-expression networks after genome duplication. GC Conant KH Wolfe, PLoS biology 2006 4 e109 16555924 10.1371/journal.pbio.0040109
105. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. G Blanc KH Wolfe, Plant Cell 2004 16 1679 1691 15208398 10.1105/tpc.021410
106. Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications. CM Gachon M Langlois-Meurinne Y Henry P Saindrenan, Plant Mol Biol 2005 58 229 245 10.1007/s11103-005-5346-5 16027976
107. Preservation of duplicate genes by complementary, degenerative mutations. A Force M Lynch FB Pickett A Amores YL Yan J Postlethwait, Genetics 1999 151 1531 1545 10101175
108. The evolutionary fate and consequences of duplicate genes. M Lynch JS Conery, Science 2000 290 5494 1151 1155 11073452 10.1126/science.290.5494.1151
109. The probability of duplicate gene preservation by subfunctionalization. M Lynch A Force, Genetics 2000 154 459 473 10629003
110. The probability of preservation of a newly arisen gene duplicate. M Lynch M O'Hely B Walsh A Force, Genetics 2001 159 1789 1804 11779815
111. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. X He J Zhang, Genetics 2005 169 1157 1164 15654095 10.1534/genetics.104.037051
112. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. S Rastogi DA Liberles, BMC Evol Biol 2005 5 28 15831095 10.1186/1471-2148-5-28
113. Paleontological evidence to date the tree of life. MJ Benton PC Donoghue, Molecular biology and evolution 2007 24 26 53 10.1093/molbev/msl150
114. Ensembl Genome Browser. http://www.ensembl.org/index.html
115. Multiple sequence alignment with Clustal X. F Jeanmougin JD Thompson M Gouy DG Higgins TJ Gibson, Trends Biochem Sci 1998 23 403 405 10.1016/S0968-0004(98)01285-7 9810230
116. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic acids research 1994 22 4673 4680 7984417 10.1093/nar/22.22.4673
117. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. S Kumar K Tamura M Nei, Brief Bioinform 2004 5 150 163 10.1093/bib/5.2.150 15260895
118. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. HA Schmidt K Strimmer M Vingron A von Haeseler, Bioinformatics 2002 18 502 504 10.1093/bioinformatics/18.3.502 11934758
119. The Pfam database. http://pfam.sanger.ac.uk