LOCUS KZ393653 1625 bp DNA linear CON 14-NOV-2017
DEFINITION Teladorsagia circumcincta strain S unplaced genomic scaffold
T_circumcincta.1.0_Cont205724, whole genome shotgun sequence.
ACCESSION KZ393653 LUHK01000000
VERSION KZ393653.1
DBLINK BioProject: PRJNA72569
BioSample: SAMN02780891
KEYWORDS WGS; HIGH_QUALITY_DRAFT.
SOURCE Teladorsagia circumcincta
ORGANISM Teladorsagia circumcincta
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditina; Rhabditomorpha; Strongyloidea; Trichostrongylidae;
Teladorsagia.
REFERENCE 1 (bases 1 to 1625)
AUTHORS Mitreva,M.
TITLE Draft genome of the parasitic nematode Teladorsagia circumcincta
isolate WARC Sus (inbred)
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1625)
AUTHORS Mitreva,M., Abubucker,S., Martin,J., Minx,P., Warren,C.,
Pepin,K.H., Palsikar,V.B., Zhang,X.W. and Wilson,R.K.
TITLE Direct Submission
JOURNAL Submitted (16-SEP-2015) The Genome Institute, Washington University
School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA
COMMENT The brown stomach worm, Teladorsagia circumcinta, is economically
the most important nematode parasite of sheep throughout temperate
regions of the world and has developed multiple resistances to
drugs. Globally, these parasites lead to millions of dollars in
economic losses due to reduced production of meat, wool and milk
and the high costs of treatment. These brownish, thread-like worms
infect the fourth stomach (abomasum) of small ruminants (sheep and
goats), causing weight loss, decreased wool production and death.
The strain sequenced here was developed in the laboratory of Dr.
Stewart Bisset (stewart.bisset@agresearch.co.nz) at AgResearch, New
Zealand, by subjecting an anthelmintic-susceptible laboratory
isolate, originally derived from field-grazed lambs in New Zealand
in the 1950s, to two generations of inbreeding (sibling mating) in
order to minimize genetic diversity. Worm isolation and DNA
extraction was performed by Stewart Bisset and/or the Genome
Institute's production team.
This assembly consists of fragments, 3kb and 8kb insert whole
genome shotgun libraries. The sequences were generating on the
Roch/454 platform and assembled using Newbler. To improve
scaffolding, the inhouse tool CIGA (Cdna tool for Improving Genome
Assembly) was used to map 454 cDNA reads using blat to the genomic
assembly to link genomic contigs based on cDNA evidence. Only joins
confirmed by additional independent data typing were accepted. Gaps
were then closed using Pygap (Gap closure tool) which utilzes the
Pyramid assembler and uses Illumina paired reads to close gaps and
extend contigs.
The repeat library was generated using Repeatmodeler (A.F.A. Smit,
R. Hubley & P. Green http://repeatmasker.org). The Ribosomal RNA
genes were identified using RNAmmer (Lagesen et. al., 2007 Nucleic
Acids Res.) and transfer RNA's were identified with tRNAscan-SE
(Lowe and Eddy, Nucleic Acids Res. 1997). Non-coding RNAs, such as
microRNAs, were identified by sequence homology search of the Rfam
database (Griffiths-Jones et. al., 2003 Nucleic Acids Res.).
Repeats and predicted RNA's were then masked using RepeatMasker
(A.Smit, R. Hubley & P. Green http://repeatmasker.org).
Protein-coding genes were predicted using a combination of ab
initio programs Snap (Korf, 2004 BCM Bioinformatics), Fgenesh
(Salamov A., Solovyev V. 2000, Genome Res.) and Augustus (M.
Stanke, et. al., 2008 Bioinformatics) and the annotation pipeline
tool Maker (M. Yandell et. al., 2007 Genomc Research) which aligns
mRNA, EST and protein information from same species or
cross-species to aid in gene structure determination and
modifications. A consensus gene set from the above prediction
algorithms was generated, using a logical, hierarchical approach
developed at the Genome institute. Gene product naming was
determined by BER (http://ber.sourceforge.net).
Our goal is to explore this WGS draft sequence of Teladorsagia
circumcincta to better define proteins involved in nematode
parasitism that impact health and disease and are relevant to both
host-parasite relationships and basic biological processes.
For information regarding this assembly or project, or any other
GSC genome project, please visit our Genome Groups web page
(http://genome.wustl.edu/genome_group_index.cgi) and email the
designated contact person. For specific questions regarding the
Teladorsagia circumcincta genome project contact Makedonka Mitreva
(mmitreva@genome.wustl.edu) at Washington University School of
Medicine. The National Human Genome Research Institute (NHGRI) of
the National Institutes of Health (NIH) provided funds for this
project.
##Genome-Assembly-Data-START##
Finishing Goal :: High-Quality Draft
Current Finishing Status :: High-Quality Draft
Assembly Method :: Newbler v. 2.6
Assembly Name :: T_circumcincta.14.0.ec.cg.pg
Genome Coverage :: 12.20x
Sequencing Technology :: 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..1625
/organism="Teladorsagia circumcincta"
/mol_type="genomic DNA"
/submitter_seqid="T_circumcincta.1.0_Cont205724"
/strain="S"
/isolation_source="developed by two generations of
inbreeding (sibling mating) of an anthelmintic-susceptible
laboratory isolate that was originally derived from
field-grazed lambs in New Zealand in the 1950s"
/host="sheep"
/db_xref="taxon:45464"
/chromosome="Unknown"
/country="New Zealand"
/lat_lon="42.0000 S 174.0000 E"
gene complement(287..>1485)
/locus_tag="TELCIR_23953"
mRNA complement(join(287..409,1383..>1485))
/locus_tag="TELCIR_23953"
/product="hypothetical protein"
CDS complement(join(287..409,1383..>1485))
/locus_tag="TELCIR_23953"
/note="KEGG: hsa:51251 4.2e-12 NT5C3, MGC27337, MGC87109,
MGC87828, P5'N-1, PN-I, PSN1, UMPH, UMPH1, cN-III;
5'-nucleotidase, cytosolic III K01081"
/codon_start=2
/product="hypothetical protein"
/protein_id="PIO54677.1"
/translation="NNVLLLGDSMGDIHMDVGVEKDGPTLKIGFLNSDVKGLLDHYMD
VYDVVLVQDQSMKVPDTIVQAVAAGYLKRL"
CONTIG join(LUHK01178289.1:1..1625)
//