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Felis_catus-6.2

Organism name:
Felis catus (domestic cat)
Infraspecific name:
Breed: Abyssinian
Isolate:
Cinnamon
Sex:
female
BioSample:
SAMN02953640
Submitter:
International Cat Genome Sequencing Consortium
Date:
2011/12/14
Synonyms:
felCat5
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000181335.2 (replaced)
RefSeq assembly accession:
GCF_000181335.1 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT.
  • Data displayed for RefSeq version
WGS Project:
AANG02
Assembly method:
Celera Assembler v. 6.1
Genome coverage:
2x Sanger; 12x 454
Sequencing technology:
Sanger; 454 Titanium

IDs: 440818 [UID] 320798 [GenBank] 440818 [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 generated 6.7M plasmid and 1.3M ... fosmid end reads, representing roughly 2X whole genome shotgun (WGS) coverage. In addition, The Genome Institute at Washington University School of Medicine, St Louis, MO, 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 software (Miller et al. Bioinformatics 2008 24:2818) to 14X Q20 coverage of the genome. 

To create a chromosomal version of this assembly we have aligned marker sequences associated with a radiation hybrid (RH) map (Davis et al. 2009) to the assembled genome sequence using Cross_match (P. Green, unpublished). In addition, the assembled cat genome was aligned against the dog genome (canFam2) and the human genome (hg19) at UCSC (B. Raney) utilizing BLASTZ (Schwartz 2003) to align and score non-repetitive cat regions against repeat-masked dog and human sequence, respectively. Alignment chains differentiated between orthologous and paralogous alignments (Kent 2003) and only "reciprocal best" alignments were retained in the alignment set. The assembled cat genome was also broken into 1kb segments and then aligned against the 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 RH map marker content from Davis et al. (2009). 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 marker assignments. And, along with assembly read pair information, alignments with the dog and human genomes were used to identify breakpoints in scaffolds when marker and alignment information confirmed a false join within the genome 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 the satellite sequences. In the last step a total of 86 finished cat BACs (totaling 14,924,681 bases) were integrated into the assembly, using BLAT and Cross-match aligners for accurate coordinates. There are 2.43Gb bases (including Ns in gaps) on ordered/oriented chromosomes, nearly 15.4 million bases on the chr*_random (unlocalized), and more than 11 million bases on chromosome Un (unplaced). The chromosomal agp contains the ordered/oriented bases for each chromosome (named after the respective linkage group). This second draft assembly is referred to as Felis_catus-6.2. After contamination screening a total of 1012 contigs, primarily Rhodobacter sphaeroides and E. coli, were removed. 

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 - The Genome Institute at Washington University School of Medicine, St Louis, MO
 Whole genome alignments - Brian Raney, University of California, Santa Cruz, CA, and The Genome Institute at Washington University School of Medicine, St Louis, MO.
 Cat RH map - Bill Murphy, Texas A&M University, College Station, TX. 

For questions regarding this cat assembly please contact Dr. Wes Warren.  more

Global statistics

Total sequence length2,455,541,136
Total assembly gap length91,244,929
Gaps between scaffolds900
Number of scaffolds6,400
Scaffold N504,658,941
Scaffold L50154
Number of contigs203,083
Contig N5020,621
Contig L5033,870
Total number of chromosomes and plasmids20

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_000181345.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome A1CM001378.1=NC_018723.158
Chromosome A2CM001379.1=NC_018724.153
Chromosome A3CM001380.1=NC_018725.158
Chromosome B1CM001381.1=NC_018726.147
Chromosome B2CM001382.1=NC_018727.144
Chromosome B3CM001383.1=NC_018728.161
Chromosome B4CM001384.1=NC_018729.147
Chromosome C1CM001385.1=NC_018730.149
Chromosome C2CM001386.1=NC_018731.151
Chromosome D1CM001387.1=NC_018732.159
Chromosome D2CM001388.1=NC_018733.128
Chromosome D3CM001389.1=NC_018734.132
Chromosome D4CM001390.1=NC_018735.123
Chromosome E1CM001391.1=NC_018736.118
Chromosome E2CM001392.1=NC_018737.115
Chromosome E3CM001393.1=NC_018738.117
Chromosome F1CM001394.1=NC_018739.122
Chromosome F2CM001395.1=NC_018740.114
Chromosome XCM001396.1=NC_018741.153
unplacedn/an/an/a4,731

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Chromosome A1AllAssembled moleculeUnlocalized scaffolds240,125,537239,302,903822,6341246658233,958,374233,159,525798,8495,828,2825,828,28244,24819,38019,3146665650
Chromosome A2AllAssembled moleculeUnlocalized scaffolds169,414,344169,043,629370,7151226953163,720,817163,356,921363,8963,733,1043,733,10410,89213,56513,5452068680
Chromosome A3AllAssembled moleculeUnlocalized scaffolds142,693,442142,459,683233,7591206258137,807,301137,575,932231,3694,088,2834,088,28310,92810,71410,7021261610
Chromosome B1AllAssembled moleculeUnlocalized scaffolds207,285,059205,241,0522,044,0071106347200,883,730198,861,7672,021,9634,502,1174,502,1171,253,70717,64117,48515662620
Chromosome B2AllAssembled moleculeUnlocalized scaffolds154,595,952154,261,789334,1631015744149,117,194148,785,170332,0243,751,5253,751,52521,18712,68612,6662056560
Chromosome B3AllAssembled moleculeUnlocalized scaffolds149,357,013148,491,654865,3591125161143,779,792142,933,721846,0714,866,9124,866,912147,22912,41812,3378150500
Chromosome B4AllAssembled moleculeUnlocalized scaffolds145,050,710144,259,557791,1531055847139,604,205138,891,385712,8204,189,3394,189,33975,23411,83511,7676857570
Chromosome C1AllAssembled moleculeUnlocalized scaffolds223,535,292221,441,2022,094,0901186949217,156,630215,112,6112,044,0197,139,1687,139,1681,109,49118,24718,04020768680
Chromosome C2AllAssembled moleculeUnlocalized scaffolds161,025,091157,659,2993,365,7921075651155,798,363152,468,3543,330,0094,778,0474,778,0471,719,17113,15912,89726255550
Chromosome D1AllAssembled moleculeUnlocalized scaffolds117,477,978116,869,131608,8471074859112,636,585112,035,993600,5925,963,8325,963,83228,1978,8558,8183747470
Chromosome D2AllAssembled moleculeUnlocalized scaffolds90,184,51089,822,065362,44562342885,825,28485,466,620358,6644,415,9264,415,92662,1666,7086,6852333330
Chromosome D3AllAssembled moleculeUnlocalized scaffolds96,085,61995,741,729343,89064323291,622,76491,285,072337,6924,234,4054,234,40517,9127,0397,0241531310
Chromosome D4AllAssembled moleculeUnlocalized scaffolds96,852,85496,020,406832,44863402392,307,85691,542,936764,9204,663,0194,663,019214,0147,4207,3724839390
Chromosome E1AllAssembled moleculeUnlocalized scaffolds63,085,42963,002,10283,32745271858,889,67758,807,62782,0502,671,0372,671,03710,4785,4465,440626260
Chromosome E2AllAssembled moleculeUnlocalized scaffolds64,103,73964,039,83863,90139241559,837,40459,775,00862,3964,279,7644,279,76415,5625,1465,142423230
Chromosome E3AllAssembled moleculeUnlocalized scaffolds43,625,85343,024,555601,29834171739,891,18239,319,762571,4202,537,8552,537,855178,1113,1753,1373816160
Chromosome F1AllAssembled moleculeUnlocalized scaffolds68,805,77168,669,167136,60447252267,564,33067,430,147134,1833,805,0533,805,05311,5095,7575,7461124240
Chromosome F2AllAssembled moleculeUnlocalized scaffolds82,833,10282,763,53669,56641271481,686,06681,618,50967,5575,518,0795,518,0799,3916,4796,471826260
Chromosome XAllAssembled moleculeUnlocalized scaffolds127,761,577126,427,0961,334,4811479453120,906,243119,642,9641,263,2793,957,7924,174,02874,29010,56810,46710193930
unplacedAssembled molecule11,625,2554,73111,285,4014,0824450
MoleculeTotal
Length
Mitochondrion MT17,009