LOCUS KZ271208 2950 bp DNA linear CON 17-AUG-2017
DEFINITION Onchocerca flexuosa isolate Red Deer unplaced genomic scaffold
O_flexuosa-1.0_Cont1295, whole genome shotgun sequence.
ACCESSION KZ271208 LQNL01000000
VERSION KZ271208.1
DBLINK BioProject: PRJNA230512
BioSample: SAMN04226856
KEYWORDS WGS; HIGH_QUALITY_DRAFT.
SOURCE Onchocerca flexuosa
ORGANISM Onchocerca flexuosa
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Spirurina; Spiruromorpha; Filarioidea; Onchocercidae; Onchocerca.
REFERENCE 1 (bases 1 to 2950)
AUTHORS Mitreva,M.
TITLE Draft genome of the nematode, Onchocerca flexuosa
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 2950)
AUTHORS Mitreva,M., Pepin,K.H., Martin,J., Ozersky,P., Zhang,X. and
Wilson,R.K.
TITLE Direct Submission
JOURNAL Submitted (17-DEC-2015) McDonnell Genome Institute, Washington
University School of Medicine, 4444 Forest Park, St. Louis, MO
63108, USA
COMMENT Onchocerca flexuosa is a filarial nematode (Nematoda) related to
Onchocerca volvulus the agent of human African river blindness. O.
flexuosa is in contrast to O. volvulus free of obligatory Wolbachia
endosymbionts. Adult worms live in subcutaneous nodules in red
deer. Infective larvae are transmitted by blackflies of the genus
Simulium. This species of filarial parasites is widespread in
Europe and parts of Asia. Adult worms for genome sequencing were
isolated from naturally infected red deer (Cervus elaphus) by
Norbert W. Brattig, Samantha McNulty and Kerstin Fischer. DNA and
RNA samples were provided by Peter U. Fischer
(Pufische@dom.wustl.edu).
This assembly consists of fragments, 3kb and 8kb insert whole
genome shotgun libraries. The sequences were generating on the
Illumina platform and assembled using Allpaths_LG. To improve
scaffolding, our in house tool Pygap (Gap closure tool), 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 O. flexuosa 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
Fasciola hepatica 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 :: AllPaths_LG v. 2012-12-28
Assembly Name :: O_flexuosa_1.0.allpaths.pg.lrna
Genome Coverage :: 66.0x
Sequencing Technology :: Illumina HiSeq 2000
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..2950
/organism="Onchocerca flexuosa"
/mol_type="genomic DNA"
/submitter_seqid="O_flexuosa-1.0_Cont1295"
/isolate="Red Deer"
/isolation_source="Subcutaneous nodules"
/host="Cervus elaphus (red deer)"
/db_xref="taxon:387005"
/chromosome="Unknown"
/country="Germany"
/collection_date="2007"
/collected_by="Norbert W. Brattig, Samantha McNulty,
Kerstin Fischer"
gene complement(1481..1846)
/locus_tag="X798_07609"
mRNA complement(join(1481..1714,1787..1846))
/locus_tag="X798_07609"
/product="collagen triple helix repeat protein"
CDS complement(join(1481..1714,1787..1846))
/locus_tag="X798_07609"
/inference="protein motif:HMMPfam:IPR008160"
/note="KEGG: scl:sce7039 0.0012 putative 5'-nucleotidase
family protein; K01081 5'-nucleotidase"
/codon_start=1
/product="collagen triple helix repeat protein"
/protein_id="OZC05418.1"
/db_xref="InterPro:IPR008160"
/translation="MPMRLFIIFLLFVCAAFMAQSCGPPQRGPPGPPGQNGQDGSSGD
RGPQGPEGEMGEQGMTGQPGPRGPPGETGVIGEGGEDGDKGMKGIRGQDVAGG"
CONTIG join(LQNL01004846.1:1..2950)
//