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Sequence Set Browser


AACT00000000.1 Ciona savignyi

# of Contigs: 66,800
# of Proteins: 0
# of Scaffolds: 3,447
Total length: 401,449,946 bp
BioProject: PRJNA1435
BioSample: SAMN02952906
Keywords: WGS
Annotation: Contigs
Organism: Ciona savignyishow lineagehide lineage
/mol_type = genomic genomic
WGS: AACT01000001:AACT01066800
Scaffolds: CH000001:CH003011, CH003012:CH003447
3,447 scaffolds, total length is 547,691,944 bases
Submitted (01-AUG-2003) Whitehead Institute/MIT Center for Genome Research, 320 Charles Street, Cambridge, MA 02142, USA – show 213 authorshide authors
Birren,B., Nusbaum,C., Abebe,A., Abouelleil,A., Adekoya,E., Ait-zahra,M., Allen,N., Allen,T., An,P., Anderson,M., Anderson,S., Arachchi,H., Armbruster,J., Bachantsang,P., Baldwin,J., Barry,A., Bayul,T., Blitshsteyn,B., Bloom,T., Blye,J., Boguslavskiy,L., Borowsky,M., Boukhgalter,B., Brunache,A., Butler,J., Calixte,N., Calvo,S., Camarata,J., Campo,K., Chang,J., Cheshatsang,Y., Citroen,M., Collymore,A., Considine,T., Cook,A., Cooke,P., Corum,B., Cuomo,C., David,R., Dawoe,T., Degray,S., Dodge,S., Dooley,K., Dorje,P., Dorjee,K., Dorris,L., Duffey,N., Dupes,A., Elkins,T., Engels,R., Erickson,J., Farina,A., Faro,S., Ferreira,P., Fischer,H., Fitzgerald,M., Foley,K., Gage,D., Galagan,J., Gearin,G., Gnerre,S., Gnirke,A., Goyette,A., Graham,J., Grandbois,E., Gyaltsen,K., Hafez,N., Hagopian,D., Hagos,B., Hall,J., Hatcher,B., Heller,A., Higgins,H., Honan,T., Horn,A., Houde,N., Hughes,L., Hulme,W., Husby,E., Iliev,I., Jaffe,D., Jones,C., Kamal,M., Kamat,A., Kamvysselis,M., Karlsson,E., Kells,C., Kieu,A., Kisner,P., Kodira,C., Kulbokas,E., Labutti,K., Lama,D., Landers,T., Leger,J., Levine,S., Lewis,D., Lewis,T., Lindblad-toh,K., Liu,X., Lokyitsang,T., Lokyitsang,Y., Lucien,O., Lui,A., Ma,L.J., Mabbitt,R., Macdonald,J., Maclean,C., Major,J., Manning,J., Marabella,R., Maru,K., Matthews,C., Mauceli,E., Mccarthy,M., Mcdonough,S., Mcghee,T., Meldrim,J., Meneus,L., Mesirov,J., Mihalev,A., Mihova,T., Mikkelsen,T., Mlenga,V., Moru,K., Mozes,J., Mulrain,L., Munson,G., Naylor,J., Newes,C., Nguyen,C., Nguyen,N., Nguyen,T., Nicol,R., Nielsen,C., Nizzari,M., Norbu,C., Norbu,N., O'donnell,P., Okoawo,O., O'leary,S., Omotosho,B., O'neill,K., Osman,S., Parker,S., Perrin,D., Phunkhang,P., Piqani,B., Purcell,S., Rachupka,T., Ramasamy,U., Rameau,R., Ray,V., Raymond,C., Retta,R., Richardson,S., Rise,C., Rodriguez,J., Rogers,J., Rogov,P., Rutman,M., Schupbach,R., Seaman,C., Settipalli,S., Sharpe,T., Sheridan,J., Sherpa,N., Shi,J., Smirnov,S., Smith,C., Sougnez,C., Spencer,B., Stalker,J., Stange-thomann,N., Stavropoulos,S., Stetson,K., Stone,C., Stone,S., Stubbs,M., Talamas,J., Tchuinga,P., Tenzing,P., Tesfaye,S., Theodore,J., Thoulutsang,Y., Topham,K., Towey,S., Tsamla,T., Tsomo,N., Vallee,D., Vassiliev,H., Venkataraman,V., Vinson,J., Vo,A., Wade,C., Wang,S., Wangchuk,T., Wangdi,T., Whittaker,C., Wilkinson,J., Wu,Y., Wyman,D., Yadav,S., Yang,S., Yang,X., Yeager,S., Yee,E., Young,G., Zainoun,J., Zembeck,L., Zimmer,A., Zody,M., Lander,E.

The Ciona savignyi whole genome shotgun (WGS) project has the project accession AACT00000000. This version of the project (01) has the accession number AACT01000000, and consists of sequences AACT01000001-AACT01066800.

The Ciona savignyi genome was sequenced by whole genome shotgun from a single individual with a high level of heterozygosity. Based on targeted finishing of homologous regions, the estimated rate of substitution between the two haplotypes is 6%, the total heterozygosity including indels is at least 19%, and these rates vary significantly between regions. The assembly of Ciona savignyi therefore required extensive adaptation of existing strategies for whole genome assembly. Novel algorithms attempted to recognize read-read overlaps between reads of opposite haplotype based on context and, by excluding such overlaps, to construct contigs and scaffolds which represent sequence from only one of the haplotypes. These scaffolds (CON records) are assigned the accession numbers CH000001-CH003011. Because there are two haplotypes, many regions of the Ciona savignyi genome are represented exactly twice within these scaffold records. To remove this redundancy, the two haplotypes were merged by constructing paired scaffold assemblies, which reference the same contigs as the separate haplotype assembly, but which switch frequently between haplotypes at homologous positions in order to choose the best-assembled haplotype at each region. These scaffolds are assigned the accession numbers CH003012-CH003447.

GenBank:AACT01.1.gbff.gz 84.9 Mb
 AACT01.2.gbff.gz 77.3 Mb
 AACT01.3.gbff.gz 18.8 Mb
FASTA:AACT01.1.fsa_nt.gz 54.1 Mb
 AACT01.2.fsa_nt.gz 46.6 Mb
 AACT01.3.fsa_nt.gz 11.9 Mb
ASN.1:AACT01.1.bbs.gz 62 Mb
 AACT01.2.bbs.gz 63.9 Mb
 AACT01.3.bbs.gz 14 Mb