The basal chordate amphioxus as a simple model for elucidating developmental mechanisms in vertebrates

Birth Defects Research Part C - Embryo Today: Reviews

Volumn 84, Issue 3, 2008, Pages 175-187

  Koop, Demian ^a   Holland, Linda Z ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Birth defects; Branchiostoma; Chordate evolution

Indexed keywords

AMPHIOXUS; BIRTH DEFECT; CHORDATE; CRANIOFACIAL MALFORMATION; DEVELOPMENTAL BIOLOGY; EMBRYO DEVELOPMENT; EMBRYONAL TISSUE; EXPERIMENTAL MODEL; GENE DUPLICATION; GENOME; GILL; MOLECULAR BIOLOGY; MUSCLE; NERVE CORD; NERVOUS SYSTEM DEVELOPMENT; NEURAL CREST; NEURULATION; NONHUMAN; NOTOCHORD; PHARYNX; PRIORITY JOURNAL; REVIEW; SENSE ORGAN; SOMITE; VERTEBRATE; YOLK SAC;

ANIMALS; CHORDATA, NONVERTEBRATE; EVOLUTION; MODELS, BIOLOGICAL; PHYLOGENY; VERTEBRATES;

BRANCHIOSTOMA; BRANCHIOSTOMA LANCEOLATUM; VERTEBRATA;

EID: 51949105729     PISSN: 1542975X     EISSN: None     Source Type: Journal    
DOI: 10.1002/bdrc.20128     Document Type: Review

References (186)

1. Abdelhak S, Kalatzis V, Heilig H, et al. 1997a. Clustering of mutations responsible for branchio-oto-renal (BOR) syndrome in the eyes absent homologous region (eyaHR) of EYA1. Hum Mol Genet 6:2247-2255.
2. Abdelhak S, Kalatzis V, Heilig R, et al. 1997b. A human homologue of the Drosophila eyes absentgene underlies branchio-oto-renal (BOR) syndrome and identifies a novel gene family. Nat Genet 15:157-164.
3. Aggarwal VS, Morrow BE. 2008. Genetic modifiers of the physical malformations in velo-cardio-facial syndrome/DiGeorge syndrome. Dev Disabil Res Rev 14:19-25.
4. Beaster-Jones L, Horton AC, Gibson-Brown JJ, et al. 2006. The amphioxus T-box gene, AmphiTbx15/18/22, illuminates the origins of chordate segmentation. Evol Dev 8:119-129.
5. Beaster-Jones L, Schubert M, Holland LZ. 2007. Cis-regulation of the amphioxus engrailed gene: Insights into evolution of a muscle-specific enhancer. Mech Dev 124:532-542.
6. Beaster-Jones L, Kalten bach SL, Koop D, et al. 2008. Evolutionary conservation of mesodermal segmentation in cephalochordates and vertebrates. Dev Genes Evol (in press).
7. Blair JE, Hedges SB. 2005. Molecular phylogeny and divergence times of deuterostome animals. Mol Biol Evol 22:2275-2284.
8. Boorman CJ, Shimeld SM. 2002. The evolution of left-right asymmetry in chordates. Bioessays 24:1004-1011.
9. Callery EM, Elinson RP. 2000. Thryoid hormone-dependent metamorphosis in a direct developing frog. Proc Natl Acad Sci USA 97:2615-2620.
10. Candiani S, Kreslova J, Benes V, et al. 2003. Cloning and developmental expression of amphioxus Dachschund. Gene Expr Patterns 3:65-69.
11. Caneparo L, Huang Y-L, Staudt N, et al. 2007. Dickkopf-1 regulates gastrulation movements by coordinated modulation of Wnt/betacatenin and Wnt/PCP activities, through interaction with the Dally-like homologue Knypek. Genes Dev 21:465-480.
12. Cañestro C, Postlethwait JH. 2007. Development of a chordate anterior-posterior axis without classical retinoic acid signaling. Dev Biol 305:522-538.
13. Chen J-Y, Dzik J, Edgecombe GD, et al. 1995. A possible early Cambrian chordate. Nature 377:720-722.
14. Chen T, Li Q, Xu J, et al. 2007. Mutation screening of BMP4, BMP7, HOXA4 and HOXB6 genes in Chinese patients with hypospadias. Eur J Hum Genet 15:23-28.
15. Chinpaisal C, Chang L, Hu X, et al. 1997. The orphan nuclear receptor TR2 suppresses a DR4 hormone response element of the mouse CRABP-I gene promoter. Biochemistry 36:14088-14095.
16. Collins MD, Mao G. 1999. Teratology of retinoids. Annu Rev Pharmacol Toxicol 39:399-430.
17. Dehal P, Satou Y, Campbell RK, et al. 2002. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298:2157-2167.
18. Delsuc F, Brinkmann H, Chourrout D, Philippe H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439:965-968.
19. Dequéant ML, Pourquié O. 2008. Segmental patterning of the vertebrate embryonic axis. Nature Rev Genet 9:370-382.
20. Dobzhansky T. 1973. Nothing in biology makes sense except in the light of evolution. Am Biol Teacher 35:125-129.
21. Donoghue PC, Graham A, Kelsh RN. 2008. The origin and evolution of the neural crest. Bioessays 30:530-541.
22. Dorsky RI, Sheldahl LC, Moon RT. 2002. A transgenic Lef1/b-catenin- dependent reporter is expressed in spatially restricted domains throughout zebrafish development. Dev Biol 241:229-237.
23. Dunn CW, Hejnol A, Matus DQ, et al. 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749.
24. Edvardsen RB, Lerat E, Maeland AD, et al. 2004. Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica. J Mol Evol 59:448-457.
25. Edvardsen RB, Seo H-C, Jensen MF, et al. 2005. Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica. Curr Biol 15:R12-R13.
26. Escriva H, Holland ND, Gronemeyer H, et al. 2002. The retinoic acid signaling pathway regulates anterior/posterior patterning in the nerve cord and pharynx of amphioxus, a chordate lacking neural crest. Development 129:2905-2916.
27. Ferrier DEK, Minguillón C, Cebrián C, Garcia- Fernàndez J. 2001. Amphioxus Evx Genes: Implications for the evolution of the midbrain-hindbrain boundary and the chordate tailbud. Dev Biol 237:270-281.
28. Ferrier DEK, Minguillon C, Holland PWH, Garcia-Femandez J. 2000. The amphioxus Hox cluster: Deuterostome posterior flexibility and Hox14. Evol Dev 2:284-293.
29. Fleischer AB, Simpson JK, McMichael A, Feldman SR. 2003. Are there racial and sex differences in the use of oral isotretinoin for acne management in the United States? J Am Acad Dermatol 49:662-666.
30. Fredriksson G, Ericson LE, Olsson R. 1984. Electron-microscopic studies of iodine-binding and peroxidase activity in the endostyle of the larval amphioxus (Branchiostoma lanceolatum). Cell Tiss Res 241:257-266.
31. Fredriksson G, Öfverholm T, Erickson LE. 1985. Ultrastructural demonstration of iodine-binding and peroxidase activity in the endostyle of Oikopleura dioica (Appendicularia). Gen Comp Endocrinol 58:319-327.
32. Fujita H. 1969. Studies on iodine metabolism of thyroid gland as revealed by electron microscopic autoradiography of Iodine-125. Virchows Arch Abt B Zellpathol 2:265-279.
33. Galli LM, Barnes T, Cheng T, Acosta L, et al. 2006. Differential inhibition of Wnt-3a by Sfrp-1, Sfrp-2, and Sfrp-3. Dev Dyn 235:681-690.
34. Garcia-Fernàndez J, Holland PWH. 1994. Archetypal organization of the amphioxus Hox gene cluster. Nature 370:563-566.
35. Garg V, Yamagishi C, Hu T, et al. 2001. Tbx1, a DiGeorge syndrome candidate gene, is regulated by Sonic Hedgehog during pharyngeal arch development. Dev Biol 235:62-73.
36. Garriock RJ, Warkman AS, Meadows SM, et al. 2007. Census of vertebrate Wnt genes: Isolation and developmental expression of Xenopus Wnt2, Wnt3, Wnt9a, Wnt9b, Wnt10a, and Wnt16. Dev Dyn 236:1249-1258.
37. Gaudet LM, MacKenzie J, Smith GN. 2006. Fat-soluble vitamin deficiency in pregnancy: A case report and review of a betalipoproteinemia. J Obstet Gynaecol Can 28:716-719.
38. Gostling NJ, Shimeld SM. 2003. Protochordate Zic genes define primitive somite compartments and highlight molecular changes underlying neural crest evolution. Evol Dev 5:136-144.
39. Graham A, Smith A. 2001. Patterning the pharyngeal arches. Bioessays 23:54-61.
40. Graham A, Okabe M, Quinlan R. 2005. The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat 207:479-487.
41. Guder C, Philipp I, Lengfeld T, et al. 2006. The Wnt code: Cnidarians signal the way. Oncogene 25:7450-7460.
42. Gunther T, Chen Z-F, Kim J, et al. 2000. Genetic ablation of parathyroid glands reveals another source of parathyroid hormone. Nature 406:199-203.
43. Halilagic A, Zile MH, Studer M. 2007. A novel role for retinoids in patterning the avian forebrain during presomite stages. Development 130:2039-2050.
44. Hanaoka R, Ohmori Y, Uyemura K, et al. 2004. Zebrafish gcmb is required for pharyngeal cartilage formation. Mech Dev 121:1235-1247.
45. Hartley KO, Hardcastle Z, Friday RV, et al. 2001. Transgenic Xenopus embryos reveal that anterior neural development requires continued suppression of BMP signaling after gastrulation. Dev Biol 238:168-184.
46. Heller N, Bràndli AW. 1997. Xenopus Pax-2 displays multiple splice forms during embryogenesis and pronephric kidney development. Mech Dev 69:83-104.
47. Hiruta J, Mazet F, Yasui K, et al. 2005. Comparative expression analysis of transcription factor genes in the endostyle of invertebrate chordates. Dev Dyn 233:1031-1037.
48. Hogan BL. 1996. Bone morphogenetic proteins: Multifunctional regulators of vertebrate development. Genes Dev 10:1580-1594.
49. Hogan BM, Hunter MP, Oates AC, et al. 2004. Zebrafish gcm2 is required for gill filament budding from pharyngeal ectoderm. Dev Biol 276:508-522.
50. Hol FA, Geurds MP, Chatkupt S, et al. 1996. PAX genes and human neural tube defects: An amino acid substitution in PAX-1 in a patient with spina bifida. J Med Genet 33:655-660.
51. Holland LZ. 2002. Heads or tails? Amphioxus and the evolution of anterior-posterior patterning in deuterostomes. Dev Biol 241:209-228.
52. Holland LZ, Gibson-Brown JJ. 2003. The Ciona intestinalis genome: When the constraints are off. Bioessays 25:529-532.
53. Holland LZ, Holland ND. 1996. Expression of AmphiHox-1 and AmphiPax-1 in amphioxus embryos treated with retinoic acid: Insights into evolution and patterning of the chordate nerve cord and pharynx. Development 122:1829-1838.
54. Holland LZ, Holland ND. 2000. Developmental expression of AmphiWnt1, an amphioxus gene in the Wnt1/wingless subfamily. Dev Genes Evol 210:522-524.
55. Holland LZ, Holland ND. 2007. A revised fate map for amphioxus and the evolution of axial patterning in chordates. Integr Comp Biol 47:360-372.
56. Holland LZ, Kene M, Williams NA, Holland ND. 1997. Sequence and embryonic expression of the amphioxus engrailed gene (AmphiEn): The metameric pattern of transcription resembles that of its segment-polarity homologue in Drosophila. Development 124:1723-1732.
57. Holland LZ, Schubert M, Kozmik Z, Holland ND. 1999. AmphiPax3/7, an amphioxus paired box gene: Insights into chordate myogenesis, neurogenesis, and the possible evolutionary precursor of definitive vertebrate neural crest. Evol Dev 1:153-165.
58. Holland LZ, Schubert M, Holland ND, Neuman T. 2000. Evolutionary conservation of the presumptive neural plate markers AmphiSox1/2/3 and AmphiNeurogenin in the invertebrate chordate amphioxus. Dev Biol 226:18-33.
59. Holland LZ, Rached LA, Tamme R, Holland ND, et al. 2001. Characterization and developmental expression of the amphioxus homologue of Notch (AmphiNotch): Evolutionary conservation of multiple expression domains in amphioxus and vertebrates. Dev Biol 232:493-507.
60. Holland LZ, Laudet V, Schubert M. 2004. The chordate amphioxus: An emerging model organism for developmental biology. Cell Mol Life Sci 61:2290-2308.
61. Holland LZ, Panfilio KA, Chastain R, et al. 2005. Nuclear beta-catenin promotes non-neural ectoderm and posterior cell fates in amphioxus embryos. Dev Dyn 233:1430-1443.
62. Holland LZ, Albalat R, Azumi K, et al. 2008. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res 18:1100-1111.
63. Holland ND, Chen J. 2001. Origin and early evolution of the vertebrates: New insights from advances in molecular biology, anatomy, and palaeontology. Bioessays 23:142-151.
64. Holland ND, Holland LZ. 2006. Stage-and tissue-specific patterns of cell division in embryonic and larval tissues of amphioxus during normal development. Evol Dev 8:142-149.
65. Holland ND, Kozmik Z, Holland LZ. 1995a. An amphioxus Pax gene, AmphiPax-1, expressed in embryonic endoderm, but not in mesoderm: Implications for the evolution of class I paired box genes. Mol Mar Biol Biotechnol 4:206-214.
66. Holland ND, Panganiban G, Henyey EL, Holland LZ. 1996. Sequence and developmental expression of AmphiDII, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: Insights into evolution of craniate forebrain and neural crest. Development 122:2911-2920.
67. Holland PWH, Koschorz B, Holland LZ, Herrmann BG. 1995b. Conservation of Brachyury (T) genes in amphioxus and vertebrates: Developmental and evolutionary implications. Development 121:4283-4291.
68. Hollander G, Gill J, Zuklys S, et al. 2006. Cellular and molecular events during early thymus development. Immunol Rev 209:28-46.
69. Honein MA, Paulozzi LJ, Erikson JD. 2001. Continued occurrence of Accutane-exposed pregnancies. Teratology 64:399-430.
70. Hoskins BE, Cramer CH, Silvius D, et al. 2007. Transcription factor SIX5 is mutated in patients with branchiooto-renal syndrome. Am J Hum Genet 80:800-804.
71. Hou XG, Aldridge RJ, Siveter DJ. 2002. New evidence on the anatomy and phylogeny of the earliest vertebrates. Proc R Soc Lond B Biol Sci 269:1865-1869.
72. Imai JH, Meinertzhagen IA. 2007. Neurons of the ascidian larval nervous system in Ciona intestinalis. I. Central nervous system. J Comp Neurol 501:316-334.
73. Ishibashi T, Usami T, Fujie M, et al. 2005. Oligonucleotide-based microarray analysis of retinoic acid target genes in the protochordate, Ciona intestinalis. Dev Dyn 233:1571-1578.
74. Jeffery WR. 2006. Ascidian neural crest-like cells: Phylogenetic distribution, relationship to larval complexity, and pigment cell fate. J Exp Zool B 306:470-480.
75. Jeffery WR, Strickler AG, Yamamoto Y. 2004. Migratory neural crest-like cells form body pigmentation in a urochordate embryo. Nature 431:696-699.
76. Joosten PHU, Hol FA, van Beersum SEC, et al. 1998. Altered regulation of platelet-derived growth factor receptor-alpha gene-transcription in vitro by spina bifida-associated mutant Pax1 proteins. Proc Natl Acad Sci USA 95:14459-14463.
77. Kawakami Y, Raya A, Raya RM, et al. 2005. Retinole acid signaling links left-right asymmetric patterning and bilaterally symmetric somitogenesis in the zebrafish embryo. Nature 435:165-171.
78. Kawano T, Wang C, Hotta Y, et al. 2007. Three novel mutations of the PAX6 gene in Japanese aniridia patients. J Hum Genet 52:571-574.
79. Kazanskaya O, Glinka A, Niehrs C. 2000. The role of Xenopus dickkopf1 in prechordal plate specification and neural patterning. Development 127:4981-4992.
80. Kiecker C, Niehrs C. 2001. A morphogen gradient of Wnt/beta-catenin signaling regulates anteroposterior neural patterning in Xenopus. Development 128:4189-4201.
81. Kingsbury BF. 1939. The question of a lateral thyroid in mammals with special reference to man. Am J Anat 65:333-356.
82. Kingsbury SR, Loddo M, Fanshawe T, et al. 2005. Repression of DNA replication licensing in quiescence is independent of geminin and may define the cell cycle state of progenitor cells. Exp Cell Res 309:56-67.
83. Kluge B, Renault N, Rohr KB. 2005. Anatomical and molecular reinvestigation of lamprey endostyle development provides new insight into thyroid gland evolution. Dev Genes Evol 215:32-40.
84. Kon T, Nohara M, Yamanoue Y, et al. 2007. Phylogenese position of a whale-fall lancelet (Cephalochordata) inferred from whole mitochondrial genome sequences. BMC Evol Biol 7:127-139.
85. Kozmik Z, Holland N, Kalousova A, et al. 1999. Characterization of an amphioxus paired box gene, AmphiPax2/5/8: Developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. Development 126:1295-1304.
86. Kozmik Z, Holland ND, Kreslova J, et al. 2007. Pax-Six-Eya-Dach network during amphioxus development: Conservation in vitro but context specificity in vivo. Dev Biol 306:143-159.
87. Kumar S, Kimberling WJ, Weston MD, et al. 1998. Identification of three novel mutations in human EYA1 protein associated with branchio-oto-renal syndrome. Hum Mutat 11:443-449.
88. Lammi L, Halonen K, Pirinen S, et al. 2003. A missense mutation in PAX9 in a family with distinct phenotype of oligodontia. Eur J Hum Genet 11:866-871.
89. Langeland JA, Tomsa JM, Jackman WR Jr, Kimmel CB. 1998. An amphioxus snail gene: Expression in paraxial mesoderm and neural plate suggests a conserved role in patterning the chordate embryo. Dev Genes Evol 208:569-577.
90. Langeland JA, Holland LZ, Chastain RA, Holland ND. 2006. An amphioxus LIM-homeobox gene, AmphiLim1/5, expressed early in the invaginating organizer region and later in differentiating cells of the kidney and central nervous system. Int J Biol Sci 2:110-116.
91. Lee PN, Pang K, Matus DQ, Martindale MQ. 2006. A WNT of things to come: Evolution of Wnt signaling and polarity in cnidarians. Sem Cell Dev Biol 17:157-167.
92. Li X, Zhang W, Chen D, Lin Y, et al. 2006. Expression of a novel somite-formation-related gene, AmphiSom, during amphioxus development. Dev Genes Evol 216:52-55.
93. Lindsay EA. 2001. Chromosomal microdeletions: Dissecting del22q11 syndrome. Nat Rev Genet 2:858-868.
94. Lindsay EA, Vitelli F, Su H, Morishima M, et al. 2001. Tbx1 haploinsufficiency in the DiGeorge syndrome region causes aortic arch defects in mice. Nature 410:97-101.
95. MacCallum CJ. 2007. Does medicine without evolution make sense? PLoS Biol 5:e112.
96. Maden M, Graham A, Zile M, Gale E. 2000. Abnormalities of somite development in the absence of retinoic acid. Int J Dev Biol 44:151-159.
97. Maden M, Gale E, Kostetskii I, Zile M. 1996. Vitamin A-deficient quail embryos have half a hindbrain and other neural defects. Curr Biol 6:417-426.
98. Mahadevan NR, Horton AC, Gibson-Brown JJ. 2004. Developmental expression of the amphioxus Tbx1/10 gene illuminates the evolution of vertebrate branchial arches and sclerotome. Dev Genes Evol 214:559-566.
99. Mallatt J, Chen J. 2003. Fossil sister group of craniates: Predicted and found. J Morph 258:1-31.
100. Manzanares M, Wada H, Hasaki N, et al. 2000. Conservation and elaboration of Hox gene regulation during evolution of the vertebrate head. Nature 408:854-857.
101. Mark M, Ghyselinck NB, Chambon P. 2004. Retinoic acid signaling in the development of branchial arches. Curr Opin Genet Dev 14:591-598.
102. Marshall H, Morrison A, Studer M, et al. 1996. Retinoids and Hox genes. FASEB J 10:969-978.
103. Mastroiacovo P, Mazzone T, Addis A, et al. 1999. High vitamin A intake in early pregnancy and major malformations: A multicenter prospective controlled study. Teratology 59:7-11.
104. Mazet F, Masood S, Luke GN, et al. 2004. Expression of AmphiCoe, an amphioxus COE/EBF gene, in the developing central nervous system and epidermal sensory neurons. Genesis 38:58-65.
105. Mazet F, Luke GN, Shimeld SM. 2005. The amphioxus FoxQ1 gene is expressed in the developing endostyle. Gene Expr Patterns 5:313-315.
106. McGaughran JM, Oates A, Donnai D, et al. 2003. Mutations in PAX1 may be associated with Klippel-Feil syndrome. Eur J Hum Genet 11:468-4674.
107. McGinnis W, Garber RL, Wirz J, et al. 1984. A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans. Cell 37:403-408.
108. Meinertzhagen IA, Okamura Y. 2001. The larval ascidian nervous system: The chordate brain from its small beginnings. Trends Neurosci 24:401-410.
109. Merscher S, Funke B, Epstein JA, et al. 2001. TBX1 is responsible for cardiovascular defects in velo-cardio-facial/DiGeorge Syndrome. Cell 104:619-629.
110. Meulemans D, Bronner-Fraser M. 2002. Amphioxus and lamprey AP-2 genes: Implications for neural crest evolution and migration patterns. Development 129:4953-4962.
111. Meulemans D, Bronner-Fraser M. 2004. Gene-regulatory interactions in neural crest evolution and Development. Dev Cell 7:291-299.
112. Meulemans D, Bronner-Fraser M. 2007. Insights from amphioxus into the evolution of vertebrate cartilage. PLoS ONE 2:e787, 781-789.
113. Meulemans D, McCauley D, Bronner-Fraser M. 2003. Id expression in amphioxus and lamprey highlights the role of gene co-option during neural crest evolution. Dev Biol 264:430-442.
114. Minguillon C, Jimenez-Delgado S, Panopoulou G, Garcia-Fernàndez J. 2003. The amphioxus Hairy family: Differential fate after duplication. Development 130:5903-5914.
115. Moreno TA, Kintner C. 2004. Regulation of segmental patterning by retinoic acid signaling during Xenopus somitogenesis. Dev Cell 6:205-218.
116. Mostowska A, Kobielak A, Trzeciak WH. 2003. Molecular basis of non-syndromic tooth agenesis: Mutations of MSX1 and PAX9 reflect their role in patterning human dentition. Eur J Oral Sci 111:365-370.
117. Mulder GB, Manley NR, Maggio-Price L. 1998. Retinoic acid-induced thymic abnormalities in the mouse are associated with altered pharyngeal morphology, thymocyte maturation defects, and altered expression of Hoxa3 and Pax1. Teratology 58:263-275.
118. Mulder GB, Manley N, Grant J, et al. 2000. Effects of excess vitamin A on development of cranial neural crest-derived structures: A neonatal and embryologic study. Teratology 62:214-226.
119. Nagatomo K-i, Ishibashi T, Satou Y, et al. 2003. Retinoic acid affects gene expression and morphogenesis without upregulating the retinoic acid receptor in the ascidian Ciona intestinalis. Mech Dev 120:363-372.
120. Nishida H, 1987. Cell lineage analysis in ascidian embryos by intracellular injection of a tracer enzyme. III. Up to the tissue restricted stage. Dev Biol 121:526-541.
121. Nissen RM, Yan J, Amsterdam A, et al. 2003. Zebrafish foxi one modulates cellular responses to Fgf signaling required for the integrity of ear and jaw patterning. Development 130:2543-2554.
122. Ogasawara M, Satoh N. 1998. Isolation and characterization of endostyle-specific genes in the ascidian Ciona intestinalis. Biol Bull 195:60-69.
123. Ogasawara M, Di Lauro R, Satoh N. 1999. Ascidian homologues of mammalian thyroid peroxidase genes are expressed in the thyroid-equivalent region of the endostyle. J Exp Zool B 285:158-169.
124. Ogasawara M, Shigetani Y, Hirano S, et al. 2000. Pax1/Pax9-related genes in an agnathan vertebrate, Lampetra japonica: Expression pattern of LjPax9 implies sequential evolutionary events toward the gnathostome body plan. Dev Biol 223:399-410.
125. Okabe M, Graham A. 2004. The origin of the parathyroid gland. Proc Natl Acad Sci USA 101:17716-17719.
126. Paris M, Escriva H, Schubert M, et al. 2008. Amphioxus postembryonic development reveals the homology of chordate metamorphosis. Curr Biol 18:825-830.
127. Pennacchio LA, Ahituv N, Moses AM, et al. 2006. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444:499-502.
128. Peters H, Neubuser A, Kratochwil K, Balling R. 1998. Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities. Genes Dev 12:2735-2747.
129. Philippe H, Lartillot N, Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol 22:1246-1253.
130. Pinho S, Niehrs C. 2007. Dkk3 is required for TGF-beta signaling during Xenopus mesoderm induction. Differentiation 75:957-967.
131. Piotrowski T, Ahn D-G, Schilling TF, et al 2003. The zebrafish van gogh mutation disrupts tbx1, which is involved in the DiGeorge deletion syndrome in humans. Development 130:5043-5052.
132. Powers TP, Amemiya CT. 2004. Evidence for a Hox14 paralog group in vertebrates. Curr Biol 14:R183-R184.
133. Putnam NH, Butts T, Ferrier DE, et al. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064-1071.
134. Quinlan R, Gale E, Maden M, Graham A. 2002. Deficits in the posterior pharyngeal endoderm in the absence of retinoids. Dev Dyn 225:54-60.
135. Rahr H. 1982. Ultrastructure of gill bars of Branchiostoma lanceolatum with special reference to gill skeleton and blood vessels (Cephalochordata). Zoomorphology 99:167-180.
136. Rasmussen SLK, Holland LZ, Schubert M, et al. 2007. Amphioxus AmphiDelta: Evolution of delta protein structure, segmentation, and neurogenesis. Genesis 45:113-122.
137. Roberts C, Ivins SM, James CT, et al. 2005. Retinoic acid down-regulates Tbx1 expression in vivo and in vitro. Dev Dyn 232:928-938.
138. Roberts C, Ivins S, Cook AC, et al. 2006. Cyp26 genes a1, b1 and c1 are down-regulated in Tbx1 null mice and inhibition of Cyp26 enzyme function produces a phenocopy of DiGeorge syndrome in the chick. Hum Mol Genet 15:3394-3410.
139. Rohr KB, Concha ML. 2000. Expression of nk2.1a during early development of the thyroid gland in zebrafish. Mech Dev 95:267-270.
140. Ruf RG, Xu PX, Silvius D, et al. 2004. SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes. Proc Natl Acad Sci USA 101:8090-8095.
141. Ryan JF, Mazza ME, Pang K, et al. 2007. Pre-bilaterian origins of the Hox cluster and the Hox code: Evidence from the sea anemone, Nematostella vectensis. PLoS ONE 2:e153.
142. Sauka-Spengler T, Le Mentec C, Lepage M, Mazan S. 2002. Embryonic expression of Tbx1, a DiGeorge syndrome candidate gene, in the lamrey Lampetra fluviatilis. Gene Expr Patterns 2:99-103.
143. Schohl A, Fagotto F. 2002. Beta-catenin, MAPK and Smad signaling during early Xenopus development. Development 129:37-52.
144. Schohl A, Fagotto F. 2003. A role for maternal beta-catenin in early mesoderm induction in Xenopus. EMBO J 22:3303-3313.
145. Schubert M, Holland LZ, Holland ND. 2000a. Characterization of an amphioxus Wnt gene, AmphiWnt11, with possible roles in myogenesis and tail outgrowth. Genesis 27:1-5.
146. Schubert M, Holland LZ, Panopoulou GD, et al. 2000b. Characterization of amphioxus AmphiWnt8: Insights into the evolution of patterning of the embryonic dorsoventral axis. Evol Dev 2:85-92.
147. Schubert M, Holland LZ, Stokes MD, Holland ND. 2001. Three amphioxus Wnt genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) associated with the tail bud: The evolution of somitogenesis in chordates. Dev Biol 240:262-273.
148. Schubert M, Yu JK, Holland ND, et al. 2005. Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxus. Development 132:61-73.
149. Schubert M, Holland ND, Laudet V, Holland LZ. 2006. A retinoic acid-Hox hierarchy controls both anterior/posterior patterning and neuronal specification in the developing central nervous system of the cephalochordate amphioxus. Dev Biol 296:190-202.
150. Schuffenhauer S, Leifheit H-J, Lichtner P, et al. 1999. De novo deletion (14)(q11.2q13) including PAX9: Clinical and molecular findings. J Med Genet 36:233-236.
151. Scott MP, Weiner AJ. 1984. Structural relationships among genes that control development: Sequence homology between the Antennapedia, Ultrabithorax, and Fushi Tarazu Loci of Drosophila. Proc Natl Acad Sci USA 81:4115-4119.
152. Sharman AC, Shimeld SM, Holland PWH. 1999. An amphioxus Msx gene expressed predominantly in the dorsal neural tube. Dev Genes Evol 209:260-263.
153. Shimeld SM. 1997. Characterisation of amphioxus HNF-3 genes: Conserved expression in the notochord and floor plate. Dev Biol 183:74-85.
154. Shimeld SM. 1999. The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog. Dev Genes Evol 209:40-47
155. Soviknes AM, Chourrout D, Glover JC. 2005. Development of putative GABAergic neurons in the appendicularian urochordate Oikopleura dioica. J Comp Neurol 490:12-28.
156. Spagnuolo A, Ristoratore F, Di Gregorio A, et al. 2003. Unusual number and genomic organization of Hox genes in the tunicate Ciona intestinalis. Gene 309:71-79.
157. Suzuki S. 1985. Iodine distribution in the thyroid follicles of the hagfish, Eptatretus burgeri and lamprey, Lampetra japonica: electron-probe X-ray microanalysis. Cell Tissue Res 241:539-543.
158. Venkatesh TV, Holland ND, Holland LZ, et al. 1999. Sequence and developmental expression of amphioxus AmphiNk2-1: Insights into the evolutionary origin of the vertebrate thyroid gland and forebrain. Dev Genes Evol 209:254-259.
159. Vermot J, Niederreither K, Garnier J-M, et al. 2003. Decreased embryonic retinoic acid synthesis results in a DiGeorge syndrome phenotype in newborn mice. Proc Natl Acad Sci USA 100:1763-1768.
160. Vincent C, Kalatzis V, Abdelhak S, et al. 1997. BOR and BO syndromes are allelic defects of EYA. Eur J Hum Genet 5:242-246.
161. Vitelli F, Taddei I, Morishima M, et al. 2002. A genetic link between Tbx1 and fibroblast growth factor signaling. Development 129:4605-4611.
162. Wada H, Escriva H, Zhang S, Laudet V. 2006a. Conserved RARE localization in amphioxus Hox clusters and implications for Hox code evolution in the vertebrate neural crest. Dev Dyn 235:1522-1531.
163. Wada H, Okuyama M, Satoh N, Zhang SC. 2006b. Molecular evolution of fibrillar collagen in chordates, with implications for the evolution of vertebrate skeletons and chordate phylogeny. Evol Dev 8:370-377.
164. Wang W, Zhong J, Su B, et al. 2007. Comparison of Pax1/9 locus reveals 500-myr-old syntenic block and evolutionary conserved noncoding regions. Mol Biol Evol 24:784-791.
165. Wang Z, Dolle P, Cardoso WV, Niederreither K. 2006. Retinoic acid regulates morphogenesis and patterning of posterior foregut derivatives. Dev Biol 297:433-445.
166. Wardle FC, Smith JC. 2004. Refinement of gene expression patterns in the early Xenopus embryo. Development 131:4687-4696.
167. Wasiak S, Lohnes D. 1999. Retinoic acid affects left-right patterning. Dev Biol 215:332-342.
168. Wendung O, Dennefeld C, Chambon P, Mark M, 2000. Retinoid signaling is essential for patterning the endoderm of the third and fourth pharyngeal arches. Development 127: 1553-1562.
169. Wikramanayake AH, Hong M, Lee PN, Pang K, Byrum CA, Bince JM, Xu R, Martindale MQ. 2003. An ancient role for nuclear β-catenin in the evolution of axial polarity and germ layer segregation. Nature 426:446-450.
170. Woolfe A, Goodson M, Goode DK, et al. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3:e7.
171. Wright GM, Youson JH. 1976. Transformation of the endostyle of the anadromous sea lamprey Petromyzon marinus during metamorphosis, Part 1: Light microscopy and autoradiography with iodine-125. Gen Comp Endocrinol 30:243-257.
172. Wysowski DK, Swann J, Vega A. 2002. Use of isotretinoin (Accutane) in the United States: Rapid increase from 1992 through 2000. J Am Acad Dermatol 46:505-509.
173. Xu P, Woo I, Her H, et al. 1997. Mouse Eya homologues of the Drosophila eyes absent gene require Pax6 for expression in lens and nasal placode. Development 124:219-231.
174. Xu P-X, Zheng W, Laclef C, et al. 2002. Eyal is required for the morphogenesis of mammalian thymus, parathyroid and thyroid. Development 129:3033-3044.
175. Yamagishi H, Maeda J, Hu T, et al. 2003. Tbx1 is regulated by tissue-specific forkhead proteins through a common Sonic hedgehog-responsive enhancer. Genes Dev 17:269-281.
176. Yasui K, Zhang SC, Uemura M, Saiga H. 2000. Left-right asymmetric expression of BbPtx, a Ptx-related gene, in a lancelet species and the developmental left-sidedness in deuterostomes. Development 127:187-195.
177. Yu J-K, Holland LZ, Holland ND. 2002a. An amphioxus nodal gene (AmphiNodal) with early symmetrical expression in the organizer and mesoderm and later asymmetrical expression associated with left-right axis formation. Evol Dev 4:418-425.
178. Yu JK, Holland ND, Holland LZ. 2002b. An amphioxus winged helix/forkhead gene, AmphiFoxD: Insights into vertebrate neural crest evolution. Dev Dyn 225:289-297.
179. Yu JK, Satou Y, Holland ND, Shin-I T, et al. 2007. Axial patterning in cephalochordates and the evolution of the organizer. Nature 445:613-617.
180. Yu JK, Meulemans D, McKeown SJ, Bronner-Fraser M. 2008. Insights from the amphioxus genome on the origin of vertebrate neural crest. Genome Res 18:1127-1132.
181. Zajac JD, Danks JA. 2008. The development of the parathyroid gland: From fish to human. Curr Opin Nephrol Hyperten 17:353-356.
182. Zhang G, Cohn MJ. 2006. Hagfish and lancelet fibrillar collagens reveal that type II collagen-based cartilage evolved in stem vertebrates. Proc Natl Acad Sci USA 103:16829-16833.
183. Zhang L, Zhong T, Wang Y, et al. 2006. TBX1, a DiGeorge syndrome candidate gene, is inhibited by retinoic acid. Int J Dev Biol 50:55-61.
184. Zhang S-c, Holland ND, Holland LZ. 1997. Topographic changes in nascent and early mesoderm in amphioxus embryos studied by DiI labeling and by in situ hybridization for a Brachyury gene. Dev Genes Evol 206:532-535.
185. Zou D, Silvius D, Davenport J, et al. 2006. Patterning of the third pharyngeal pouch into thymus/parathyroid by Six and Eyal. Dev Biol 293:499-512.
186. Zweier C, Sticht H, Aydin-Yaylagül I, et al. 2007. Human TBX1 missense mutations cause gain of function resulting in the same phenotype as 22q11.2 deletions. Am J Hum Genet 80:510-517.