Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol. 2009;10(8):513–25.
Article
CAS
PubMed
Google Scholar
Diekmann Y, Seixas E, Gouw M, Tavares-Cadete F, Seabra MC, Pereira-Leal JB. Thousands of rab GTPases for the cell biologist. PLoS Comput Biol. 2011;7(10), e1002217.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brighouse A, Dacks JB, Field MC. Rab protein evolution and the history of the eukaryotic endomembrane system. Cell Mol Life Sci. 2010;67(20):3449–65.
Article
PubMed Central
CAS
PubMed
Google Scholar
Park HH. Structural basis of membrane trafficking by rab family small g protein. Int J Mol Sci. 2013;14(5):8912–23.
Article
PubMed Central
PubMed
Google Scholar
Klopper TH, Kienle N, Fasshauer D, Munro S. Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis. BMC Biol. 2012;10:71.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bright LJ, Kambesis N, Nelson SB, Jeong B, Turkewitz AP. Comprehensive analysis reveals dynamic and evolutionary plasticity of Rab GTPases and membrane traffic in Tetrahymena thermophila. PLoS Genet. 2010;6(10), e1001155.
Article
PubMed Central
PubMed
Google Scholar
Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. 2007;315(5809):207–12.
Article
PubMed Central
PubMed
Google Scholar
Saito-Nakano Y, Nakahara T, Nakano K, Nozaki T, Numata O. Marked amplification and diversification of products of ras genes from rat brain, Rab GTPases, in the ciliates Tetrahymena thermophila and Paramecium tetraurelia. J Eukaryot Microbiol. 2010;57(5):389–99.
Article
CAS
PubMed
Google Scholar
Pereira-Leal JB, Seabra MC. Evolution of the Rab family of small GTP-binding proteins. J Mol Biol. 2001;313(4):889–901.
Article
CAS
PubMed
Google Scholar
Rutherford S, Moore I. The Arabidopsis Rab GTPase family: another enigma variation. Curr Opin Plant Biol. 2002;5(6):518–28.
Article
CAS
PubMed
Google Scholar
Elias M, Brighouse A, Gabernet-Castello C, Field MC, Dacks JB. Sculpting the endomembrane system in deep time: high resolution phylogenetics of Rab GTPases. J Cell Sci. 2012;125(Pt 10):2500–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wasmeier C, Romao M, Plowright L, Bennett DC, Raposo G, Seabra MC. Rab38 and Rab32 control post-Golgi trafficking of melanogenic enzymes. J Cell Biol. 2006;175(2):271–81.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nilsson Skold H, Aspengren S, Wallin M. Rapid color change in fish and amphibians - function, regulation, and emerging applications. Pigment Cell Melanoma Res. 2013;26(1):29–38.
Article
PubMed
Google Scholar
Esposito R, D’Aniello S, Squarzoni P, Pezzotti MR, Ristoratore F, Spagnuolo A. New insights into the evolution of metazoan tyrosinase gene family. PLoS One. 2012;7(4), e35731.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bultema JJ, Ambrosio AL, Burek CL, Di Pietro SM. BLOC-2, AP-3, and AP-1 proteins function in concert with Rab38 and Rab32 proteins to mediate protein trafficking to lysosome-related organelles. J Biol Chem. 2012;287(23):19550–63.
Article
PubMed Central
CAS
PubMed
Google Scholar
Loftus SK, Larson DM, Baxter LL, Antonellis A, Chen Y, Wu X, et al. Mutation of melanosome protein RAB38 in chocolate mice. Proc Natl Acad Sci U S A. 2002;99(7):4471–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H. Evidence of en bloc duplication in vertebrate genomes. Nat Genet. 2002;31(1):100–5.
Article
CAS
PubMed
Google Scholar
Dehal P, Boore JL. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 2005;3(10), e314.
Article
PubMed Central
PubMed
Google Scholar
Ohno S. Patterns in genome evolution. Curr Opin Genet Dev. 1993;3(6):911–4.
Article
CAS
PubMed
Google Scholar
Oiso N, Riddle SR, Serikawa T, Kuramoto T, Spritz RA. The rat Ruby (R) locus is Rab38: identical mutations in Fawn-hooded and Tester-Moriyama rats derived from an ancestral Long Evans rat sub-strain. Mamm Genome. 2004;15(4):307–14.
Article
CAS
PubMed
Google Scholar
Wei ML. Hermansky-Pudlak syndrome: a disease of protein trafficking and organelle function. Pigment Cell Res. 2006;19(1):19–42.
Article
CAS
PubMed
Google Scholar
Hermansky F, Pudlak P. Albinism associated with hemorrhagic diathesis and unusual pigmented reticular cells in the bone marrow: report of two cases with histochemical studies. Blood. 1959;14(2):162–9.
CAS
PubMed
Google Scholar
Park M, Serpinskaya AS, Papalopulu N, Gelfand VI. Rab32 regulates melanosome transport in Xenopus melanophores by protein kinase a recruitment. Curr Biol. 2007;17(23):2030–4.
Article
PubMed Central
CAS
PubMed
Google Scholar
Delsuc F, Brinkmann H, Chourrout D, Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 2006;439(7079):965–8.
Article
CAS
PubMed
Google Scholar
Racioppi C, Kamal AK, Razy-Krajka F, Gambardella G, Zanetti L, di Bernardo D, et al. Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis. Nat Commun. 2014;5:4830.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tsuda M, Sakurai D, Goda M. Direct evidence for the role of pigment cells in the brain of ascidian larvae by laser ablation. J Exp Biol. 2003;206(Pt 8):1409–17.
Article
PubMed
Google Scholar
Wang C, Liu Z, Huang X. Rab32 is important for autophagy and lipid storage in Drosophila. PLoS One. 2012;7(2), e32086.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ma J, Plesken H, Treisman JE, Edelman-Novemsky I, Ren M. Lightoid and Claret: a rab GTPase and its putative guanine nucleotide exchange factor in biogenesis of Drosophila eye pigment granules. Proc Natl Acad Sci U S A. 2004;101(32):11652–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008;453(7198):1064–71.
Article
CAS
PubMed
Google Scholar
Lacalli TC. Sensory systems in amphioxus: a window on the ancestral chordate condition. Brain Behav Evol. 2004;64(3):148–62.
Article
PubMed
Google Scholar
Vopalensky P, Pergner J, Liegertova M, Benito-Gutierrez E, Arendt D, Kozmik Z. Molecular analysis of the amphioxus frontal eye unravels the evolutionary origin of the retina and pigment cells of the vertebrate eye. Proc Natl Acad Sci U S A. 2012;109(38):15383–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yu JK, Meulemans D, McKeown SJ, Bronner-Fraser M. Insights from the amphioxus genome on the origin of vertebrate neural crest. Genome Res. 2008;18(7):1127–32.
Article
PubMed Central
CAS
PubMed
Google Scholar
Braasch I, Schartl M, Volff JN. Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evol Biol. 2007;7:74.
Article
PubMed Central
PubMed
Google Scholar
Sugimoto M. Morphological color changes in fish: regulation of pigment cell density and morphology. Microsc Res Tech. 2002;58(6):496–503.
Article
CAS
PubMed
Google Scholar
Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004;431(7011):946–57.
Article
PubMed
Google Scholar
Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y. Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res. 2003;13(3):382–90.
Article
PubMed Central
CAS
PubMed
Google Scholar
Taylor JS, Van de Peer Y, Braasch I, Meyer A. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci. 2001;356(1414):1661–79.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hoegg S, Brinkmann H, Taylor JS, Meyer A. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol. 2004;59(2):190–203.
Article
CAS
PubMed
Google Scholar
Kuraku S, Meyer A. The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication. Int J Dev Biol. 2009;53(5-6):765–73.
Article
CAS
PubMed
Google Scholar
Braasch I, Brunet F, Volff JN, Schartl M. Pigmentation pathway evolution after whole-genome duplication in fish. Genome Biol Evol. 2009;1:479–93.
Article
PubMed Central
PubMed
Google Scholar
Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, et al. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014;505(7482):174–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics. 2011;188(4):799–808.
Article
PubMed Central
CAS
PubMed
Google Scholar
Namkoong J, Shin SS, Lee HJ, Marin YE, Wall BA, Goydos JS, et al. Metabotropic glutamate receptor 1 and glutamate signaling in human melanoma. Cancer Res. 2007;67(5):2298–305.
Article
CAS
PubMed
Google Scholar
Shin SS, Namkoong J, Wall BA, Gleason R, Lee HJ, Chen S. Oncogenic activities of metabotropic glutamate receptor 1 (Grm1) in melanocyte transformation. Pigment Cell Melanoma Res. 2008;21(3):368–78.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fatemi SH, Folsom TD, Rooney RJ, Thuras PD. mRNA and protein expression for novel GABAA receptors theta and rho2 are altered in schizophrenia and mood disorders; relevance to FMRP-mGluR5 signaling pathway. Transl Psychiatry. 2013;3, e271.
Article
PubMed Central
CAS
PubMed
Google Scholar
Skafidas E, Testa R, Zantomio D, Chana G, Everall IP, Pantelis C. Predicting the diagnosis of autism spectrum disorder using gene pathway analysis. Mol Psychiatry. 2014;19(4):504–10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Leinders-Zufall T, Ishii T, Chamero P, Hendrix P, Oboti L, Schmid A, et al. A family of nonclassical class I MHC genes contributes to ultrasensitive chemodetection by mouse vomeronasal sensory neurons. J Neurosci. 2014;34(15):5121–33.
Article
PubMed Central
PubMed
Google Scholar
Godfrey PA, Malnic B, Buck LB. The mouse olfactory receptor gene family. Proc Natl Acad Sci U S A. 2004;101(7):2156–61.
Article
PubMed Central
CAS
PubMed
Google Scholar
Carthagena L, Bergamaschi A, Luna JM, David A, Uchil PD, Margottin-Goguet F, et al. Human TRIM gene expression in response to interferons. PLoS One. 2009;4(3), e4894.
Article
PubMed Central
PubMed
Google Scholar
Muhlenbein N, Hofmann S, Rothbauer U, Bauer MF. Organization and function of the small Tim complexes acting along the import pathway of metabolite carriers into mammalian mitochondria. J Biol Chem. 2004;279(14):13540–6.
Article
PubMed
Google Scholar
Thisse B, Pflumio S, Fürthauer M, Loppin B, Heyer V, Degrave A, et al. Expression of the zebrafish genome during embryogenesis (NIH R01 RR15402). ZFIN Direct Data Submission (http://zfinorg). 2001.
Virta VC, Cooper MS. Structural components and morphogenetic mechanics of the zebrafish yolk extension, a developmental module. J Exp Zool B Mol Dev Evol. 2011;316(1):76–92.
Article
PubMed
Google Scholar
D’Aniello S, Irimia M, Maeso I, Pascual-Anaya J, Jimenez-Delgado S, Bertrand S, et al. Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus. Mol Biol Evol. 2008;25(9):1841–54.
Article
PubMed
Google Scholar
Ravi V, Lam K, Tay BH, Tay A, Brenner S, Venkatesh B. Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes. Proc Natl Acad Sci U S A. 2009;106(38):16327–32.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bultema JJ, Di Pietro SM. Cell type-specific Rab32 and Rab38 cooperate with the ubiquitous lysosome biogenesis machinery to synthesize specialized lysosome-related organelles. Small GTPases. 2013;4(1):16–21.
Article
PubMed Central
PubMed
Google Scholar
Irimia M, Tena JJ, Alexis MS, Fernandez-Minan A, Maeso I, Bogdanovic O, et al. Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res. 2012;22(12):2356–67.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cohen-Solal KA, Sood R, Marin Y, Crespo-Carbone SM, Sinsimer D, Martino JJ, et al. Identification and characterization of mouse Rab32 by mRNA and protein expression analysis. Biochim Biophys Acta. 2003;1651(1-2):68–75.
Article
CAS
PubMed
Google Scholar
Osanai K, Takahashi K, Nakamura K, Takahashi M, Ishigaki M, Sakuma T, et al. Expression and characterization of Rab38, a new member of the Rab small G protein family. Biol Chem. 2005;386(2):143–53.
Article
CAS
PubMed
Google Scholar
Zhang L, Yu K, Robert KW, DeBolt KM, Hong N, Tao JQ, et al. Rab38 targets to lamellar bodies and normalizes their sizes in lung alveolar type II epithelial cells. Am J Physiol Lung Cell Mol Physiol. 2011;301(4):L461–77.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ellis K, Bagwell J, Bagnat M. Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis. J Cell Biol. 2013;200(5):667–79.
Article
PubMed Central
CAS
PubMed
Google Scholar
Torday JS, Rehan VK. Deconvoluting lung evolution using functional/comparative genomics. Am J Respir Cell Mol Biol. 2004;31(1):8–12.
Article
CAS
PubMed
Google Scholar
Gertz EM, Yu YK, Agarwala R, Schaffer AA, Altschul SF. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 2006;4:41.
Article
PubMed Central
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–80.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol. 2012;61(6):1061–7.
Article
PubMed
Google Scholar
Fuentes M, Benito E, Bertrand S, Paris M, Mignardot A, Godoy L, et al. Insights into spawning behavior and development of the European amphioxus (Branchiostoma lanceolatum). J Exp Zool B Mol Dev Evol. 2007;308(4):484–93.
Article
PubMed
Google Scholar
Irimia M, Pineiro C, Maeso I, Gomez-Skarmeta JL, Casares F, Garcia-Fernandez J. Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer. Evodevo. 2010;1(1):7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Thisse C, Thisse B. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat Protoc. 2008;3(1):59–69.
Article
CAS
PubMed
Google Scholar