LOCUS EPB73268.1 129 aa PRT CON 06-JUN-2013
DEFINITION Ancylostoma ceylanicum hypothetical protein protein.
ACCESSION KE124997-6
PROTEIN_ID EPB73268.1
SOURCE Ancylostoma ceylanicum
ORGANISM Ancylostoma ceylanicum
Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
Rhabditina; Rhabditomorpha; Strongyloidea; Ancylostomatidae;
Ancylostomatinae; Ancylostoma.
REFERENCE 1 (bases 1 to 444250)
AUTHORS Mitreva,M.
TITLE Draft genome of the parasitic nematode Anyclostoma ceylanicum
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 444250)
AUTHORS Mitreva,M., Abubucker,S., Martin,J., Minx,P., Warren,C.,
Pepin,K.H., Palsikar,V.B., Zhang,X.W.E. and Wilson,R.K.
TITLE Direct Submission
JOURNAL Submitted (14-MAY-2013) The Genome Institute, Washington University
School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA
COMMENT Ancylostoma ceylanicum is a parasite of humans and carnivores in
Asia. The parasite was adapted to the Syrian golden hamster
(Mesocricetus auratus) in 1972 by Ray and Bhopale. The strain
(Indian) was distributed worldwide from the lab of Dr. Jerzy Behnke
in the 1980's. The sequenced strain was obtained by Dr. John M.
Hawdon (jhawdon@gwu.edu) from Dr. Ricardo Fujiwara at the Federal
University of Minas Gerais, Brazil. The strain was maintained in
Dr. Hawdon's lab in dogs and hamsters since 2007. Worm isolation
and extraction of nucleic acids was performed by Dr. Verena
Gelmedin and others in the Hawdon lab, or the Genome Institute
production team. Voucher specimens are on deposit in the U.S.
National Parasite Collection (accession number 102954). For the
original isolation and adaptation to hamsters see Ray, D.K.,
Bhopale, K.K., 1972. Complete development of Ancylostoma ceylanicum
(Looss, 1911) in golden hamsters, Mesocricetus auratus. Experientia
28, 359-361
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, 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 A. ceylanicum 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.
ceylanicum 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.
MapAsmResearch-04/19/2010-patch-
08/17/2010
Assembly Name :: A_ceylanicum1.3.ec.cg.pg
Genome Coverage :: 26.10x
Sequencing Technology :: 454
##Genome-Assembly-Data-END##
FEATURES Qualifiers
source /organism="Ancylostoma ceylanicum"
/mol_type="genomic DNA"
/submitter_seqid="A_ceylanicum-1.0_Cont223"
/specimen_voucher="USDA:USNPC:102954"
/db_xref="taxon:53326"
/chromosome="Unknown"
protein /locus_tag="ANCCEY_07638"
intron_pos 97:0 (1/1)
BEGIN
1 MEYVNTTKFG QADGLSRLMR KHQVESEDVV IAAVENDVCT LLKECIRRLP VTVDDVESYT
61 RTDAVLGKVI SCVNTEKWPK ANQKLAYFQN RCKTLSPNYF ANFGYYGEQS QRGDNFIIQS
121 FGLDGRTII
//