skip to main content

Sequence Set Browser

 

AAWT00000000.1 Schmidtea mediterranea

Master
# of Contigs: 94,682
# of Proteins: 0
Total length: 865,587,040 bp
BioProject: PRJNA12585
BioSample: SAMN02953673
Keywords: WGS
Annotation: Contigs
Organism: Schmidtea mediterraneashow lineagehide lineage
Biosource:
/dev_stage = adult; juvenile
/mol_type = genomic
/note = clonal line
/strain = S2F2
WGS: AAWT01000001:AAWT01094682
Reference:
PCAP assembly of Schmidtea mediterranea S2F2 : Unpublished – show 9 authorshide authors
Clifton,S.W., Fulton,L., Yang,S.-P., Sanchez Alvarado,A., Reddien,P., Newmark,P., Chinwalla,A., Mardis,E., Wilson,R.K.
Submission:
Submitted (14-NOV-2006) Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd, St. Louis, MO 63108, USA – show 9 authorshide authors
Clifton,S.W., Fulton,L., Yang,S.-P., Sanchez Alvarado,A., Reddien,P., Newmark,P., Chinwalla,A., Mardis,E., Wilson,R.K.

The Schmidtea mediterranea whole genome shotgun (WGS) project has the project accession AAWT00000000. This version of the project (01) has the accession number AAWT01000000, and consists of sequences AAWT01000001-AAWT01094682.

DNA Source: Genomic DNA was purified from whole animals of the S2F2 line, clonally derived from a single animal. Both adult and juvenile DNA was used for this project. Although the genome size was originally estimated at 480 Mb, a more recent estimate performed by Spencer Johnston of Texas A&M University reported the size at 800 Mb. Assembly Description: This draft assembly contains read pairs from plasmid libraries from both adult and juvenile genomic DNA plus a fosmid library (322,506 reads) equivalent to 11.60X Q20 sequence coverage of the genome. The PCAP.rep whole genome assembler was used (Huang et al, Nucleic Acids Res. 2006 Jan 5;34(1):201-5). Additional filtering following assembly removed contigs less than 2000 bases as well as potential contaminants. 186381 supercontigs (including singletons) were removed by this process, with 43,294 supercontigs remaining. Other comments: This genome has proven to be A/T rich (69%), very repetitive (46% of total genome), and heterozygous (even though the animals used for DNA preparation were clonally derived) with portions that recombine, making automated assembly of the genome very difficult. BAC library preparations have been unsuccessful, as the DNA degrades during the preparation process. The genome size calculated using this assembly is 865 Mb (compared to the newly estimated 800 Mb size). We are supplying this draft assembly to the public, but investigators should be aware that due to the nature of this genome, this should be considered preliminary data.

Contigs
Download
GenBank:AAWT01.1.gbff.gz 77.5 Mb
 AAWT01.2.gbff.gz 77.3 Mb
 AAWT01.3.gbff.gz 77.2 Mb
 AAWT01.4.gbff.gz 81.9 Mb
 AAWT01.5.gbff.gz 50.7 Mb
ASN.1:AAWT01.1.bbs.gz 61 Mb
 AAWT01.2.bbs.gz 61.4 Mb
 AAWT01.3.bbs.gz 61.2 Mb
 AAWT01.4.bbs.gz 63 Mb
 AAWT01.5.bbs.gz 33.9 Mb