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; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
Trypanosomatida; 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"
/submitter_seqid="Scaffold97"
/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)
//