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IDs: 472391 [UID] 2209228 [GenBank] 2305458 [RefSeq]
Background: The killifish DNA for shotgun sequencing is derived from a single three-month old male (Austrofundulus limnaeus) taken from a laboratory stock maintained by Dr. Jason Podrabsky, Portland State University, Portland, OR. The stock originated from near Quisiro, Maracaibo ... basin, Venezuela. This stock has been maintained since 1995 as described by Podrabsky (1999) (Environmental biology of fishes, 54:421-431). Total genomic DNA was extracted from brain, liver, and white muscle. Total assembled sequence coverage of Illumina instrument reads was 94X, including 26X fragments, and 68X long insert reads. The combined sequence reads were assembled using the ALLPATHS-LG software (Gnerre 2011). The estimated genome size is 974Mb. This recalcitrant genome has an estimated 46% repeat content, which is high compared to other fishes. For instance, Poecilia formosa has a repeat content of just 18%. Post assembly improvements included merging (GAA.pl, Yao 2011) the assembly with a JR-Assembler (Chu 2013) assembly of A. limnaeus. The contigs of the merged assembly were reordered by L_RNA_scaffolder (Xue 2013), and SSPACE (Boetzer 2010) was used to further improve scaffolding. Finally, a custom script was used to close gaps. This version has been screened and cleaned of contaminating contigs, and all contigs 200bp or smaller were removed. The assembly is made up of a total of 29,785 scaffolds with an N50 scaffold length of 983,489bp, which includes singletons (single contigs scaffolds). The N50 contig length is 8097bp. This assembly spans 867Mb including gaps, and singleton scaffolds. This work was supported by an NSF grant, NSF IOS-1354549, and a faculty enhancement award from Portland State University to Jason Podrabsky, Portland State University. For questions regarding this A. limnaeus 1.0 assembly please contact Jason Podrabsky, Portland State University, podrabsj(at)pdx.edu. DNA samples can be obtained from: Jason Podrabsky lab 1719 SW 10th Avenue SRTC rm 246 Department of Biology, Portland State University Portland, OR 97201 Sequence and Assembly Credits: source DNA - Jason Podrabsky, Portland State University, Portland, OR Genome Sequence - The HighThroughput DNA Sequencing and Genomics facility, University of Oregon, Eugene, OR Sequence Assembly - Jason Podrabsky, Josiah Wagner, and Kristin Culpepper, Department of Biology, Portland State University It is requested that users of this Australofundulus limneaus 1.0 sequence assembly acknowledge Jason Podrabsky and Portland State University in any publications that result from use of this sequence assembly. Assembly Statistics *** Contiguity: Contig *** Total contig number: 168369 Total contig bases: 695045378 bp Average contig length: 4128 bp Maximum contig length: 133211 bp N50 contig length: 8097 bp N50 contig number: 24011 *** Contiguity: Supercontig *** Total supercontig number: 29785 Average supercontig length: 23335 bp Maximum supercontig length: 10068867 bp N50 supercontig length: 983489 bp (includes singletons) N50 supercontig number: 159 *** Scaffold Distribution *** Scaffolds > 1M: 156 Scaffold 250K--1M: 387 Scaffold 100K--250K: 398 Scaffold 10--100K: 1860 Scaffold 5--10K: 343 Scaffold 2--5K: 798 Scaffold 0--2K: 25843 more
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