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Sequence Set Browser

 

ABIR00000000.2 Trichinella spiralis

Master
# of Contigs: 9,267
# of Proteins: 16,380
# of Scaffolds: 6,863
Total length: 58,541,486 bp
BioProject: PRJNA12603
BioSample: SAMN02953711
Keywords: WGS
Annotation: Contigs
Organism: Trichinella spiralisshow lineagehide lineage
Biosource:
/mol_type = genomic
/strain = ISS 195
WGS: ABIR02000001:ABIR02009267
Scaffolds: GL622784:GL629646
6,863 scaffolds, total length is 63,525,422 bases
Reference:
The draft genome of the parasitic nematode Trichinella spiralis : Nat. Genet. 43 (3), 228-235 (2011) – show 21 authorshide authors
Mitreva,M., Jasmer,D.P., Zarlenga,D.S., Wang,Z., Abubucker,S., Martin,J., Taylor,C.M., Yin,Y., Fulton,L., Minx,P., Yang,S.P., Warren,W.C., Fulton,R.S., Bhonagiri,V., Zhang,X., Hallsworth-Pepin,K., Clifton,S.W., McCarter,J.P., Appleton,J., Mardis,E.R., Wilson,R.K.
Submission:
Submitted (16-OCT-2007) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Parkway, St. Louis, MO 63108, USA – Wilson,R.K.
Submission:
Submitted (11-MAR-2010) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA – show 16 authorshide authors
Mitreva,M., Wang,Z., Abubucker,S., Martin,J., Taylor,C., Fulton,L., Minx,P., Wesley,C., Warren,C., Fulton,R., Pepin,K.H., Bhonagiri,V., Zhang,X.W.E., Clifton,S., Mardis,E.R., Wilson,R.K.

On Jan 4, 2011 this sequence version replaced gi:162732758.

The Trichinella spiralis whole genome shotgun (WGS) project has the project accession ABIR00000000. This version of the project (02) has the accession number ABIR02000000, and consists of sequences ABIR02000001-ABIR02009267.

Trichinella spiralis is a roundworm that cause most of the human trichinella infections and deaths around the world. Its pathogenicity is higher than that of other trichinella species due to the higher number of newborn larvae produced by the females and for the stronger immune reaction induced in humans. The life cycle of the parasite begins when a person or an animal eats contaminated meat containing larvae. T. spiralis is a basal nematode with a well-defined phylogenetic position near the root of the phylum Nematoda. The genome size estimate based on flow sorted nuclei stained with PI (Spencer Johnston, Texas A&M University) is 1C = 71.3 +/1 1.2 Mb. The strain being sequenced (ISS 195) was obtained from the laboratory of Judith Appleton (Cornell University) and has been maintained in rats since 1970. Worm isolation and DNA extraction was performed by Dante Zarlenga (USDA) This assembly consists of plasmid, fosmid and BAC end sequences. The data were assembled using the assembly engine, PCAP (Xiaoqiu Huang et. al. 2006). Our goal is to explore this WGS draft sequence of T. spiralis in several ways: i) to provide a better understanding of evolutionary biology by identifying gene loss or gain across the phylum Nematoda and clarify evolution of genome architecture (synteny, operons); ii) help identify RNA genes and regulatory regions; and iii) better define proteins involved in nematode parasitism that impact health and disease and are relevant to both host-parasite relationships and basic biological processes.. We masked the repeats by using RECON (Bao and Eddy, 2002) and RepeatMasker (A.F.A. Smit, R. Hubley & P. Green RepeatMasker at http://repeatmasker.org). Then the Ribosomal RNA genes were identified using RNAmmer ((http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer ). Transfer RNA genes 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). Protein-coding genes were predicted using a combination of ab initio programs (Snap, Korf, 2004 and Fgenesh, Softberry, Corp) and an inhouse evidence based program Eannot (Eannot Ding et al., 2004) which uses mRNA, EST and protein alignment information from same species or cross-species to aid in gene structure determination. A consensus gene set from the above prediction algorithms will be generated, using a logical, hierarchical approach. Gene product naming was determined by BER (JCVI: http://ber.sourceforge.net ). 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 T. spiralis genome project contact Makedonka Mitreva mmitreva@watson.wustl.edu (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##
Assembly Method : PCAP v. January 12, 2007
Assembly Name : Trichinella spiralis-3.7.1
Genome Coverage : 34.6x
Sequencing Technology : ABI 3730
##Genome-Assembly-Data-END##
Contigs
Proteins
Download
GenBank:ABIR02.1.gbff.gz 32.4 Mb
FASTA:ABIR02.1.fsa_nt.gz 17 Mb
ASN.1:ABIR02.1.bbs.gz 25.7 Mb