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

Satou, Yutaka; Mineta, Katsuhiko; Ogasawara, Michio et al.

Genome Biology, 2008, 9(10), R152

Permalink : https://hdl.handle.net/2115/50047

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アクセス権
open access
URI
https://hdl.handle.net/2115/50047
タイトル
Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis : new insight into intron and operon populations
著者
Satou, Yutaka ; Mineta, Katsuhiko ; Ogasawara, Michio ; Sasakura, Yasunori ; Shoguchi, Eiichi ; Ueno, Keisuke ; Yamada, Lixy ; Matsumoto, Jun ; Wasserscheid, Jessica ; Dewar, Ken ; Wiley, Graham B ; Macmil, Simone L ; Roe, Bruce A ; Zeller, Robert W ; Hastings, Kenneth EM ; Lemaire, Patrick ; Lindquist, Erika ; Endo, Toshinori ; Hotta, Kohji ; Inaba, Kazuo
著者名
Satou, Yutaka
著者名
Mineta, Katsuhiko
著者名
Ogasawara, Michio
著者名
Sasakura, Yasunori
著者名
Shoguchi, Eiichi
著者名
Ueno, Keisuke
著者名
Yamada, Lixy
著者名
Matsumoto, Jun
著者名
Wasserscheid, Jessica
著者名
Dewar, Ken
著者名
Wiley, Graham B
著者名
Macmil, Simone L
著者名
Roe, Bruce A
著者名
Zeller, Robert W
著者名
Hastings, Kenneth EM
著者名
Lemaire, Patrick
著者名
Lindquist, Erika
著者名
Endo, Toshinori
著者名
Hotta, Kohji
著者名
Inaba, Kazuo
言語
英語
発行日
2008-10
出版者
BioMed Central
収録物名
Genome Biology
巻(号)
9(10)
ページ
R152
抄録
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.
資源タイプ
学術雑誌論文
出版タイプ
Version of Record
権利情報
Creative Commons Attribution 2.0 Generic
PISSN
1465-6906
関連情報 (isIdenticalTo)
出版社版DOI
https://doi.org/10.1186/gb-2008-9-10-r152