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Sequence Set Browser

 

AADE00000000.1 Drosophila pseudoobscura pseudoobscura

Master
# of Contigs: 17,507
# of Proteins: 23,456
# of Scaffolds: 4,896
Total length: 171,310,798 bp
BioProject: PRJNA10626
BioSample: SAMN00779672
Keywords: WGS
Annotation: Contigs, Scaffolds
Organism: Drosophila pseudoobscura pseudoobscurashow lineagehide lineage
Biosource:
/mol_type = genomic genomic
/strain = MV2-25
/sub_species = pseudoobscura
WGS: AADE01000001:AADE01017507
Scaffolds: CH379058:CH379070, CH475397:CH476252, CH672438:CH676462, CM000070:CM000071
4,896 scaffolds, 23,456 proteins, total length is 152,696,384 bases
Reference:
Mind the Gap: Building Phase-3 Finished Genomes with Pacific Biosciences RS Long-Read Sequencing Technology : Unpublished – show 11 authorshide authors
English,A.C., Richards,S., Han,Y., Wang,M., Vee,V., Qu,J., Qin,X., Muzny,D.M., Worley,K.C., Reid,J.G., Gibbs,R.A.
Reference:
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution : Genome Res. 15 (1), 1-18 (2005) – show 52 authorshide authors
Richards,S., Liu,Y., Bettencourt,B.R., Hradecky,P., Letovsky,S., Nielsen,R., Thornton,K., Hubisz,M.J., Chen,R., Meisel,R.P., Couronne,O., Hua,S., Smith,M.A., Zhang,P., Liu,J., Bussemaker,H.J., van Batenburg,M.F., Howells,S.L., Scherer,S.E., Sodergren,E., Matthews,B.B., Crosby,M.A., Schroeder,A.J., Ortiz-Barrientos,D., Rives,C.M., Metzker,M.L., Muzny,D.M., Scott,G., Steffen,D., Wheeler,D.A., Worley,K.C., Havlak,P., Durbin,K.J., Egan,A., Gill,R., Hume,J., Morgan,M.B., Miner,G., Hamilton,C., Huang,Y., Waldron,L., Verduzco,D., Clerc-Blankenburg,K.P., Dubchak,I., Noor,M.A., Anderson,W., White,K.P., Clark,A.G., Schaeffer,S.W., Gelbart,W., Weinstock,G.M., Gibbs,R.A.
Reference:
Evolution of genes and genomes on the Drosophila phylogeny : Nature 450 (7167), 203-218 (2007) – show 418 authorshide authors
Drosophila 12 Genomes Consortium, Clark,A.G., Eisen,M.B., Smith,D.R., Bergman,C.M., Oliver,B., Markow,T.A., Kaufman,T.C., Kellis,M., Gelbart,W., Iyer,V.N., Pollard,D.A., Sackton,T.B., Larracuente,A.M., Singh,N.D., Abad,J.P., Abt,D.N., Adryan,B., Aguade,M., Akashi,H., Anderson,W.W., Aquadro,C.F., Ardell,D.H., Arguello,R., Artieri,C.G., Barbash,D.A., Barker,D., Barsanti,P., Batterham,P., Batzoglou,S., Begun,D., Bhutkar,A., Blanco,E., Bosak,S.A., Bradley,R.K., Brand,A.D., Brent,M.R., Brooks,A.N., Brown,R.H., Butlin,R.K., Caggese,C., Calvi,B.R., Bernardo de Carvalho,A., Caspi,A., Castrezana,S., Celniker,S.E., Chang,J.L., Chapple,C., Chatterji,S., Chinwalla,A., Civetta,A., Clifton,S.W., Comeron,J.M., Costello,J.C., Coyne,J.A., Daub,J., David,R.G., Delcher,A.L., Delehaunty,K., Do,C.B., Ebling,H., Edwards,K., Eickbush,T., Evans,J.D., Filipski,A., Findeiss,S., Freyhult,E., Fulton,L., Fulton,R., Garcia,A.C., Gardiner,A., Garfield,D.A., Garvin,B.E., Gibson,G., Gilbert,D., Gnerre,S., Godfrey,J., Good,R., Gotea,V., Gravely,B., Greenberg,A.J., Griffiths-Jones,S., Gross,S., Guigo,R., Gustafson,E.A., Haerty,W., Hahn,M.W., Halligan,D.L., Halpern,A.L., Halter,G.M., Han,M.V., Heger,A., Hillier,L., Hinrichs,A.S., Holmes,I., Hoskins,R.A., Hubisz,M.J., Hultmark,D., Huntley,M.A., Jaffe,D.B., Jagadeeshan,S., Jeck,W.R., Johnson,J., Jones,C.D., Jordan,W.C., Karpen,G.H., Kataoka,E., Keightley,P.D., Kheradpour,P., Kirkness,E.F., Koerich,L.B., Kristiansen,K., Kudrna,D., Kulathinal,R.J., Kumar,S., Kwok,R., Lander,E., Langley,C.H., Lapoint,R., Lazzaro,B.P., Lee,S.J., Levesque,L., Li,R., Lin,C.F., Lin,M.F., Lindblad-Toh,K., Llopart,A., Long,M., Low,L., Lozovsky,E., Lu,J., Luo,M., Machado,C.A., Makalowski,W., Marzo,M., Matsuda,M., Matzkin,L., McAllister,B., McBride,C.S., McKernan,B., McKernan,K., Mendez-Lago,M., Minx,P., Mollenhauer,M.U., Montooth,K., Mount,S.M., Mu,X., Myers,E., Negre,B., Newfeld,S., Nielsen,R., Noor,M.A., O'Grady,P., Pachter,L., Papaceit,M., Parisi,M.J., Parisi,M., Parts,L., Pedersen,J.S., Pesole,G., Phillippy,A.M., Ponting,C.P., Pop,M., Porcelli,D., Powell,J.R., Prohaska,S., Pruitt,K., Puig,M., Quesneville,H., Ram,K.R., Rand,D., Rasmussen,M.D., Reed,L.K., Reenan,R., Reily,A., Remington,K.A., Rieger,T.T., Ritchie,M.G., Robin,C., Rogers,Y.H., Rohde,C., Rozas,J., Rubenfield,M.J., Ruiz,A., Russo,S., Salzberg,S.L., Sanchez-Gracia,A., Saranga,D.J., Sato,H., Schaeffer,S.W., Schatz,M.C., Schlenke,T., Schwartz,R., Segarra,C., Singh,R.S., Sirot,L., Sirota,M., Sisneros,N.B., Smith,C.D., Smith,T.F., Spieth,J., Stage,D.E., Stark,A., Stephan,W., Strausberg,R.L., Strempel,S., Sturgill,D., Sutton,G., Sutton,G.G., Tao,W., Teichmann,S., Tobari,Y.N., Tomimura,Y., Tsolas,J.M., Valente,V.L., Venter,E., Venter,J.C., Vicario,S., Vieira,F.G., Vilella,A.J., Villasante,A., Walenz,B., Wang,J., Wasserman,M., Watts,T., Wilson,D., Wilson,R.K., Wing,R.A., Wolfner,M.F., Wong,A., Wong,G.K., Wu,C.I., Wu,G., Yamamoto,D., Yang,H.P., Yang,S.P., Yorke,J.A., Yoshida,K., Zdobnov,E., Zhang,P., Zhang,Y., Zimin,A.V., Baldwin,J., Abdouelleil,A., Abdulkadir,J., Abebe,A., Abera,B., Abreu,J., Acer,S.C., Aftuck,L., Alexander,A., An,P., Anderson,E., Anderson,S., Arachi,H., Azer,M., Bachantsang,P., Barry,A., Bayul,T., Berlin,A., Bessette,D., Bloom,T., Blye,J., Boguslavskiy,L., Bonnet,C., Boukhgalter,B., Bourzgui,I., Brown,A., Cahill,P., Channer,S., Cheshatsang,Y., Chuda,L., Citroen,M., Collymore,A., Cooke,P., Costello,M., D'Aco,K., Daza,R., De Haan,G., DeGray,S., DeMaso,C., Dhargay,N., Dooley,K., Dooley,E., Doricent,M., Dorje,P., Dorjee,K., Dupes,A., Elong,R., Falk,J., Farina,A., Faro,S., Ferguson,D., Fisher,S., Foley,C.D., Franke,A., Friedrich,D., Gadbois,L., Gearin,G., Gearin,C.R., Giannoukos,G., Goode,T., Graham,J., Grandbois,E., Grewal,S., Gyaltsen,K., Hafez,N., Hagos,B., Hall,J., Henson,C., Hollinger,A., Honan,T., Huard,M.D., Hughes,L., Hurhula,B., Husby,M.E., Kamat,A., Kanga,B., Kashin,S., Khazanovich,D., Kisner,P., Lance,K., Lara,M., Lee,W., Lennon,N., Letendre,F., LeVine,R., Lipovsky,A., Liu,X., Liu,J., Liu,S., Lokyitsang,T., Lokyitsang,Y., Lubonja,R., Lui,A., MacDonald,P., Magnisalis,V., Maru,K., Matthews,C., McCusker,W., McDonough,S., Mehta,T., Meldrim,J., Meneus,L., Mihai,O., Mihalev,A., Mihova,T., Mittelman,R., Mlenga,V., Montmayeur,A., Mulrain,L., Navidi,A., Naylor,J., Negash,T., Nguyen,T., Nguyen,N., Nicol,R., Norbu,C., Norbu,N., Novod,N., O'Neill,B., Osman,S., Markiewicz,E., Oyono,O.L., Patti,C., Phunkhang,P., Pierre,F., Priest,M., Raghuraman,S., Rege,F., Reyes,R., Rise,C., Rogov,P., Ross,K., Ryan,E., Settipalli,S., Shea,T., Sherpa,N., Shi,L., Shih,D., Sparrow,T., Spaulding,J., Stalker,J., Stange-Thomann,N., Stavropoulos,S., Stone,C., Strader,C., Tesfaye,S., Thomson,T., Thoulutsang,Y., Thoulutsang,D., Topham,K., Topping,I., Tsamla,T., Vassiliev,H., Vo,A., Wangchuk,T., Wangdi,T., Weiand,M., Wilkinson,J., Wilson,A., Yadav,S., Young,G., Yu,Q., Zembek,L., Zhong,D., Zimmer,A., Zwirko,Z., Jaffe,D.B., Alvarez,P., Brockman,W., Butler,J., Chin,C., Gnerre,S., Grabherr,M., Kleber,M., Mauceli,E., MacCallum,I.
Submission:
Submitted (18-DEC-2003) Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA – Human Genome Sequencing Center
Submission:
Submitted (09-OCT-2012) Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA – show 12 authorshide authors
English,A.C., Richards,S., Han,Y., Wang,M., Batterton,M.N., Vee,V., Qu,J., Qin,X., Muzny,D.M., Worley,K.C., Reid,J.G., Gibbs,R.A.
Submission:
Submitted (30-APR-2012) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave., Cambridge, MA 02138, USA – FlyBase
Submission:
Submitted (28-MAR-2013) FlyBase, Harvard University, Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA – FlyBase

The Drosophila pseudoobscura pseudoobscura whole genome shotgun (WGS) project has the project accession AADE00000000. This version of the project (01) has the accession number AADE01000000, and consists of sequences AADE01000001-AADE01017507.

4681 contigs from PacBio sequences were added to the end of AADE01000000 in Sept 2012 and updated in Oct 2012. Assembly version Dpse_3.0 has 4790 chromosomes plus scaffolds, 106 fewer than were in the previous version, Dpse_2.0. Those 104 scaffolds are interspersed within the listed ranges of the CH* accessions.

##Genome-Assembly-Data-START##
Assembly Method : PBJelly v. 12.8.2; Atlas genome assembly
Assembly Name : Dpse_3.0
Genome Coverage : 9.7x Sanger; 24x PacBio
Sequencing Technology : Sanger; PacBio
##Genome-Assembly-Data-END##
##Genome-Annotation-Data-START##
Annotation Provider : FlyBase
Annotation Status : Full annotation
Annotation Version : Release 3.1
URL : http://flybase.org
##Genome-Annotation-Data-END##
Contigs
Download
GenBank:AADE01.1.gbff.gz 83.3 Mb
FASTA:AADE01.1.fsa_nt.gz 50 Mb
ASN.1:AADE01.1.bbs.gz 64.6 Mb