LOCUS KN550008 65767 bp DNA linear CON 15-DEC-2014
DEFINITION Oesophagostomum dentatum strain OD-Hann unplaced genomic scaffold
O_dentatum_1.0_Cont809, whole genome shotgun sequence.
ACCESSION KN550008 JOOK01000000
VERSION KN550008.1
DBLINK BioProject: PRJNA72579
BioSample: SAMN02866218
KEYWORDS WGS; HIGH_QUALITY_DRAFT.
SOURCE Oesophagostomum dentatum
ORGANISM Oesophagostomum dentatum
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditina; Rhabditomorpha; Strongyloidea; Strongylidae;
Oesophagostomum.
REFERENCE 1 (bases 1 to 65767)
AUTHORS Mitreva,M.
TITLE Draft genome of the hookworm Oesophagostomum dentatum
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 65767)
AUTHORS Mitreva,M., Pepin,K.H., Abubucker,S., Martin,J., Minx,P.,
Warren,C., Palsikar,V.B., Zhang,X. and Wilson,R.K.
TITLE Direct Submission
JOURNAL Submitted (29-MAR-2014) The Genome Institute, Washington University
School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA
COMMENT Oesophagostomum dentatum, a Nodule worm, infects various livestock
species and can also be found in humans. The larval stages invade
the large intestinal wall and cause granulomatous inflammatory
reactions. O. dentatum infects pigs in all production systems
worldwide. Due to the lack of effective immune reactions worm
burdens can be high and the parasite is found in pigs of all age
groups. O. dentatum can be cultivated in vitro in all life cycle
stages and serves as a model for strongylid nematodes which
constitute a group of parasites most closely related to C. elegans.
The sequenced strain (OD-Hann) was collected in Lower Saxony,
Germany, around 1990 by Prof. Dr. Arwid Daugschies, and is since
maintained in pigs, currently at the Institute of Parasitology,
Vetmeduni Vienna, Austria. Material for sequencing was obtained
from Prof Dr Anja Joachim (Anja.Joachim@vetmeduni.ac.at) of the
Vetmeduni Vienna where it has been maintained since 2003. Worm
isolation and extraction of nucleic acids was done by Prof Joachim
and coworkers at the Institute of Parasitology, Vetmeduni Vienna,
or the Genome Institute 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, in house tools CIGA (Cdna tool for Improving Genome
Assembly) and Pygap (Gap closure tool) were 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 and used to close gaps,
followed by the Pyramid assembler using Illumina paired reads to
close gaps and extending contigs.
The repeat library was generated using Repeatmodeler (A. Smit, R.
Hubley http://www.systemsbiology.org/). The Ribosomal RNA genes
were identified using RNAmmer
((http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer ) and
transfer RNA's were identified with tRNAscan-SE (Lowe and Eddy,
1997). Non-coding RNAs, such as microRNAs, were identified by
sequence homology search of the Rfam database
(http://selab.janelia.org/software.html). 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 (I. Korf, 2004),
Fgenesh (Softberry, Corp) and Augustus (M. Stanke, et. Al 2008) and
the annotation pipeline tool Maker (M. Yandell et. al., 2007) 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 (JCVI: http://ber.sourceforge.net).
Our goal is to explore this WGS draft sequence of Oesophagostomum
dentatum 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
Oesophagostomum dentatum 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. MapAsmResearch-10/14/2011
Assembly Name :: O_dentatum_10.0.ec.cg.pg
Genome Coverage :: 15.0x
Sequencing Technology :: LaRoche 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..65767
/organism="Oesophagostomum dentatum"
/mol_type="genomic DNA"
/submitter_seqid="O_dentatum_1.0_Cont809"
/strain="OD-Hann"
/db_xref="taxon:61180"
/chromosome="Unknown"
/lab_host="pig"
/country="Germany: Lower Saxony"
/collection_date="1990"
/collected_by="Arwid Daugschies"
assembly_gap 2628..2727
/estimated_length=100
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 4971..8316
/estimated_length=3346
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 9730..10049
/estimated_length=320
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 21131..21230
/estimated_length=100
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
gene 22334..26039
/locus_tag="OESDEN_04737"
mRNA join(22334..22380,22433..22733,22786..22871,24579..24668,
24736..24901,24978..25078,25741..25843,25899..26039)
/locus_tag="OESDEN_04737"
/product="HAD hydrolase, family IE"
CDS join(22334..22380,22433..22733,22786..22871,24579..24668,
24736..24901,24978..25078,25741..25843,25899..26039)
/locus_tag="OESDEN_04737"
/inference="protein motif:HMMTigr:IPR018012"
/note="KEGG: ecb:100055382 1.6e-52 hypothetical protein
LOC100055382; K01081 5'-nucleotidase"
/codon_start=1
/product="HAD hydrolase, family IE"
/protein_id="KHJ95314.1"
/db_xref="InterPro:IPR018012"
/translation="MPTPVAFPLPVIDENRTIVEPNFNAIFNRPNVMMRDREAVERKL
KIMVEGGKQKLMVGLENRRSIEVVKDKSSFQVISDFDYTLSRFEDSRGARCWTTHGVF
DHCAMEVDPMLADKFQTLRAKYFPIEFDPKLSLEQKIPYMEEWWNKSHNHIVSARFSK
PTIENFVRNSKIILRDQAEVMLQRLHHLGVPLVVFSAGIGNIIEMFLQQKFGQMPANV
HIISNMMNFNDKGVVVSFSQPLIHTFCKNSSVIRKEAEFFHEVRGRNNVILLGDSMGD
IHMDVGVEKQGPTLKIGFLNSDIDNLLEHYLDAYDVVLVRDQSMAIPDAIVQIIAEGY
IKERESSLIS"
assembly_gap 29803..30453
/estimated_length=651
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
gene 31086..33143
/locus_tag="OESDEN_04738"
mRNA join(31086..31235,31636..31720,32413..32541,32594..32692,
32746..32963,33030..33143)
/locus_tag="OESDEN_04738"
/product="collagen triple helix repeat protein"
CDS join(31086..31235,31636..31720,32413..32541,32594..32692,
32746..32963,33030..33143)
/locus_tag="OESDEN_04738"
/inference="protein motif:HMMPfam:IPR008160"
/note="KEGG: isc:IscW_ISCW014473 2.5e-36 basement membrane
collagen, putative"
/codon_start=1
/product="collagen triple helix repeat protein"
/protein_id="KHJ95315.1"
/db_xref="InterPro:IPR008160"
/translation="MTENNADRLAWVVSAACLVFVAGTVAVVATLHSEISSVAERAER
ELPKYNQTYNTYSTSQCECPGGPRGPPGLNGYDGVPGVPGEDGRNGNDDHTLRLHYSD
SCATCPAGPPGPPGEPGPEGETGPKGFQGPPGSDGAPGIPGPKGPDGDKGVPGPPGLP
GPPGNPGANGRRNTPVPGPQGPPGPAGEAGSIGEPGAPGLPGPEGPAGPGGWPGHPGS
RGADGAYGPPGDPGASGEGGYCPCVSRNTRNSNDATDDYKKTDGIS"
gene complement(33524..36643)
/locus_tag="OESDEN_04739"
mRNA complement(join(33524..33535,33981..34109,34633..34824,
34916..35096,36621..36643))
/locus_tag="OESDEN_04739"
/product="hypothetical protein"
CDS complement(join(33524..33535,33981..34109,34633..34824,
34916..35096,36621..36643))
/locus_tag="OESDEN_04739"
/codon_start=1
/product="hypothetical protein"
/protein_id="KHJ95316.1"
/translation="MLRVITFLRELAGLWRAYVHSYSFQAKPTLCRMCVLQARANKLT
SLAGVAISSHEHSGQKRKREEKKKKRFNEYFFLKTDKSQGEPAKVAKRDPFADSGENV
LLVQQLRDQITKLHSLVAQKEAAMLEKDKKIATLQADLMSAERKHREKVEQLLKEKDE
AIQMVIERQRQANKQVKK"
assembly_gap 39300..40086
/estimated_length=787
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 40941..42756
/estimated_length=1816
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 43920..44124
/estimated_length=205
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 48242..49878
/estimated_length=1637
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
gene 50284..50837
/locus_tag="OESDEN_04740"
mRNA join(50284..50327,50432..50837)
/locus_tag="OESDEN_04740"
/product="hypothetical protein"
CDS join(50284..50327,50432..50837)
/locus_tag="OESDEN_04740"
/codon_start=1
/product="hypothetical protein"
/protein_id="KHJ95317.1"
/translation="MKTTKSGNREETDVATVDRIYDTYAHAPRAAGYLNDDSYYETSM
EEAIRFHMPAELCSFFSSLICFCLWERHKRDVSEDFINGGFRTGLAETLAFHEIAERA
ALHSVKLNEVLNVNYPPVADSVNKRSMLRYIEIGCIDYKNQPSGVNV"
assembly_gap 50943..51522
/estimated_length=580
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 53622..54905
/estimated_length=1284
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
gene complement(61370..62011)
/locus_tag="OESDEN_04741"
mRNA complement(join(61370..61532,61854..62011))
/locus_tag="OESDEN_04741"
/product="hypothetical protein"
CDS complement(join(61370..61532,61854..62011))
/locus_tag="OESDEN_04741"
/codon_start=1
/product="hypothetical protein"
/protein_id="KHJ95318.1"
/translation="MPWCAKGESHVLFNKQNDPEPSFHILIIEDSFTALGDENKLGKN
FTFEAKHKTTGRSFIFAAEDFKTLEPWVELLMITTVDYVLLLKQSFGEQIDHIQYSEA
EPGN"
assembly_gap 62160..64142
/estimated_length=1983
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
CONTIG join(JOOK01127775.1:1..2627,gap(100),JOOK01127780.1:1..2243,
gap(3346),JOOK01127781.1:1..1413,gap(320),JOOK01127782.1:1..11081,
gap(100),JOOK01127783.1:1..8572,gap(651),JOOK01127784.1:1..8846,
gap(787),JOOK01127785.1:1..854,gap(1816),JOOK01127786.1:1..1163,
gap(205),JOOK01127787.1:1..4117,gap(1637),JOOK01127776.1:1..1064,
gap(580),JOOK01127777.1:1..2099,gap(1284),JOOK01127778.1:1..7254,
gap(1983),JOOK01127779.1:1..1625)
//