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1 (bases 1 to 444250) AUTHORS Mitreva,M. TITLE Draft genome of the parasitic nematode Anyclostoma ceylanicum JOURNAL Unpublished REFERENCE 2 (bases 1 to 444250) AUTHORS Mitreva,M., Abubucker,S., Martin,J., Minx,P., Warren,C., Pepin,K.H., Palsikar,V.B., Zhang,X.W.E. and Wilson,R.K. TITLE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 //