LOCUS       KB222973               73523 bp    DNA     linear   CON 19-MAR-2015
DEFINITION  Trypanosoma cruzi JR cl. 4 unplaced genomic scaffold Scaffold97,
            whole genome shotgun sequence.
ACCESSION   KB222973 AODP01000000
VERSION     KB222973.1
DBLINK      BioProject: PRJNA59941
            BioSample: SAMN02953827
KEYWORDS    WGS.
SOURCE      Trypanosoma cruzi JR cl. 4
  ORGANISM  Trypanosoma cruzi JR cl. 4
            Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae;
            Trypanosoma; Schizotrypanum.
REFERENCE   1  (bases 1 to 73523)
  AUTHORS   Warren,W., Weinstock,G., Wilson,R.K. and Buck,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-JAN-2013) The Genome Institute, Washington University
            School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA
COMMENT     Background:
            
             The Trypanosome cruzi JR strain cl4 was obtained from Dr. Gregory
            Buck, Center for the Study of Biological Complexity, Microbiology
            and Immunology, Virginia Commonwealth University.  This strain, a
            representative of the TcI lineage of T. cruzi (Hamilton et al.,
            2011), was isolated from a male patient, age 55, in chronic
            symptomatic stage of disease in Anzoategui, Venezuela by Dr. Hernan
            Carrasco and his colleagues at the Universidad Central de Venezuela
            (Lewis et al., 2009). A clonal derivative was prepared from
            epimastigote culture by plating on blood agar plates (M. Lewis) and
            used for sequencing.
             Genomic DNA was depleted for kinetoplast (mitochondrial) DNA
            (kDNA), which represents up to 30-50% of the total DNA in the cell,
            by Dr. Andrey Matveyev. In brief, total DNA was extracted from
            cultured late log phase T. cruzi JR epimastigote forms and
            submitted to low voltage electrophoresis in 0.8% low melting
            agarose. The gDNA-containing agarose blocks were excised from the
            gel, leaving the kDNA networks intact in the gel. Purified gDNA was
            recovered from the agarose blocks after digestion using
            Beta-agarase I.
            
             The gDNA was fragmented and sequenced using the Roche 454 FLX
            Titanium technology and a draft assembly was produced. Total
            sequence coverage from the Roche 454 technology was  approximately
            50X (fragments @ 22X, 3 Kb paired end (PE) @20X, 8 Kb PE @ 6.5X)
            using a genome size estimate of 40 Mbp. The combined sequence reads
            were assembled using the Newbler software (Roche 454). This first
            draft assembly was referred to as T._cruzi_JR cl4-1.1. The
            T._cruzi_JR cl4-1.1 version was manually edited to create version
            T._cruzi_JR cl4-1.1.1. In the T._cruzi_JR cl4-1.1.1 assembly 2962
            scaffold gaps were closed with Illumina read mapping and local
            assembly. Assembly error correction was done by aligning Illumina
            reads to correct insertion and deletion errors (6500). Finally, 22
            contaminating contigs were removed to yield version  T._cruzi_JR
            cl4-1.1.4. The T._cruzi_JR cl4-1.1.4 assembly is made up of a total
            of 18,177 scaffolds with an N50 scaffold length of over 72kb (N50
            contig length is 7.1 kb) and assembled size spans 40.5 Mb.
            
             This work was supported by NSF DEB-0830056 grant to Gregory Buck
            and by NIH-NHGRI grant 5U54HG00307907 to RKW, Director of The
            Genome Institute at Washington University School of Medicine.
            
             For questions regarding this T._cruzi_JR cl4-1.1.4 assembly please
            contact Dr. Wes Warren, Washington University School of Medicine
            (wwarren@genome.wustl.edu). Downloads of the sequence data are
            available via the TriTrypDB genome browser server. Funding for the
            sequence characterization of the Trypanosoma cruzi JR cl4 strain
            genome was provided by the National Human Genome Research Institute
            (NHGRI), National Institutes of Health (NIH).
            
             Credits:
            
             DNA source: Myrna G. Serrano, Andrey Matveyev, Ana Lara and
            Gregory Buck, Center for the Study of Biological Complexity & the
            Department of Microbiology and Immunology, Virginia Commonwealth
            University, Richmond, VA
            
             Parasite source: Michael Miles and Michael D. Lewis, Medical
            Protozoology, London School of Hygiene & Tropical Medicine, London,
            England. The original strain was isolated and cloned by Dr. Hernan
            Carrasco and his colleagues at the Universidad Central de
            Venezuela.
            
             Sequencing - The Genome Institute, Washington University School of
            Medicine, St Louis, MO.
            
             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 Trypanosoma cruzi JR cl4 strain
            sequence assembly acknowledge Gregory A. Buck, Virginia
            Commonwealth University, and The Genome Institute, Washington
            University School of Medicine.
            
             Miles MA, Toye PJ, Oswald SC, Godfrey DG. The identification by
            isoenzyme patterns of two distinct strain-groups of Trypanosoma
            cruzi, circulating independently in a rural area of Brazil. Trans R
            Soc Trop Med Hyg. 1977, 71: 217-25.
             Brisse S, Barnabe C, Tibayrenc M. Identification of six
            Trypanosoma cruzi phylogenetic lineages by random amplified
            polymorphic DNA and multilocus enzyme electrophoresis. Int J
            Parasitol. 2000; 30: 35-44.
             Zingales B, Andrade SG, Briones MR, Campbell DA, Chiari E,
            Fernandes O, Guhl F, Lages-Silva E, Macedo AM, Machado CR, Miles
            MA, Romanha AJ, Sturm NR, Tibayrenc M, Schijman AG; Second
            Satellite Meeting. A new consensus for Trypanosoma cruzi
            intraspecific nomenclature: second revision meeting recommends TcI
            to TcVI. Mem Inst Oswaldo Cruz. 2009; 104: 1051-4.
            
              Lewis M.D. Llewellyn M.S., Gaunt M.W., Yeo M., Carrasco H.J., et
            al. (2009). Flow cytometric analysis and microsatellite genotyping
            reveal extensive DNA content variation in Trypanosoma cruzi
            populations and expose contrasts between natural and experimental
            hybrids. Int. J. Parasitol. 39: 1305-13.
            
            ##Genome-Assembly-Data-START##
            Assembly Method       :: Newbler v. March 2012
            Assembly Name         :: Trypanosoma_cruzi_JR_cl4-1.1.4
            Genome Coverage       :: 69x
            Sequencing Technology :: Roche 454
            ##Genome-Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..73523
                     /organism="Trypanosoma cruzi JR cl. 4"
                     /mol_type="genomic DNA"
                     /strain="JR cl. 4"
                     /isolation_source="55 year old mail patient in chronic
                     syptomatic stage of disease"
                     /host="Homo sapiens"
                     /db_xref="taxon:914063"
                     /chromosome="Unknown"
                     /country="Venezuela: Anzoategui"
     assembly_gap    4466..4475
                     /estimated_length=10
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
     assembly_gap    7402..7743
                     /estimated_length=342
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
     assembly_gap    9776..9971
                     /estimated_length=196
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
     assembly_gap    11652..11696
                     /estimated_length=45
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
     assembly_gap    36012..36659
                     /estimated_length=648
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
     assembly_gap    45590..45991
                     /estimated_length=402
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
     assembly_gap    57320..57401
                     /estimated_length=82
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
     assembly_gap    59795..60794
                     /estimated_length=1000
                     /gap_type="within scaffold"
                     /linkage_evidence="unspecified"
CONTIG      join(AODP01001803.1:1..4465,gap(10),AODP01001804.1:1..2926,
            gap(342),AODP01001805.1:1..2032,gap(196),AODP01001806.1:1..1680,
            gap(45),AODP01001807.1:1..24315,gap(648),AODP01001808.1:1..8930,
            gap(402),AODP01001809.1:1..11328,gap(82),AODP01001810.1:1..2393,
            gap(1000),AODP01001811.1:1..12729)
//