{"PubmedArticle":{"MedlineCitation":{"@attributes":{"Status":"MEDLINE","Owner":"NLM","IndexingMethod":"Manual"},"PMID":{"@attributes":{"Version":"1"},"@text":"12736825"},"DateCompleted":{"Year":"2004","Month":"02","Day":"27"},"DateRevised":{"Year":"2025","Month":"01","Day":"04"},"Article":{"@attributes":{"PubModel":"Print-Electronic"},"Journal":{"ISSN":{"@attributes":{"IssnType":"Print"},"@text":"0949-944X"},"JournalIssue":{"@attributes":{"CitedMedium":"Print"},"Volume":"213","Issue":"5-6","PubDate":{"Year":"2003","Month":"Jun"}},"Title":"Development genes and evolution","ISOAbbreviation":"Dev Genes Evol"},"ArticleTitle":"A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors.","Pagination":{"StartPage":"222","EndPage":"234","MedlinePgn":"222-34"},"Abstract":{"AbstractText":["Homeobox-containing genes play crucial roles in various developmental processes, including body-plan specification, pattern formation and cell-type specification. The present study searched the draft genome sequence and cDNA\/EST database of the basal chordate Ciona intestinalis to identify 83 homeobox-containing genes in this animal. This number of homeobox genes in the Ciona genome is smaller than that in the Caenorhabditis elegans, Drosophila melanogaster, human and mouse genomes. Of the 83 genes, 76 have possible human orthologues and 7 may be unique to Ciona. The ascidian homeobox genes were classified into 11 classes, including Hox class, NK class, Paired class, POU class, LIM class, TALE class, SIX class, Prox class, Cut class, ZFH class and HNF1 class, according to the classification scheme devised for known homeobox genes. As to the Hox cluster, the Ciona genome contains single copies of each of the paralogous groups, suggesting that there is a single Hox cluster, if any, but genes orthologous to Hox7, 8, 9 and 11 were not found in the genome. In addition, loss of genes had occurred independently in the Ciona lineage and was noticed in Gbx of the EHGbox subclass, Sax, NK3, Vax and vent of the NK class, Cart, Og9, Anf and Mix of the Paired class, POU-I, III, V and VI of the POU class, Lhx6\/7 of the LIM class, TGIF of the TALE class, Cux and SATB of the Cut class, and ZFH1 of the ZFH class, which might have reduced the number of Ciona homeobox genes. Interestingly, one of the newly identified Ciona intestinalis genes and its vertebrate counterparts constitute a novel subclass of HNF1 class homeobox genes. Furthermore, evidence for the gene structures and expression of 54 of the 83 homeobox genes was provided by analysis of ESTs, suggesting that cDNAs for these 54 genes are available. The present data thus reveal the repertoire of homeodomain-containing transcription factors in the Ciona genome, which will be useful for future research on the development and evolution of chordates."]},"AuthorList":{"@attributes":{"CompleteYN":"Y"},"Author":[{"@attributes":{"ValidYN":"Y"},"LastName":"Wada","ForeName":"Shuichi","Initials":"S","AffiliationInfo":[{"Affiliation":"Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan."}]},{"@attributes":{"ValidYN":"Y"},"LastName":"Tokuoka","ForeName":"Miki","Initials":"M"},{"@attributes":{"ValidYN":"Y"},"LastName":"Shoguchi","ForeName":"Eiichi","Initials":"E"},{"@attributes":{"ValidYN":"Y"},"LastName":"Kobayashi","ForeName":"Kenji","Initials":"K"},{"@attributes":{"ValidYN":"Y"},"LastName":"Di Gregorio","ForeName":"Anna","Initials":"A"},{"@attributes":{"ValidYN":"Y"},"LastName":"Spagnuolo","ForeName":"Antonietta","Initials":"A"},{"@attributes":{"ValidYN":"Y"},"LastName":"Branno","ForeName":"Margherita","Initials":"M"},{"@attributes":{"ValidYN":"Y"},"LastName":"Kohara","ForeName":"Yuji","Initials":"Y"},{"@attributes":{"ValidYN":"Y"},"LastName":"Rokhsar","ForeName":"Daniel","Initials":"D"},{"@attributes":{"ValidYN":"Y"},"LastName":"Levine","ForeName":"Michael","Initials":"M"},{"@attributes":{"ValidYN":"Y"},"LastName":"Saiga","ForeName":"Hidetoshi","Initials":"H"},{"@attributes":{"ValidYN":"Y"},"LastName":"Satoh","ForeName":"Nori","Initials":"N"},{"@attributes":{"ValidYN":"Y"},"LastName":"Satou","ForeName":"Yutaka","Initials":"Y"}]},"Language":["eng"],"PublicationTypeList":{"PublicationType":[{"@attributes":{"UI":"D003160"},"@text":"Comparative Study"},{"@attributes":{"UI":"D016428"},"@text":"Journal Article"},{"@attributes":{"UI":"D013485"},"@text":"Research Support, Non-U.S. Gov't"}]},"ArticleDate":[{"@attributes":{"DateType":"Electronic"},"Year":"2003","Month":"05","Day":"08"}]},"MedlineJournalInfo":{"Country":"Germany","MedlineTA":"Dev Genes Evol","NlmUniqueID":"9613264","ISSNLinking":"0949-944X"},"CitationSubset":["IM"],"MeshHeadingList":{"MeshHeading":[{"DescriptorName":{"@attributes":{"UI":"D000818","MajorTopicYN":"N"},"@text":"Animals"}},{"DescriptorName":{"@attributes":{"UI":"D002938","MajorTopicYN":"N"},"@text":"Ciona intestinalis"},"QualifierName":[{"@attributes":{"UI":"Q000196","MajorTopicYN":"N"},"@text":"embryology"},{"@attributes":{"UI":"Q000235","MajorTopicYN":"Y"},"@text":"genetics"}]},{"DescriptorName":{"@attributes":{"UI":"D016000","MajorTopicYN":"N"},"@text":"Cluster Analysis"}},{"DescriptorName":{"@attributes":{"UI":"D030541","MajorTopicYN":"N"},"@text":"Databases, Genetic"}},{"DescriptorName":{"@attributes":{"UI":"D005801","MajorTopicYN":"N"},"@text":"Genes, Homeobox"},"QualifierName":[{"@attributes":{"UI":"Q000235","MajorTopicYN":"Y"},"@text":"genetics"}]},{"DescriptorName":{"@attributes":{"UI":"D016678","MajorTopicYN":"Y"},"@text":"Genome"}},{"DescriptorName":{"@attributes":{"UI":"D010802","MajorTopicYN":"Y"},"@text":"Phylogeny"}}]}},"PubmedData":{"History":{"PubMedPubDate":[{"@attributes":{"PubStatus":"received"},"Year":"2002","Month":"12","Day":"17"},{"@attributes":{"PubStatus":"accepted"},"Year":"2003","Month":"3","Day":"11"},{"@attributes":{"PubStatus":"pubmed"},"Year":"2003","Month":"5","Day":"9","Hour":"5","Minute":"0"},{"@attributes":{"PubStatus":"medline"},"Year":"2004","Month":"2","Day":"28","Hour":"5","Minute":"0"},{"@attributes":{"PubStatus":"entrez"},"Year":"2003","Month":"5","Day":"9","Hour":"5","Minute":"0"}]},"PublicationStatus":"ppublish","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"12736825"},{"@attributes":{"IdType":"doi"},"@text":"10.1007\/s00427-003-0321-0"}]},"ReferenceList":[{"Reference":[{"Citation":"Development. 1999 Jun;126(11):2539-50","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10226012"}]}},{"Citation":"Trends Genet. 2002 Jan;18(1):41-7","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11750700"}]}},{"Citation":"Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1469-74","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"9990047"}]}},{"Citation":"Nucleic Acids Res. 1997 Nov 1;25(21):4173-80","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"9336443"}]}},{"Citation":"Mech Dev. 1999 Oct;88(1):123-6","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10525197"}]}},{"Citation":"Nucleic Acids Res. 2003 Jan 1;31(1):133-7","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"12519966"}]}},{"Citation":"Science. 2002 Dec 13;298(5601):2157-67","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"12481130"}]}},{"Citation":"Mech Dev. 1998 Nov;78(1-2):199-202","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"9858732"}]}},{"Citation":"Nucleic Acids Res. 2001 Aug 1;29(15):3258-69","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11470884"}]}},{"Citation":"Mol Phylogenet Evol. 2002 Sep;24(3):412-7","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"12220984"}]}},{"Citation":"Gene. 2000 Apr 18;247(1-2):145-51","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10773454"}]}},{"Citation":"Mech Dev. 1999 May;83(1-2):127-39","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10381573"}]}},{"Citation":"Nature. 1994 Aug 18;370(6490):563-6","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"7914353"}]}},{"Citation":"Cell. 1992 Nov 13;71(4):551-3","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"1358459"}]}},{"Citation":"J Biol Chem. 1998 May 29;273(22):13552-62","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"9593691"}]}},{"Citation":"Genesis. 2002 Aug;33(4):153-4","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"12203911"}]}},{"Citation":"Development. 1998 Jul;125(14):2599-610","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"9636075"}]}},{"Citation":"Dev Biol. 2001 Aug 15;236(2):289-303","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11476572"}]}},{"Citation":"Gene. 2002 Apr 3;287(1-2):107-13","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11992728"}]}},{"Citation":"Dev Genes Evol. 1998 Feb;207(8):515-23","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"9510546"}]}},{"Citation":"Curr Biol. 2000 Sep 7;10(17):1059-62","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10996074"}]}},{"Citation":"Science. 2000 Mar 24;287(5461):2204-15","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10731134"}]}},{"Citation":"Development. 1999 Nov;126(21):4737-48","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10518491"}]}},{"Citation":"Int J Dev Biol. 2002 Jan;46(1):115-23","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11902672"}]}},{"Citation":"Mech Dev. 2001 Feb;100(2):189-203","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11165477"}]}},{"Citation":"Dev Genes Evol. 1999 Mar;209(3):186-97","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10079362"}]}},{"Citation":"Mech Dev. 2001 Apr;102(1-2):271-4","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11287209"}]}},{"Citation":"J Exp Zool. 2000 Dec 15;288(4):345-51","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11144283"}]}},{"Citation":"Gene. 1991 Feb 15;98(2):253-7","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"1673109"}]}},{"Citation":"Trends Genet. 2000 Feb;16(2):75-83","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"10652534"}]}},{"Citation":"Dev Biol. 2001 Sep 15;237(2):270-81","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11543613"}]}},{"Citation":"Mol Biol Evol. 1996 Oct;13(8):1078-86","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"8865662"}]}},{"Citation":"Development. 2001 Mar;128(5):779-90","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11171402"}]}},{"Citation":"Nature. 1998 Apr 30;392(6679):920-2","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"9582071"}]}},{"Citation":"Development. 1993 Jul;118(3):719-29","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"7915669"}]}},{"Citation":"Curr Opin Genet Dev. 2002 Aug;12(4):403-8","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"12100884"}]}},{"Citation":"Mol Cell. 2002 Nov;10(5):1129-37","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"12453420"}]}},{"Citation":"Evol Dev. 2000 Sep-Oct;2(5):284-93","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11252557"}]}},{"Citation":"Mech Dev. 2000 Dec;99(1-2):173-6","ArticleIdList":{"ArticleId":[{"@attributes":{"IdType":"pubmed"},"@text":"11091088"}]}}]}]}}}