An improved assembly of the Ciona intestinalis genome reveals that it contains non-canonical introns and that about 20% of Ciona genes reside in operons

Dewar, Ken

Endo, Toshinori

Hastings, Kenneth EM

Hotta, Kohji

Inaba, Kazuo

Lemaire, Patrick

Lindquist, Erika

Macmil, Simone L

Matsumoto, Jun

Mineta, Katsuhiko

Ogasawara, Michio

Roe, Bruce A

Sasakura, Yasunori

Satou, Yutaka

Shoguchi, Eiichi

Ueno, Keisuke

Wasserscheid, Jessica

Wiley, Graham B

Yamada, Lixy

Zeller, Robert W

English

PubMed

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

Hokkaido University Collection of Scholarly and Academic Papers

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

Springer - Publisher Connector

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

International audienceBackground: 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

Satou, Y.

Mineta, K.

Ogasawara, M.

Sasakura, Y.

Shoguchi, E.

Ueno, K.

Yamada, L.

Matsumoto, J.

Wasserscheid, J.

Dewar, K.

Wiley, G. B.

Macmil, S. L.

Roe, B. A.

Zeller, R. W.

Hastings, K. E.

Lindquist, E.

Endo, T.

Hotta, K.

Inaba, K.

HAL: Hyper Article en Ligne

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

HAL AMU

Yutaka Satou

Katsuhiko Mineta

Michio Ogasawara

Yasunori Sasakura

Eiichi Shoguchi

Keisuke Ueno

Lixy Yamada

Jun Matsumoto

Jessica Wasserscheid

Ken Dewar

Graham B Wiley

Simone L Macmil

Bruce A Roe

Robert W Zeller

Kenneth EM Hastings

Patrick Lemaire

Erika Lindquist

Toshinori Endo

Kohji Hotta

Kazuo Inaba

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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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Hokkaido University Collection of Scholarly and Academic Papers

Springer - Publisher Connector

HAL: Hyper Article en Ligne

HAL AMU

Springer - Publisher Connector

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