LOCUS KN783927 1309 bp DNA linear CON 16-JAN-2015
DEFINITION Ancylostoma duodenale strain Zhejiang unplaced genomic scaffold
A_duodenale-1.0_Cont255559, whole genome shotgun sequence.
ACCESSION KN783927 JHON01000000
VERSION KN783927.1
DBLINK BioProject: PRJNA72581
BioSample: SAMN03277212
KEYWORDS WGS; HIGH_QUALITY_DRAFT.
SOURCE Ancylostoma duodenale
ORGANISM Ancylostoma duodenale
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditina; Rhabditomorpha; Strongyloidea; Ancylostomatidae;
Ancylostomatinae; Ancylostoma.
REFERENCE 1 (bases 1 to 1309)
AUTHORS Mitreva,M.
TITLE Draft genome of the parsitic nematode Ancylostoma duodenale
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1309)
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-DEC-2013) The Genome Institute, Washington University
School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA
COMMENT Ancylostoma duodenale is one of two major species of hookworm that
infect humans worldwide. An Indian A. dudoenale isolate was first
adapted to dogs by Dr. G.A. Schad in 1979 (Schad 1979) using
corticosteroid treatment. This strain has been lost. The sequenced
strain of A. duodenale (Zhejiang) was isolated from humans in
Zhejiang Province, China by Dr. Wen Li-yong and passaged once
through a dog (unpublished). Genomic DNA was isolated by Dr. John
M. Hawdon and confirmed as A. duodenale by PCR. No voucher has been
deposited. This strain has also been lost, and no laboratories are
known to be currently maintaining A. duodenale in animals. For the
original isolation and adaptation to dogs see Schad, G.A. 1979.
Ancylostoma duodenale: maintenance through six generations in
helminth-native pups. Experimental Parasitology 47(2), 246-253.
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. CIGA mapped 454
cDNA reads using blat to the genomic assembly linking genomic
contigs based on cDNA evidence with only joins confirmed by
additional independent data typing accepted. PyGap closed gaps and
extended contigs using the Pyramid assembler with Illumina paired
end reads.
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 A. duodenale 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 A.
duodenale 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 Version MapAsmResearch v.
04/19/2010-patch-08/17/2010
Assembly Name :: A_duodenale_2.2.ec.cg.pg
Genome Coverage :: 19.00x
Sequencing Technology :: 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..1309
/organism="Ancylostoma duodenale"
/mol_type="genomic DNA"
/submitter_seqid="A_duodenale-1.0_Cont255559"
/strain="Zhejiang"
/host="Homo sapiens"
/db_xref="taxon:51022"
/chromosome="Unknown"
/lab_host="dog"
/country="China: Zhejiang Province"
gene <35..769
/locus_tag="ANCDUO_26338"
mRNA join(<35..249,276..341,428..482,558..769)
/locus_tag="ANCDUO_26338"
/product="hypothetical protein"
CDS join(<35..249,276..341,428..482,558..769)
/locus_tag="ANCDUO_26338"
/note="KEGG: ret:RHE_CH03555 3.0e-11 ypch01255;
5'-nucleotidase protein K01081"
/codon_start=3
/product="hypothetical protein"
/protein_id="KIH43651.1"
/translation="PAPVVVPAPAPAPVVVPAPAPASVVVPAPAPVVHPVPVVVPAPA
PAPVVIPAPAPAPVVVPAPAPVVAPAPPAPVVVPAPAPVPVPVPAPVAVHHYHPRTKV
HNVASAYKKESHHRSDTVMVSGDDHHFDHFSGSLDFFPHDHLLDHAAYPVPLRARVNR
KKLASKKAAKARKSFEKKKKN"
CONTIG join(JHON01087832.1:1..1309)
//