LOCUS KN716699 75662 bp DNA linear CON 12-MAR-2015
DEFINITION Dictyocaulus viviparus strain HannoverDv2000 unplaced genomic
scaffold D_viviparus-1.0_Cont550, whole genome shotgun sequence.
ACCESSION KN716699 AZAF01000000
VERSION KN716699.1
DBLINK BioProject: PRJNA72587
BioSample: SAMN02873952
KEYWORDS WGS; HIGH_QUALITY_DRAFT.
SOURCE Dictyocaulus viviparus (bovine lungworm)
ORGANISM Dictyocaulus viviparus
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditina; Rhabditomorpha; Strongyloidea; Metastrongylidae;
Dictyocaulus.
REFERENCE 1 (bases 1 to 75662)
AUTHORS Mitreva,M.
TITLE Draft genome of the bovine lungworm Dictyocaulus viviparus
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 75662)
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 (12-NOV-2013) The Genome Institute, Washington University
School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA
COMMENT Dictyocaulus viviparus, the bovine lungworm, is the cause of
parasitic bronchitis in cattle (husk, verminous pneumonia,
dictyocaulosis) with a world wide distribution in temperate areas.
The predominant hosts are cattle, but it can also infect deers.
Infection occurs on pasture as infective larvae develop from L1
that are shed with the feces to free-living infective L3 that are
ingested by cattle while grazing. Free-living larvae do not feed;
survival on pasture is therefore limited to a few months depending
on temperature and humidity. The parasite is able to interrupt
development inside the host. Infective larvae that have been
exposed to low temperatures on pasture before infection
subsequently develop only to preadult larval stages that survive
winter conditions as hypobiotic larvae in the lung and resume
development in spring. These animals contaminate pastures the
following spring and represent the major source of infection for
other susceptible cattle. The strain being sequenced
(HannoverDv2000) was obtained from the laboratory of Drs. Thomas
Schnieder and Christina Strube (Christina.Strube@tiho-hannover.de)
and has been maintained in calves since August 2000. Worm isolation
and DNA extraction was performed by Christina Strube and/or the
Genome Institute's production team.
This assembly consists of fragments, 3kb and 8kb insert whole
genome shotgun libraries. The sequences were generated on the
Roch/454 platform and assembled using Newbler. To improve
scaffolding, inhouse 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 close gaps followed by
the Pyramid assembler and Illumina paired reads to closing gaps and
extending 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 D. viviparus 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 D.
viviparus 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##
Current Finishing Status :: High-Quality Draft
Assembly Method :: Newbler v. 2.6
Assembly Name :: D_viviparus_9.2.1.ec.pg
Genome Coverage :: 12.20x
Sequencing Technology :: 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..75662
/organism="Dictyocaulus viviparus"
/mol_type="genomic DNA"
/submitter_seqid="D_viviparus-1.0_Cont550"
/strain="HannoverDv2000"
/isolation_source="Cow lung"
/host="cattle"
/db_xref="taxon:29172"
/chromosome="Unknown"
/country="Germany"
/lat_lon="51.00 N 9.00 E"
/collection_date="Aug-2000"
/collected_by="Drs. Thomas Schnieder and Christina Strube"
gene 3999..11729
/locus_tag="DICVIV_11832"
mRNA join(3999..4061,4430..4579,5131..5259,5801..5944,
6949..7081,7135..7244,7563..7694,7771..7833,7925..8085,
8269..8365,8472..8661,8732..8874,8937..9032,9615..9794,
10369..10425,10519..10616,11278..11395,11521..11570,
11627..11729)
/locus_tag="DICVIV_11832"
/product="CRAL/TRIO domain protein"
CDS join(3999..4061,4430..4579,5131..5259,5801..5944,
6949..7081,7135..7244,7563..7694,7771..7833,7925..8085,
8269..8365,8472..8661,8732..8874,8937..9032,9615..9794,
10369..10425,10519..10616,11278..11395,11521..11570,
11627..11729)
/locus_tag="DICVIV_11832"
/inference="protein motif:HMMPfam:IPR001251"
/inference="protein motif:HMMPfam:IPR006797"
/inference="protein motif:HMMPfam:IPR008273"
/note="KEGG: isc:IscW_ISCW023769 5.6e-27 retinal-binding
protein, putative"
/codon_start=1
/product="CRAL/TRIO domain protein"
/protein_id="KJH42177.1"
/db_xref="InterPro:IPR001251"
/db_xref="InterPro:IPR006797"
/db_xref="InterPro:IPR008273"
/translation="MVQTYQSPVRVYKHPFELVMAAYEKRFPTCPQIPIFVGSEVTYE
YHSEDGAQWVIERKCQLNVDAPYLVKKVHPDNPEWTCFEQNAALDVKSFFGFETAVEK
LAMKQYAANLAKGKEILEYFIDELIKSGVTYIPQFEHKDSGSSADSAIDISKEHSSDE
TWRRAFTEERREFFIIALRFVTYWLPMLARRYDKTGKRRRSVKFVIAESKLEAEYIRR
FLGQLSPLEESRLCELKYGLHAHHKGKLPNDAHLLRFLRARDFDVAKAKELVHNSIIW
RKQHNVDRILQEWTPPSVMTQFFPGCWHHNDKEGRPLYLLRLGNLDMKGMLRSCGLEN
IVKLTLSICEEGLIKTAEATRQIGAPISTWSLLVDLEGLSMRHLWRPGVQSLLRIIEI
VEAHYPETMGQVLVVRAPRVFPILWTLISPFIDETTRNKFMINSGELVKGEISKYVDD
QYIPDFLGGTCLVSCPSGGHIPKSQYRPVQELPDDADVLRSMYTTASVTRGYPVEVII
PVTSMGCVLTWDFDILKSECEFIVYHTPKIIQEAMTPHSPSMLKPVEMVTAAIANNPL
PVVISDPSLTLGLDLTIEEKPVVFQEGDSMQGSHFCSRSGTYILQWRIPEISGQHNTT
FDFSIGTHKCRLMYYHELLNSADFRKGGSNFLNISKSCRCCLQYKKVSKEAKSHWLVF
CQFIHNFDSLLSRWEMFNISQTVGSVASLESCRSSFSSIAPPSQPGTPCVGSKIAK"
assembly_gap 9340..9520
/estimated_length=181
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 17384..17877
/estimated_length=494
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 20400..21171
/estimated_length=772
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
gene 34753..38263
/locus_tag="DICVIV_11833"
mRNA join(34753..34807,34918..35076,35236..35340,35776..35858,
35914..35998,36230..36369,36617..36747,36890..36971,
37097..37238,37339..37462,37638..37754,37824..37906,
38211..38263)
/locus_tag="DICVIV_11833"
/product="hypothetical protein"
CDS join(34753..34807,34918..35076,35236..35340,35776..35858,
35914..35998,36230..36369,36617..36747,36890..36971,
37097..37238,37339..37462,37638..37754,37824..37906,
38211..38263)
/locus_tag="DICVIV_11833"
/inference="protein motif:HMMPfam:IPR017442"
/note="KEGG: phu:Phum_PHUM368540 1.3e-30
serine/threonine-protein kinase NIM1, putative"
/codon_start=1
/product="hypothetical protein"
/protein_id="KJH42178.1"
/db_xref="InterPro:IPR017442"
/translation="MLRTWCGSPPYAAPELLLGKEYDGLKADIWSLGVILYILVTGGF
PFPGDNVENLKRAVLSCHMKIPYWVSVECADLIKKMLVIHPFKRLSINAVMQHRFVVK
SSPLYRRPLKLNPTVLLFMQQHGLWTEEQIVDDVLKHNFESSIFATYEMLCDKIEKNS
LKGLTNDYPRRGSRGSILSGKANVEADSLKATVSTHHLAQLNFSTSIECDSDDSSASD
IYEESPSSSNNGKKQERCQFGLAMKEELGNRGEIRRHTLCASEKILSPDMMAQLPVSS
PLYQAVLNHSAFTDLNTSPGGTNLVTSQLPLFFALPLMPMLDYAQMLPVPNSERRASA
GENLLNPGTIESVNHIIHSAPTGNVARSIEEEGEGYLSKHAGKRNTVHTASSAFGPSS
PAPRHCPYTKASSTERRSSWASPTITMQQQQQLERMHRQASNSEVLESSTVAFSDMKS
IL"
gene <39450..40447
/locus_tag="DICVIV_11834"
mRNA join(<39450..39587,39655..39786,40093..40204,40269..40447)
/locus_tag="DICVIV_11834"
/product="hypothetical protein"
CDS join(<39450..39587,39655..39786,40093..40204,40269..40447)
/locus_tag="DICVIV_11834"
/codon_start=1
/product="hypothetical protein"
/protein_id="KJH42179.1"
/translation="AGRSPTHFEHRSAPFGCPQISITDEHNRSLAPGSSSFDPISFFE
QKVNEVVCGQRPATVIGFSPASKSGASSPEQSVKVDEGDGNDDRVKSFVSTLPLADVV
HELKNCLNEMHIQFEETSEVVYMDQEMNRLSLSTGVEIGCATLPPEHKSHVEFAIVAG
VSPNSELLCEELISRLRVLDPTASYE"
assembly_gap 41442..41541
/estimated_length=100
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
gene complement(42402..43660)
/locus_tag="DICVIV_11835"
mRNA complement(join(42402..42539,42627..42728,42896..42982,
43071..43153,43296..43418,43600..43660))
/locus_tag="DICVIV_11835"
/product="hypothetical protein"
CDS complement(join(42402..42539,42627..42728,42896..42982,
43071..43153,43296..43418,43600..43660))
/locus_tag="DICVIV_11835"
/inference="protein motif:HMMPfam:IPR002524"
/codon_start=1
/product="hypothetical protein"
/protein_id="KJH42180.1"
/db_xref="InterPro:IPR002524"
/translation="MGLHPIPRLILHSLSPLVVIGAYVSGLTIPQWVGESWMWRHADP
ILAVVLTLLFLLLIIPSFKEMMPYIFAHTPAKFHVESFQNEISETFPDVTCTHIHAYR
LWPGNVFEALIHLNFLVDKSKQAWSSDAAIRYTEVRQNVTSVLTRAGAQKVVVEPCFL
DATEIGRPWVGCVGVTCFRQDRGCCKVDEKLEVQVAR"
assembly_gap 52203..52395
/estimated_length=193
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
assembly_gap 58456..58555
/estimated_length=100
/gap_type="within scaffold"
/linkage_evidence="paired-ends"
gene 64134..67833
/locus_tag="DICVIV_11836"
mRNA join(64134..64305,64359..64452,64519..64665,65703..65802,
67648..67833)
/locus_tag="DICVIV_11836"
/product="HAD superfamily hydrolase, 5'-nucleotidase"
CDS join(64134..64305,64359..64452,64519..64665,65703..65802,
67648..67833)
/locus_tag="DICVIV_11836"
/inference="protein motif:HMMPfam:IPR008380"
/note="KEGG: phu:Phum_PHUM227090 2.1e-64 Cytosolic purine
5'-nucleotidase, putative"
/codon_start=1
/product="HAD superfamily hydrolase, 5'-nucleotidase"
/protein_id="KJH42181.1"
/db_xref="InterPro:IPR008380"
/translation="MKVSNLSINVLIIYHILEYKSPDLEILSFDLAVQRLIDIGYPEE
IRKFKYDPIFPVRGLWFDYSYGNLLKVDGFGNILVGMHGFKFLKAAEIEEIYPNRYLQ
LSESRVFVLNTLFNLPETHLLAYLIDFFDNHPEYTPLEDKTGLRGGDVLMSYKSIFYD
CRSALDWVHLESNMKEIILENMEKYVMPDDRAPLLLRQLREAGRQTFLLTNSDYGYTD
VINFDFILGTLLPN"
gene 67900..73172
/locus_tag="DICVIV_11837"
mRNA join(67900..68001,68173..68181,70843..70918,71000..71087,
71470..71665,72025..72032,72524..72696,72874..72968,
73056..73172)
/locus_tag="DICVIV_11837"
/product="5' nucleotidase family protein"
CDS join(67900..68001,68173..68181,70843..70918,71000..71087,
71470..71665,72025..72032,72524..72696,72874..72968,
73056..73172)
/locus_tag="DICVIV_11837"
/inference="protein motif:HMMPfam:IPR008380"
/note="KEGG: ssc:100154612 4.6e-53 cytosolic IMP-GMP
specific 5-nucleotidase; K01081 5'-nucleotidase"
/codon_start=1
/product="5' nucleotidase family protein"
/protein_id="KJH42182.1"
/db_xref="InterPro:IPR008380"
/translation="MTFLLGHKWRSFFNITVVNARKPKWFAEGTVFRECTKVDTSTGA
VKLGFHTGPLKEGVVYSGGSCDAFHKIVKARGKDVLYIGDHIFGDVLRSKKSRGWRTF
LVVPELDHELMVWTDRRPLFEQLNQLDNTLADIYKHLDATARRKPQIHNILQKVKVER
YADLYASSCYNLAHYPSFYFFRAAMQLLPHESTVDHASVVNSSKKDLLERKETIGQQV
RGWTQKTSNENEFCHEEEEDEQSISDGEVHMTCTLRHSKSFSDDVTEHEVADTDIVVV
PPAYVEQEQQM"
CONTIG join(AZAF01013451.1:1..9339,gap(181),AZAF01013452.1:1..7863,
gap(494),AZAF01013453.1:1..2522,gap(772),AZAF01013454.1:1..20270,
gap(100),AZAF01013455.1:1..10661,gap(193),AZAF01013456.1:1..6060,
gap(100),AZAF01013457.1:1..17107)
//