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Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis : new insight into intron and operon populations

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Please use this identifier to cite or link to this item:http://hdl.handle.net/2115/50047

Title: Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis : new insight into intron and operon populations
Authors: Satou, Yutaka Browse this author
Mineta, Katsuhiko Browse this author
Ogasawara, Michio Browse this author
Sasakura, Yasunori Browse this author
Shoguchi, Eiichi Browse this author
Ueno, Keisuke Browse this author
Yamada, Lixy Browse this author
Matsumoto, Jun Browse this author
Wasserscheid, Jessica Browse this author
Dewar, Ken Browse this author
Wiley, Graham B Browse this author
Macmil, Simone L Browse this author
Roe, Bruce A Browse this author
Zeller, Robert W Browse this author
Hastings, Kenneth EM Browse this author
Lemaire, Patrick Browse this author
Lindquist, Erika Browse this author
Endo, Toshinori Browse this author
Hotta, Kohji Browse this author
Inaba, Kazuo Browse this author
Issue Date: Oct-2008
Publisher: BioMed Central
Journal Title: Genome Biology
Volume: 9
Issue: 10
Start Page: R152
Publisher DOI: 10.1186/gb-2008-9-10-r152
Abstract: Background : The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly. Results : We have prepared a less-fragmented assembly on the basis of scaffold-joining guided by paired-end EST and bacterial artificial chromosome (BAC) sequences, and BAC chromosomal in situ hybridization data. The new assembly (115.2 Mb) is similar in length to the initial assembly (116.7 Mb) but contains 1,272 (approximately 50%) fewer scaffolds. The largest scaffold in the new assembly incorporates 95 initial-assembly scaffolds. In conjunction with the new assembly, we have prepared a greatly improved global gene model set strictly correlated with the extensive currently available EST data. The total gene number (15,254) is similar to that of the initial set (15,582), but the new set includes 3,330 models at genomic sites where none were present in the initial set, and 1,779 models that represent fusions of multiple previously incomplete models. In approximately half, 5'-ends were precisely mapped using 5'-full-length ESTs, an important refinement even in otherwise unchanged models. Conclusion : Using these new resources, we identify a population of non-canonical (non-GT-AG) introns and also find that approximately 20% of Ciona genes reside in operons and that operons contain a high proportion of single-exon genes. Thus, the present dataset provides an opportunity to analyze the Ciona genome much more precisely than ever.
Rights: http://creativecommons.org/licenses/by/2.0
Type: article
URI: http://hdl.handle.net/2115/50047
Appears in Collections:情報科学院・情報科学研究院 (Graduate School of Information Science and Technology / Faculty of Information Science and Technology) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 遠藤 俊徳

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