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Felis_catus_8.0

Organism name:
Felis catus (domestic cat)
Infraspecific name:
Breed: Abyssinian
Isolate:
Cinnamon
Sex:
female
BioSample:
SAMN02953640
BioProject:
PRJNA16726
Submitter:
International Cat Genome Sequencing Consortium
Date:
2014/11/07
Synonyms:
felCat8
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000181335.3 (replaced)
RefSeq assembly accession:
GCF_000181335.2 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
AANG03
Assembly method:
CABOG v. 6.2; MaSuRCA assembler v. 8.0; GAA v. 1.0
Genome coverage:
2x Sanger; 14x 454, 20x Illumina
Sequencing technology:
Sanger; 454 Titanium; Illumina

IDs: 250841 [UID] 1373248 [GenBank] 1513828 [RefSeq]

See Genome Information for Felis catus

There are 2 assemblies for this organism

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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

Total sequence length2,641,342,258
Total assembly gap length41,625,436
Gaps between scaffolds303
Number of scaffolds267,928
Scaffold N5018,072,971
Scaffold L5045
Number of contigs367,672
Contig N5045,189
Contig L5016,252
Total number of chromosomes and plasmids20
Number of component sequences (WGS or clone)367,856

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
non-nuclear
Assembly Unit: Primary Assembly (GCF_000181345.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome A1CM001378.2=NC_018723.214,905
Chromosome A2CM001379.2=NC_018724.29,317
Chromosome A3CM001380.2=NC_018725.212,760
Chromosome B1CM001381.2=NC_018726.215,201
Chromosome B2CM001382.2=NC_018727.211,658
Chromosome B3CM001383.2=NC_018728.213,578
Chromosome B4CM001384.2=NC_018729.29,494
Chromosome C1CM001385.2=NC_018730.214,505
Chromosome C2CM001386.2=NC_018731.212,356
Chromosome D1CM001387.2=NC_018732.27,204
Chromosome D2CM001388.2=NC_018733.29,424
Chromosome D3CM001389.2=NC_018734.25,960
Chromosome D4CM001390.2=NC_018735.23,621
Chromosome E1CM001391.2=NC_018736.25,189
Chromosome E2CM001392.2=NC_018737.25,298
Chromosome E3CM001393.2=NC_018738.22,274
Chromosome F1CM001394.2=NC_018739.27,113
Chromosome F2CM001395.2=NC_018740.26,163
Chromosome XCM001396.2=NC_018741.26,350
unplacedn/an/an/a95,235

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,641,325,249267,9272,599,699,81318,072,97199,744303
Chromosome A1AllAssembled moleculeUnlocalized scaffolds252,288,802240,380,22311,908,57914,9231814,905249,107,578237,353,82911,753,74923,309,77823,309,7787298,4238,25416917170
Chromosome A2AllAssembled moleculeUnlocalized scaffolds177,416,460168,638,7998,777,6619,343269,317174,745,722166,129,4298,616,29312,417,77514,197,5967996,6016,41618525250
Chromosome A3AllAssembled moleculeUnlocalized scaffolds151,512,697140,925,89810,586,79912,7721212,760149,243,684138,904,48210,339,20219,678,23419,678,2347525,6845,44623811110
Chromosome B1AllAssembled moleculeUnlocalized scaffolds218,782,166206,538,55412,243,61215,2191815,201215,576,425203,537,90712,038,51825,414,70725,414,7077337,8667,64022617170
Chromosome B2AllAssembled moleculeUnlocalized scaffolds162,214,809152,998,5039,216,30611,6761811,658159,896,387150,858,8639,037,52420,269,40520,269,4057305,8765,71116517170
Chromosome B3AllAssembled moleculeUnlocalized scaffolds159,456,556148,068,39511,388,16113,5901213,578156,635,120145,534,53411,100,58630,988,38230,988,3827546,6626,37728511110
Chromosome B4AllAssembled moleculeUnlocalized scaffolds150,944,392142,431,0588,513,3349,509159,494148,667,746140,408,4658,259,28133,995,19133,995,1917735,8125,60620614140
Chromosome C1AllAssembled moleculeUnlocalized scaffolds233,918,182222,198,62911,719,55314,5252014,505231,167,986219,666,54611,501,44016,878,81117,787,2057378,6908,47721319190
Chromosome C2AllAssembled moleculeUnlocalized scaffolds169,430,381159,252,93210,177,44912,3762012,356167,247,673157,272,7649,974,90922,491,02322,491,0237435,8895,66822119190
Chromosome D1AllAssembled moleculeUnlocalized scaffolds121,809,529115,468,7416,340,7887,222187,204119,957,245113,902,8436,054,40211,167,41814,181,6167704,5354,40612917170
Chromosome D2AllAssembled moleculeUnlocalized scaffolds95,723,78388,096,1247,627,6599,43399,42494,425,88086,936,3037,489,57725,790,33025,790,3307443,7063,556150880
Chromosome D3AllAssembled moleculeUnlocalized scaffolds99,146,99794,101,1115,045,8865,971115,96097,863,70292,906,1724,957,53021,134,13221,134,1327503,6303,5359510100
Chromosome D4AllAssembled moleculeUnlocalized scaffolds97,919,51694,492,5133,427,0033,641203,62196,528,11793,281,3473,246,77012,267,17448,060,0297923,4093,3189119190
Chromosome E1AllAssembled moleculeUnlocalized scaffolds65,576,12461,081,8164,494,3085,199105,18964,585,90760,188,1724,397,73511,429,88211,429,8827643,3273,221106990
Chromosome E2AllAssembled moleculeUnlocalized scaffolds66,223,68961,960,2434,263,4465,312145,29865,194,43960,999,6904,194,7497,344,8568,573,2077363,2073,1268113130
Chromosome E3AllAssembled moleculeUnlocalized scaffolds44,138,15241,224,3832,913,7692,28062,27443,575,04240,732,1372,842,90515,915,12715,915,1271,3252,1151,888227550
Chromosome F1AllAssembled moleculeUnlocalized scaffolds76,004,27670,119,2295,885,0477,125127,11374,613,68568,851,4175,762,26811,233,05311,501,5737513,3513,21014111110
Chromosome F2AllAssembled moleculeUnlocalized scaffolds89,069,21283,953,3895,115,8236,16856,16387,835,26282,831,2215,004,04129,335,23529,335,2357453,1343,015119440
Chromosome XAllAssembled moleculeUnlocalized scaffolds133,725,990127,282,3706,443,6206,408586,350129,122,798122,879,5756,243,2239,458,1169,458,1168655,3915,22716457570
unplacedAssembled molecule76,023,53695,23573,709,4157502,4360
MoleculeTotal
Length
Mitochondrion MT17,009
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