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Sequence Set Browser

 

ABRM00000000.1 Hydra vulgaris

Master
# of Contigs: 236,667
# of Proteins: 0
# of Scaffolds/Chrs: 25,828
Total length: 1,189,606,931 bp
BioProject: PRJNA12876
BioSample: SAMN00000081
Keywords: WGS
Organism: Hydra vulgarisshow lineagehide lineage
Biosource:
/mol_type = genomic
/strain = 105
WGS: ABRM01000001:ABRM01236667
Scaffolds: EQ235847:EQ261674
25,828 scaffolds, total length is 1,075,859,387 bases
Reference:
The dynamic genome of Hydra : Nature 464 (7288), 592-596 (2010) – show 74 authorshide authors
Chapman,J.A., Kirkness,E.F., Simakov,O., Hampson,S.E., Mitros,T., Weinmaier,T., Rattei,T., Balasubramanian,P.G., Borman,J., Busam,D., Disbennett,K., Pfannkoch,C., Sumin,N., Sutton,G.G., Viswanathan,L.D., Walenz,B., Goodstein,D.M., Hellsten,U., Kawashima,T., Prochnik,S.E., Putnam,N.H., Shu,S., Blumberg,B., Dana,C.E., Gee,L., Kibler,D.F., Law,L., Lindgens,D., Martinez,D.E., Peng,J., Wigge,P.A., Bertulat,B., Guder,C., Nakamura,Y., Ozbek,S., Watanabe,H., Khalturin,K., Hemmrich,G., Franke,A., Augustin,R., Fraune,S., Hayakawa,E., Hayakawa,S., Hirose,M., Hwang,J.S., Ikeo,K., Nishimiya-Fujisawa,C., Ogura,A., Takahashi,T., Steinmetz,P.R., Zhang,X., Aufschnaiter,R., Eder,M.K., Gorny,A.K., Salvenmoser,W., Heimberg,A.M., Wheeler,B.M., Peterson,K.J., Bottger,A., Tischler,P., Wolf,A., Gojobori,T., Remington,K.A., Strausberg,R.L., Venter,J.C., Technau,U., Hobmayer,B., Bosch,T.C., Holstein,T.W., Fujisawa,T., Bode,H.R., David,C.N., Rokhsar,D.S., Steele,R.E.
Submission:
Submitted (14-JUL-2008) J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA – Kirkness,E., Walenz,B., Sutton,G., Strausberg,R.

The Hydra vulgaris whole genome shotgun (WGS) project has the project accession ABRM00000000. This version of the project (01) has the accession number ABRM01000000, and consists of sequences ABRM01000001-ABRM01236667.

The 105 strain of Hydra magnipapillata originated from a single polyp collected by T. Sugiyama in September, 1973 in a swamp adjacent to the National Institute of Genetics in Mishima, Japan (T. Fujisawa, unpublished information). This strain of H. magnipapillata has been propagated in labs in Japan, Europe, and North America since then. For isolation of DNA for genome sequencing, the 105 strain was re-cloned from a single polyp in the Bode lab at UC Irvine using standard culture conditions. About 1000 polyps were harvested from the resulting culture and used to prepare DNA for genome sequencing. Approximately 10.3 million sequence traces were derived from plasmids with inserts of 3-4 kb (48%), 8-10 kb (21%), and 10-12 kb (31%). This version of the assembly, h7, is derived from approximately 6x sequence coverage of the 1.3 Gb genome. This version of the assembly is known to contain bacterial sequences that may derive from an endosymbiont. The ACZU00000000 WGS project of the Hydra magnipapillata strain 105 genome is a haploid type assembly, in which each locus is represented once. This assembly, the ABRM00000000 WGS project, is a more stringent assembly in which the multiple haplotypes may be represented as separate records. Assembly Name: h7 Genome Coverage: 6x.

Contigs
Download
GenBank:ABRM01.1.gbff.gz 216.3 Mb
 ABRM01.2.gbff.gz 194.2 Mb
 ABRM01.3.gbff.gz 83.4 Mb
FASTA:ABRM01.1.fsa_nt.gz 141.2 Mb
 ABRM01.2.fsa_nt.gz 138.6 Mb
 ABRM01.3.fsa_nt.gz 55.8 Mb
ASN.1:ABRM01.1.bbs.gz 108.6 Mb
 ABRM01.2.bbs.gz 107.2 Mb
 ABRM01.3.bbs.gz 44.7 Mb