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<PubmedArticle><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">20849572</PMID><DateCompleted><Year>2011</Year><Month>07</Month><Day>14</Day></DateCompleted><DateRevised><Year>2021</Year><Month>10</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2041-9139</ISSN><JournalIssue CitedMedium="Internet"><Volume>1</Volume><Issue>1</Issue><PubDate><Year>2010</Year><Month>Sep</Month><Day>01</Day></PubDate></JournalIssue><Title>EvoDevo</Title><ISOAbbreviation>Evodevo</ISOAbbreviation></Journal><ArticleTitle>Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer.</ArticleTitle><Pagination><StartPage>7</StartPage><MedlinePgn>7</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/2041-9139-1-7</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The zona limitans intrathalamica (ZLI) and the isthmus organizer (IsO) are two major secondary organizers of vertebrate brain development. These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively). To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In this paper, we identified a conserved sequence motif (Fezf box) in all bilaterians. We report the expression pattern of Fezf in amphioxus and Drosophila and compare it with those of Gbx, Otx and Irx. We found that the relative expression patterns of these genes in vertebrates are fully conserved in amphioxus and flies, indicating that the genetic subdivisions defining the location of both secondary organizers in early vertebrate brain development were probably present in the last common ancestor of extant bilaterians. However, in contrast to vertebrates, we found that Irx-defective flies do not show an affected Fezf expression pattern.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The absence of expression of the corresponding morphogens from cells at these conserved genetic boundaries in invertebrates suggests that the organizing properties might have evolved specifically in the vertebrate lineage by the recruitment of key morphogens to these conserved genetic locations.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Irimia</LastName><ForeName>Manuel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Departament de Gen&#xe8;tica and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain. mirimia@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pi&#xf1;eiro</LastName><ForeName>Cristina</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Maeso</LastName><ForeName>Ignacio</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>G&#xf3;mez-Skarmeta</LastName><ForeName>Jos&#xe9; Luis</ForeName><Initials>JL</Initials></Author><Author ValidYN="Y"><LastName>Casares</LastName><ForeName>Fernando</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Garcia-Fern&#xe0;ndez</LastName><ForeName>Jordi</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>09</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Evodevo</MedlineTA><NlmUniqueID>101525836</NlmUniqueID><ISSNLinking>2041-9139</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2010</Year><Month>3</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2010</Year><Month>9</Month><Day>1</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>9</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>9</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2010</Year><Month>9</Month><Day>21</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="pmc-release"><Year>2010</Year><Month>9</Month><Day>1</Day></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">20849572</ArticleId><ArticleId IdType="pmc">PMC2942887</ArticleId><ArticleId IdType="doi">10.1186/2041-9139-1-7</ArticleId><ArticleId IdType="pii">2041-9139-1-7</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Kiecker C, Lumsden A. Compartments and their boundaries in vertebrate brain development. Nat Rev Neurosci. 2005;6:553&#x2013;564. doi: 10.1038/nrn1702.</Citation><ArticleIdList><ArticleId IdType="doi">10.1038/nrn1702</ArticleId><ArticleId IdType="pubmed">15959467</ArticleId></ArticleIdList></Reference><Reference><Citation>Scholpp S, Wolf O, Brand M, Lumsden A. Hedgehog signalling from the zona limitans intrathalamica orchestrates patterning of the zebrafish diencephalon. Development. 2006;133:855&#x2013;864. doi: 10.1242/dev.02248.</Citation><ArticleIdList><ArticleId IdType="doi">10.1242/dev.02248</ArticleId><ArticleId IdType="pubmed">16452095</ArticleId></ArticleIdList></Reference><Reference><Citation>Martinez S. The isthmic organizer and brain regionalization. Int J Dev Biol. 2001;45:367&#x2013;371.</Citation><ArticleIdList><ArticleId IdType="pubmed">11291867</ArticleId></ArticleIdList></Reference><Reference><Citation>Osorio J, Mazan S, Retaux S. Organisation of the lamprey (Lampetra fluviatilis) embryonic brain: Insights from LIM-homeodomain, Pax and hedgehog genes. Dev Biol. 2005;288:100&#x2013;112. doi: 10.1016/j.ydbio.2005.08.042.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.ydbio.2005.08.042</ArticleId><ArticleId IdType="pubmed">16289025</ArticleId></ArticleIdList></Reference><Reference><Citation>Murakami Y, Uchida K, Rijli FM, Kuratani S. Evolution of the brain developmental plan: Insights from agnathans. Dev Biol. 2005;280:249&#x2013;259. doi: 10.1016/j.ydbio.2005.02.008.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.ydbio.2005.02.008</ArticleId><ArticleId IdType="pubmed">15882571</ArticleId></ArticleIdList></Reference><Reference><Citation>Lowe CJ, Terasaki M, Wu M, Freeman RM, Runft L, Kwan K, Haigo S, Aronowicz J, Lander E, Gruber C, Smith M, Kirschner M, Gerhart J. Dorsoventral patterning in hemichordates: insights into early chordate evolution. PLoS Biol. 2006;4:e291. doi: 10.1371/journal.pbio.0040291.</Citation><ArticleIdList><ArticleId IdType="doi">10.1371/journal.pbio.0040291</ArticleId><ArticleId IdType="pmc">PMC1551926</ArticleId><ArticleId IdType="pubmed">16933975</ArticleId></ArticleIdList></Reference><Reference><Citation>Shimeld SM. The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog. Dev Genes and Evol. 1999;209:40&#x2013;47. doi: 10.1007/s004270050225.</Citation><ArticleIdList><ArticleId IdType="doi">10.1007/s004270050225</ArticleId><ArticleId IdType="pubmed">9914417</ArticleId></ArticleIdList></Reference><Reference><Citation>Meulemans D, Bronner-Fraser M. Insights from amphioxus into the evolution of vertebrate cartilage. PLoS One. 2007;2:e787. doi: 10.1371/journal.pone.0000787.</Citation><ArticleIdList><ArticleId IdType="doi">10.1371/journal.pone.0000787</ArticleId><ArticleId IdType="pmc">PMC1950077</ArticleId><ArticleId IdType="pubmed">17726517</ArticleId></ArticleIdList></Reference><Reference><Citation>Holland LZ, Short S. Gene duplication, co-option and recruitment during the origin of the vertebrate brain from the invertebrate chordate brain. Brain Behav Evol. 2008;72:91&#x2013;105. doi: 10.1159/000151470.</Citation><ArticleIdList><ArticleId IdType="doi">10.1159/000151470</ArticleId><ArticleId IdType="pubmed">18836256</ArticleId></ArticleIdList></Reference><Reference><Citation>Holland LZ, Satoh N, Azumi K, Benito-Guti&#xe9;rrez &#xc8;, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LD, Ferrier DEK, Garcia-Fern&#xe0;ndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallbrook F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, Mchardy AC, Meulemans D. et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008;18:1100&#x2013;1111. doi: 10.1101/gr.073676.107.</Citation><ArticleIdList><ArticleId IdType="doi">10.1101/gr.073676.107</ArticleId><ArticleId IdType="pmc">PMC2493399</ArticleId><ArticleId IdType="pubmed">18562680</ArticleId></ArticleIdList></Reference><Reference><Citation>Castro LFC, Rasmussen SLK, Holland PWH, Holland ND, Holland LZ. A Gbx homeobox gene in amphioxus: Insights into ancestry of the ANTP class and evolution of the midbrain/hindbrain boundary. Dev Biol. 2006;295:40&#x2013;51. doi: 10.1016/j.ydbio.2006.03.003.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.ydbio.2006.03.003</ArticleId><ArticleId IdType="pubmed">16687133</ArticleId></ArticleIdList></Reference><Reference><Citation>Hirth F, Kammermeier L, Frei E, Walldorf U, Noll M, Reichert H. An urbilaterian origin of the tripartite brain: developmental genetic insights from Drosophila. Development. 2003;130:2365&#x2013;2373. doi: 10.1242/dev.00438.</Citation><ArticleIdList><ArticleId IdType="doi">10.1242/dev.00438</ArticleId><ArticleId IdType="pubmed">12702651</ArticleId></ArticleIdList></Reference><Reference><Citation>Hirata T, Nakazawa M, Muraoka O, Nakayama R, Suda Y, Hibi M. Zinc-finger genes Fez and Fez-like function in the establishment of diencephalon subdivisions. Development. 2006;133:3993&#x2013;4004. doi: 10.1242/dev.02585.</Citation><ArticleIdList><ArticleId IdType="doi">10.1242/dev.02585</ArticleId><ArticleId IdType="pubmed">16971467</ArticleId></ArticleIdList></Reference><Reference><Citation>Jeong J-Y, Einhorn Z, Mathur P, Chen L, Lee S, Kawakami K, Guo S. Patterning the zebrafish diencephalon by the conserved zinc-finger protein Fezl. Development. 2007;134:127&#x2013;136. doi: 10.1242/dev.02705.</Citation><ArticleIdList><ArticleId IdType="doi">10.1242/dev.02705</ArticleId><ArticleId IdType="pubmed">17164418</ArticleId></ArticleIdList></Reference><Reference><Citation>Rodr&#xed;guez-Seguel E, Alarc&#xf3;n P, G&#xf3;mez-Skarmeta JL. The Xenopus Irx genes are essential for neural patterning and define the border between prethalamus and thalamus through mutual antagonism with the anterior repressors Fezf and Arx. Dev Biol. 2009;329:258&#x2013;268. doi: 10.1016/j.ydbio.2009.02.028.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.ydbio.2009.02.028</ArticleId><ArticleId IdType="pubmed">19268445</ArticleId></ArticleIdList></Reference><Reference><Citation>Barrallo-Gimeno A, Nieto MA. Evolutionary history of the Snail/Scratch superfamily. Trends Genet. 2009;25:248&#x2013;252. doi: 10.1016/j.tig.2009.04.001.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.tig.2009.04.001</ArticleId><ArticleId IdType="pubmed">19427053</ArticleId></ArticleIdList></Reference><Reference><Citation>Kerner P, Hung J, B&#xe9;hague J, Le Gouar M, Balavoine G, Vervoort M. Insights into the evolution of the snail superfamily from metazoan wide molecular phylogenies and expression data in annelids. BMC Evol Biol. 2009;9:94. doi: 10.1186/1471-2148-9-94.</Citation><ArticleIdList><ArticleId IdType="doi">10.1186/1471-2148-9-94</ArticleId><ArticleId IdType="pmc">PMC2688512</ArticleId><ArticleId IdType="pubmed">19426549</ArticleId></ArticleIdList></Reference><Reference><Citation>Shimeld SM. C2H2 zinc finger genes of the Gli, Zic, KLF, SP, Wilms' tumour, Huckebein, Snail, Ovo, Spalt, Odd, Blimp-1, Fez and related gene families from Branchiostoma floridae. Dev Genes Evol. 2008;218:639&#x2013;649. doi: 10.1007/s00427-008-0248-6.</Citation><ArticleIdList><ArticleId IdType="doi">10.1007/s00427-008-0248-6</ArticleId><ArticleId IdType="pubmed">18795322</ArticleId></ArticleIdList></Reference><Reference><Citation>Sullivan JC, Reitzel AM, Finnerty JR. A high percentage of introns in human genes were present early in animal evolution: evidence from the basal metazoan Nematostella vectensis. Genome Inform. 2006;17:219&#x2013;229.</Citation><ArticleIdList><ArticleId IdType="pubmed">17503371</ArticleId></ArticleIdList></Reference><Reference><Citation>Coulombe-Huntington J, Majewski J. Characterization of intron loss events in mammals. Genome Res. 2007;17:23&#x2013;32. doi: 10.1101/gr.5703406.</Citation><ArticleIdList><ArticleId IdType="doi">10.1101/gr.5703406</ArticleId><ArticleId IdType="pmc">PMC1716263</ArticleId><ArticleId IdType="pubmed">17108319</ArticleId></ArticleIdList></Reference><Reference><Citation>Roy SW, Fedorov A, Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci USA. 2003;100:7158&#x2013;7162. doi: 10.1073/pnas.1232297100.</Citation><ArticleIdList><ArticleId IdType="doi">10.1073/pnas.1232297100</ArticleId><ArticleId IdType="pmc">PMC165846</ArticleId><ArticleId IdType="pubmed">12777620</ArticleId></ArticleIdList></Reference><Reference><Citation>Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007;317:86&#x2013;94. doi: 10.1126/science.1139158.</Citation><ArticleIdList><ArticleId IdType="doi">10.1126/science.1139158</ArticleId><ArticleId IdType="pubmed">17615350</ArticleId></ArticleIdList></Reference><Reference><Citation>Putnam N, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Guti&#xe9;rrez E, Dubchak I, Garcia-Fern&#xe0;ndez J, Grigoriev IV, Horton AV, de Jong PJ, Jurka J, Kapitonov V, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Asaf Salamov A, Satou Y, Sauka-Spengler T, Schmutz T, Shin-I T, Toyoda A. et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008;453:1064&#x2013;1071. doi: 10.1038/nature06967.</Citation><ArticleIdList><ArticleId IdType="doi">10.1038/nature06967</ArticleId><ArticleId IdType="pubmed">18563158</ArticleId></ArticleIdList></Reference><Reference><Citation>Kozmik Z, Holland ND, Kreslova J, Oliveri D, Schubert M, Jonasova K, Holland LZ, Pestarino M, Benes V, Candiani S. Pax-Six-Eya-Dach network during amphioxus development: conservation in vitro but context specificity in vivo. Dev Biol. 2007;306:149&#x2013;159. doi: 10.1016/j.ydbio.2007.03.009.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.ydbio.2007.03.009</ArticleId><ArticleId IdType="pubmed">17477914</ArticleId></ArticleIdList></Reference><Reference><Citation>Schubert M, Holland LZ, Stokes MD, Holland ND. Three amphioxus Wnt genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) associated with the tail bud: the evolution of somitogenesis in chordates. Dev Biol. 2001;240:262&#x2013;273. doi: 10.1006/dbio.2001.0460.</Citation><ArticleIdList><ArticleId IdType="doi">10.1006/dbio.2001.0460</ArticleId><ArticleId IdType="pubmed">11784062</ArticleId></ArticleIdList></Reference><Reference><Citation>Weng M, Golden KL, Lee CY. dFezf/Earmuff maintains the restricted developmental potential of intermediate neural progenitors in Drosophila. Dev Cell. 2010;18:126&#x2013;135. doi: 10.1016/j.devcel.2009.12.007.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.devcel.2009.12.007</ArticleId><ArticleId IdType="pmc">PMC6699514</ArticleId><ArticleId IdType="pubmed">20152183</ArticleId></ArticleIdList></Reference><Reference><Citation>Pfeiffer BD, Jenett A, Hammonds AS, Ngo TT, Misra S, Murphy C, Scully A, Carlson JW, Wan KH, Laverty TR, Mungall C, Svirskas R, Kadonaga JT, Doe CQ, Eisen MB, Celniker SE, Rubin GM. Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci USA. 2008;105:9715&#x2013;9720. doi: 10.1073/pnas.0803697105.</Citation><ArticleIdList><ArticleId IdType="doi">10.1073/pnas.0803697105</ArticleId><ArticleId IdType="pmc">PMC2447866</ArticleId><ArticleId IdType="pubmed">18621688</ArticleId></ArticleIdList></Reference><Reference><Citation>Gomez-Skarmeta JL, Diez del Corral R, de la Calle-Mustienes E, Ferr&#xe9;-Marc&#xf3; D, Modolell J. Araucan and caupolican, two members of the novel iroquois complex, encode homeoproteins that control proneural and vein-forming genes. Cell. 1996;85:95&#x2013;105. doi: 10.1016/S0092-8674(00)81085-5.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/S0092-8674(00)81085-5</ArticleId><ArticleId IdType="pubmed">8620542</ArticleId></ArticleIdList></Reference><Reference><Citation>Kaltenbach SL, Holland LZ, Holland ND, Koop D. Developmental expression of the three iroquois genes of amphioxus (BfIrxA, BfIrxB, and BfIrxC) with special attention to the gastrula organizer and anteroposterior boundaries in the central nervous system. Gene Expr Patterns. 2009;9:329&#x2013;334. doi: 10.1016/j.gep.2009.02.003.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.gep.2009.02.003</ArticleId><ArticleId IdType="pubmed">19233318</ArticleId></ArticleIdList></Reference><Reference><Citation>Cavodeassi F, Modolell J, Gomez-Skarmeta JL. The Iroquois family of genes: from body building to neural patterning. Development. 2001;128:2847&#x2013;2855.</Citation><ArticleIdList><ArticleId IdType="pubmed">11532909</ArticleId></ArticleIdList></Reference><Reference><Citation>Reichert H. A tripartite organization of the urbilaterian brain: developmental genetic evidence from Drosophila. Brain Res Bull. 2005;66:491&#x2013;494. doi: 10.1016/j.brainresbull.2004.11.028.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.brainresbull.2004.11.028</ArticleId><ArticleId IdType="pubmed">16144638</ArticleId></ArticleIdList></Reference><Reference><Citation>Lichtneckert R, Reichert H. Insights into the urbilaterian brain: conserved genetic patterning mechanisms in insect and vertebrate brain development. Heredity. 2005;94:465&#x2013;477. doi: 10.1038/sj.hdy.6800664.</Citation><ArticleIdList><ArticleId IdType="doi">10.1038/sj.hdy.6800664</ArticleId><ArticleId IdType="pubmed">15770230</ArticleId></ArticleIdList></Reference><Reference><Citation>Seo HC, Drivenes Ellingsen S, Fjose A. Expression of two zebrafish homologues of the murine Six3 gene demarcates the initial eye primordia. Mech Dev. 1998;73:45&#x2013;57. doi: 10.1016/S0925-4773(98)00028-8.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/S0925-4773(98)00028-8</ArticleId><ArticleId IdType="pubmed">9545529</ArticleId></ArticleIdList></Reference><Reference><Citation>Kobayashi D, Kobayashi M, Matsumoto K, Ogura T, Nakafuku M, Shimamura K. Early subdivisions in the neural plate define distinct competence for inductive signals. Development. 2002;129:83&#x2013;93.</Citation><ArticleIdList><ArticleId IdType="pubmed">11782403</ArticleId></ArticleIdList></Reference><Reference><Citation>Mazet F, Shimeld SM. Characterisation of an amphioxus Fringe gene and the evolution of the vertebrate segmentation clock. Dev Genes Evol. 2003;V213:505&#x2013;509. doi: 10.1007/s00427-003-0351-7.</Citation><ArticleIdList><ArticleId IdType="doi">10.1007/s00427-003-0351-7</ArticleId><ArticleId IdType="pubmed">12928900</ArticleId></ArticleIdList></Reference><Reference><Citation>Schubert M, Holland LZ, Panopoulou GD, Lehrach H, Holland ND. Characterization of amphioxus AmphiWnt8: insights into the evolution of patterning of the embryonic dorsoventral axis. Evol Dev. 2000;2:85&#x2013;92. doi: 10.1046/j.1525-142x.2000.00047.x.</Citation><ArticleIdList><ArticleId IdType="doi">10.1046/j.1525-142x.2000.00047.x</ArticleId><ArticleId IdType="pubmed">11258394</ArticleId></ArticleIdList></Reference><Reference><Citation>Lowe CJ, Wu M, Salic A, Evans L, Lander E, Stange-Thomann N, Gruber CE, Gerhart J, Kirschner M. Anteroposterior patterning in hemichordates and the origins of the chordate nervous system. Cell. 2003;113:853&#x2013;865. doi: 10.1016/S0092-8674(03)00469-0.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/S0092-8674(03)00469-0</ArticleId><ArticleId IdType="pubmed">12837244</ArticleId></ArticleIdList></Reference><Reference><Citation>Yeh R-F, Lim LP, Burge CB. Computational inference of homologous gene structures in the human genome. Genome Res. 2001;11:803&#x2013;816. doi: 10.1101/gr.175701.</Citation><ArticleIdList><ArticleId IdType="doi">10.1101/gr.175701</ArticleId><ArticleId IdType="pmc">PMC311055</ArticleId><ArticleId IdType="pubmed">11337476</ArticleId></ArticleIdList></Reference><Reference><Citation>Birney E, Durbin R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 2000;10:547&#x2013;548. doi: 10.1101/gr.10.4.547.</Citation><ArticleIdList><ArticleId IdType="doi">10.1101/gr.10.4.547</ArticleId><ArticleId IdType="pmc">PMC310858</ArticleId><ArticleId IdType="pubmed">10779496</ArticleId></ArticleIdList></Reference><Reference><Citation>Irimia M, Roy SW. Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res. 2008;36:1703&#x2013;1712. doi: 10.1093/nar/gkn012.</Citation><ArticleIdList><ArticleId IdType="doi">10.1093/nar/gkn012</ArticleId><ArticleId IdType="pmc">PMC2275149</ArticleId><ArticleId IdType="pubmed">18263615</ArticleId></ArticleIdList></Reference><Reference><Citation>D'Aniello S, Irimia M, Maeso I, Pascual-Anaya J, Jim&#xe9;nez-Delgado S, Bertrand S, Garcia-Fern&#xe0;ndez J. Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus. Mol Biol Evol. 2008;25:1841&#x2013;1854. doi: 10.1093/molbev/msn132.</Citation><ArticleIdList><ArticleId IdType="doi">10.1093/molbev/msn132</ArticleId><ArticleId IdType="pubmed">18550616</ArticleId></ArticleIdList></Reference><Reference><Citation>Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for several sequence alignments. Methods Enzymol. 1996;266:383&#x2013;402. full_text.</Citation><ArticleIdList><ArticleId IdType="pubmed">8743695</ArticleId></ArticleIdList></Reference><Reference><Citation>Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001;17:754&#x2013;755. doi: 10.1093/bioinformatics/17.8.754.</Citation><ArticleIdList><ArticleId IdType="doi">10.1093/bioinformatics/17.8.754</ArticleId><ArticleId IdType="pubmed">11524383</ArticleId></ArticleIdList></Reference><Reference><Citation>Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572&#x2013;1574. doi: 10.1093/bioinformatics/btg180.</Citation><ArticleIdList><ArticleId IdType="doi">10.1093/bioinformatics/btg180</ArticleId><ArticleId IdType="pubmed">12912839</ArticleId></ArticleIdList></Reference><Reference><Citation>Drummond A, Strimmer K. PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics. 2001;17:662&#x2013;663. doi: 10.1093/bioinformatics/17.7.662.</Citation><ArticleIdList><ArticleId IdType="doi">10.1093/bioinformatics/17.7.662</ArticleId><ArticleId IdType="pubmed">11448888</ArticleId></ArticleIdList></Reference><Reference><Citation>Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005;21:2104&#x2013;2105. doi: 10.1093/bioinformatics/bti263.</Citation><ArticleIdList><ArticleId IdType="doi">10.1093/bioinformatics/bti263</ArticleId><ArticleId IdType="pubmed">15647292</ArticleId></ArticleIdList></Reference><Reference><Citation>Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696&#x2013;704. doi: 10.1080/10635150390235520.</Citation><ArticleIdList><ArticleId IdType="doi">10.1080/10635150390235520</ArticleId><ArticleId IdType="pubmed">14530136</ArticleId></ArticleIdList></Reference><Reference><Citation>Irimia M, Maeso I, Garcia-Fernandez J. Convergent evolution of clustering of Iroquois homeobox genes across metazoans. Mol Biol Evol. 2008;25:1521&#x2013;1525. doi: 10.1093/molbev/msn109.</Citation><ArticleIdList><ArticleId IdType="doi">10.1093/molbev/msn109</ArticleId><ArticleId IdType="pubmed">18469332</ArticleId></ArticleIdList></Reference><Reference><Citation>Harland R. In situ hybridization: an improved whole mount method for Xenopus embryos. Methods Cell Biol. 1991;36:685&#x2013;695. full_text.</Citation><ArticleIdList><ArticleId IdType="pubmed">1811161</ArticleId></ArticleIdList></Reference><Reference><Citation>Tena JJ, Neto A, de la Calle-Mustienes E, Bras-Pereira C, Casares F, Gomez-Skarmeta JL. Odd-skipped genes encode repressors that control kidney development. Dev Biol. 2007;301:518&#x2013;531. doi: 10.1016/j.ydbio.2006.08.063.</Citation><ArticleIdList><ArticleId IdType="doi">10.1016/j.ydbio.2006.08.063</ArticleId><ArticleId IdType="pubmed">17011543</ArticleId></ArticleIdList></Reference><Reference><Citation>Yu JK, Holland LZ. Amphioxus whole-mount in situ hybridization. CSH Protoc. 2009;2009 pdb.prot5286.</Citation><ArticleIdList><ArticleId IdType="pubmed">20147271</ArticleId></ArticleIdList></Reference><Reference><Citation>Nusslein-Volhard C. A rapid method for screening eggs from single Drosophila females. Drosophila I&amp;I Serv. 1977;52:166.</Citation></Reference><Reference><Citation>Jekely G, Arendt D. Cellular resolution expression profiling using confocal detection of NBT/BCIP precipitate by reflection microscopy. Biotechniques. 2007;42:751&#x2013;755. doi: 10.2144/000112462.</Citation><ArticleIdList><ArticleId IdType="doi">10.2144/000112462</ArticleId><ArticleId IdType="pubmed">17612299</ArticleId></ArticleIdList></Reference><Reference><Citation>Dohrmann C, Azpiazu N, Frasch M. A new Drosophila homeo box gene is expressed in mesodermal precursor cells of distinct muscles during embryogenesis. Genes Dev. 1990;4:2098&#x2013;2111. doi: 10.1101/gad.4.12a.2098.</Citation><ArticleIdList><ArticleId IdType="doi">10.1101/gad.4.12a.2098</ArticleId><ArticleId IdType="pubmed">1980118</ArticleId></ArticleIdList></Reference><Reference><Citation>G&#xf3;mez-Skarmeta JL, Modolell J. Araucan and caupolican provide a link between compartment subdivisions and patterning of sensory organs and veins in the Drosophila wing. Genes Dev. 1996;10:2935&#x2013;2946. doi: 10.1101/gad.10.22.2935.</Citation><ArticleIdList><ArticleId IdType="doi">10.1101/gad.10.22.2935</ArticleId><ArticleId IdType="pubmed">8918894</ArticleId></ArticleIdList></Reference><Reference><Citation>McNeill H, Yang CH, Brodsky M, Ungos J, Simon MA. Mirror encodes a novel PBX-class homeoprotein that functions in the definition of the dorso-ventral border of the Drosophila eye. Genes Dev. 1997;11:1073&#x2013;1082. doi: 10.1101/gad.11.8.1073.</Citation><ArticleIdList><ArticleId IdType="doi">10.1101/gad.11.8.1073</ArticleId><ArticleId IdType="pubmed">9136934</ArticleId></ArticleIdList></Reference><Reference><Citation>Hartenstein V, Posakony JW. The development adult sensilla on the wing and notum of Drosophila melanogaster. Development. 1989;107:389&#x2013;405.</Citation><ArticleIdList><ArticleId IdType="pubmed">2517255</ArticleId></ArticleIdList></Reference><Reference><Citation>Holland LZ. Chordate roots of the vertebrate nervous system: expanding the molecular toolkit. Nat Rev Neurosci. 2009;10:736&#x2013;746. doi: 10.1038/nrn2703.</Citation><ArticleIdList><ArticleId IdType="doi">10.1038/nrn2703</ArticleId><ArticleId IdType="pubmed">19738625</ArticleId></ArticleIdList></Reference><Reference><Citation>Campos-Ortega J, Hartenstein V. The Embryonic Development of Drosophila melanogaster. Heidelberg: Springer-Verlag; 1997.</Citation></Reference></ReferenceList></PubmedData></PubmedArticle></PubmedArticleSet>