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IDs: 326038 [UID] 326038 [GenBank] 807718 [RefSeq]
The platyfish DNA for shotgun sequencing and for BAC libraries is derived from a single female (Xiphophorus maculates, Strain - JP 163 A, sample id: XMAC-090115_JP163A) from the laboratory of Dr. Ron Walter, Texas State University, San Marcos, Texas, ... USA. Fish have been mated and given rise to generation 105. Two brother-sister matings of the 105 generation have dropped broods from which the female was chosen for sequencing. These fish are bred and maintained at the Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas. All sequences were generated on the Roche 454 Titanium instrument with the exception of the BAC-end sequences which were generated on the ABI3730 instrument. Two independent assemblies were built with all sequence data, using the Newbler and PCAP algorithms from roughly 19.6X total sequence coverage in whole-genome shotgun reads, a combination of 12x fragments, 9x 3kb, .38x 20kb and .02x BAC-end read pairs. The physical map of Xiphophorus maculatus was constructed by generating fingerprints from the WLC-1247 BAC library (http://bacpac.chori.org). The map consists of 43,192 BAC clones with an average insert size of 160kb. A merged assembly was achieved by identifying through Blat unique sequences in the PCAP assembly. The unique sequences from the PCAP assembly were then merged into the Newbler assembly. The final assembly was checked for consistency by renaming redundant reads and contigs. To merge unique contigs from the PCAP assembly into the Newbler assembly the Newbler assembly served as the reference and all contigs were aligned by blat to the Newbler contigs. Only unique contigs not found in the Newbler assembly were added in. Any redundant reads found in contigs were removed then all contigs were renamed. The merged assembly was screened for contamination and 410 contigs were removed. A total of 23,144 contigs were added to the Newbler assembly (about 7Mb). Illumina Genome sequence reads were generated on the same DNA source for use in assembly error correction (XMAC-090115_JP163A_gDNA_tube1-lib4). These are paired end reads, insert size of 200bp, of 75 base pair read length. A total of 7.7Gb of raw data was produced. These reads were aligned to the platyfish 4.4 version to correct insertion and deletion errors. Overall, we have on average corrected 1 nucleotide every 2000 bases in the assembly. Xiphophorus maculatus Sequence and Assembly Credits DNA source - Dr. Ron Walter, Texas State University Genome Sequence - The Genome Institute, Washington University School of Medicine Sequence Assembly and Chromosomal Sequence Construction - The Genome Institute, Washington University School of Medicine Fingerprint Map - The Genome Institute, Washington University School of Medicine BAC library - Dr. Pieter DeJong, BACPAC resources center Platyfish assembly error correction - Dr. Jeffery Boore, Genome Project Solutions Platyfish cDNA data - RNA sources was Dr. Ron Walter, Texas State University. cDNA sequencing on the 454 Titanium platform was done at The Genome Institute, Washington University School of Medicine. cDNA sequencing was done on the Illumina platform at the University of Oregon. Funding for the sequence characterization of the platyfish genome is being provided by grants to Dr. Ron Walter through the National Institutes of Health (NIH) and Dr. Manfred Schartl at the Universitat Wurzburg, Germany. more
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