History (Show revision history)

Comment

A female Abyssinian cat named Cinnamon kept by Dr. Kristina Narfstrom at the University of Missouri was used as the DNA source for all sequencing reads. From this source the Broad Institute and Agencourt have generated 6.7M plasmid and ... 1.3M fosmid end reads, representing 
2X whole genome shotgun (WGS) coverage. In addition, we, at The Genome Institute at Washington University School of Medicine, St Louis, MO, have completed 6X of fragment and 6X of 3kb paired end read coverage, both on the 454 Titanium platform. A BAC library was constructed by the Amplicon Express group from the same DNA source used for sequencing. All BACs were end sequenced. The combined sequence reads were assembled using the CABOG version 6.2 software (Miller et al. Bioinformatics 2008 24:2818) to 14X Q20 coverage of the genome to create our initial assembly release, version 6.2. Additional cat data were sequenced on the Illumina platform to 20X coverage and combined with the Sanger and 454 data described above and a denovo assembly was produced using the MaSuRCA assembler v 8.0 (Zimin et al., 2013). Using GAA version 1.0 (Yao et al. 2011), the version 6.2 assembly was merged with the MaSuRCA assembly to create the final assembly, version 8.0. We filled small (<1kb) within scaffold gaps using custom scripts to align and assemble Illumina reads.



To create a chromosomal version of the 8.0 assembly we used BLASTN to align marker sequences associated with a high-density SNP array-based genetic linkage map (Li et al., unpublished) to the assembled genome sequence. In addition, the assembled cat genome was aligned against the previous cat release (Felis catus 6.2), the dog genome (camFam3) and the human genome (hg19). The assembled cat genome was broken into 1kb segments and then aligned against the cat, dog and human genomes using BLAT (Kent 2002) to identify uniquely aligning segments of the cat genome to aid in identifying breakpoints.


Scaffolds were initially ordered and oriented along the cat chromosomes using the alignments to the previous 6.2 cat release in combination with the new linkage map to validate and modify order and orientation. BLASTZ and BLAT alignments with the dog and human genomes were then used to refine the order and orientation information as well as to insert additional scaffolds into the conditional scaffold framework provided by the initial alignments and marker assignments. Alignments with the cat, dog and human genomes were used to identify breakpoints in scaffolds when marker and alignment information confirmed a false join within the genome assembly. Finished BAC clones were also integrated into the assembly. Finally, satellite sequences were identified in the genome, and centromeres were placed along each chromosome using the localization data from Davis et al. (2009) in combination with the localization of cat satellite sequences.


There are 2.44Gb bases (including Ns in gaps) on ordered/oriented chromosomes, 222Mb on the chr*_random, and 79Mb on chromosome Un. The scaffold N50 length is 180.7Mb (count=45) and the contig N50 length is 44,955 (count=16,463). The chromosomal agp contains the ordered/oriented bases for each chromosome (named after the respective linkage group). This draft assembly is referred to as Felis_catus_8.0.


Credits:


DNA source - Dr. Kristina Narfstrom, University of Missouri, Columbia, MO.


454 Production sequencing - The Genome Institute at Washington University School of Medicine, St Louis, MO


BAC sequencing - The Genome Institute at Washington University School of Medicine, St Louis, MO


Plasmid and fosmid sequencing - The Broad Institute, Cambridge, MA and Agencourt.


Sequence assembly and data integration for creation of chromosomal AGP files - Aleksey Zimin (denovo MaSuRCA assembly) and The Genome Institute at Washington University School of Medicine, St Louis, MO


Cat RH and linkage maps - Bill Murphy and Gang Li, Texas A&M University, College Station, TX; Lesie Lyons, University of Missouri, Columbia, MO.


For questions regarding this cat assembly please contact Dr. Wes Warren (wwarren@wustl.edu).  more

Global statistics