AEQU00000000.2 Python bivittatus
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# of Contigs: 274,243 # of Proteins: 0 # of Scaffolds/Chrs: 39,112 Total length: 1,384,532,810 bp BioProject: PRJNA61243 BioSample: SAMN02981298 Keywords: WGS Organism: Python bivittatus – show lineagehide lineage Biosource: /country = USA: Texas/mol_type = genomic/sex = female/tissue_type = liverWGS: AEQU02000001:AEQU02274243 Scaffolds: KE952971:KE992082 39,112 scaffolds, total length is 1,435,034,535 basesReference: Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes : Genome Biol. 12 (7), 406 (2011) – show 16 authorshide authorsCastoe,T.A., de Koning,J.A., Hall,K.T., Yokoyama,K.D., Gu,W., Smith,E.N., Feschotte,C., Uetz,P., Ray,D.A., Dobry,J., Bogden,R., Mackessy,S.P., Bronikowski,A.M., Warren,W.C., Secor,S.M., Pollock,D.D.Reference: The Burmese python genome reveals the molecular basis for extreme adaptation in snakes : Proc. Natl. Acad. Sci. U.S.A. 110 (51), 20645-20650 (2013) – show 39 authorshide authorsCastoe,T.A., de Koning,A.P., Hall,K.T., Card,D.C., Schield,D.R., Fujita,M.K., Ruggiero,R.P., Degner,J.F., Daza,J.M., Gu,W., Reyes-Velasco,J., Shaney,K.J., Castoe,J.M., Fox,S.E., Poole,A.W., Polanco,D., Dobry,J., Vandewege,M.W., Li,Q., Schott,R.K., Kapusta,A., Minx,P., Feschotte,C., Uetz,P., Ray,D.A., Hoffmann,F.G., Bogden,R., Smith,E.N., Chang,B.S., Vonk,F.J., Casewell,N.R., Henkel,C.V., Richardson,M.K., Mackessy,S.P., Bronikowski,A.M., Yandell,M., Warren,W.C., Secor,S.M., Pollock,D.D.Submission: Submitted (04-JAN-2011) Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, 12801 E. 17th Ave, MS 8101, PO Box 6511, Aurora, CO 80045, USA – Castoe,T.A., de Koning,A.P.J., Pollock,D.D.Submission: Submitted (04-SEP-2013) The Genome Institute, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – Castoe,T.A., Koning,A.P., Minx,P., Warren,W., Pollack,D.D.The Python bivittatus whole genome shotgun (WGS) project has the project accession AEQU00000000. This version of the project (02) has the accession number AEQU02000000, and consists of sequences AEQU02000001-AEQU02274243.
Background section: The Burmese python was obtained from the pet trade by Carl Franklin (Biological Curator for the University of Texas at Arlington Amphibian and Reptile Diversity Research Center). A voucher of the remaining specimen has been permanently cataloged in the collection at UTA. The snake was a female. All DNA used for genome sequencing was obtained from DNA extracted from snap-frozen liver tissue from this single animal. This assembly of Burmese python was composed of both Illumina instrument reads (frags, 3kbs, and 8kbs) and Roche 454 reads. A 20X input coverage of Illumina sequence reads were assembled using the Soap deNovo software (Beijing Genome Institute). The 454 reads were assembled with the Newbler assembler (Roche). The assemblies were merged using GAA (Yao et al 2011). The Soap assembly served as the reference assembly in the merge and represents the majority of the final assembly. This draft assembly was referred to as Burmese python assembly 5.0.2. This version has been gap filled and cleaned of contaminating contigs. The assembly is made up of a total of 39,115 scaffolds with an N50 scaffold length of 207,524 (N50 contig length was 10,658). The assembly spans 1.44Gb. For questions regarding this Python molurus bivittatus 5.0.2 assembly please contact Todd Castoe, University of Texas Arlington (todd.castoe@uta.edu). Source DNA requests - address: Todd Castoe Univ. Texas Arlington 500 UTA Blvd. Engineering Research Bldg., Rm 334 Arlington, TX 76019 Credits: DNA source - Carl Franklin Biological Curator for the University of Texas at Arlington. Sequencing - The Genome Institute, Washington University School of Medicine, St Louis, MO, and the University of Colorado School of Medicine, Denver, CO. Sequence assembly - The Genome Institute, Washington University School of Medicine, St Louis, MO. Citation upon use of this assembly in a manuscript: It is requested that users of this Python molurus bivittatus 5.0.2 sequence assembly acknowledge Todd Castoe and the University of Texas at Arlington in any publications that result from use of this sequence assembly.
##Genome-Assembly-Data-START## Assembly Method : Soap deNovo v. March 2012 Assembly Name : Python_molurus_bivittatus-5.0.2 Genome Coverage : 20x Sequencing Technology : Illumina; 454 ##Genome-Assembly-Data-END## - Contigs
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