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ROS_Cfam_1.0

Organism name:
Canis lupus familiaris (dog)
Infraspecific name:
Breed: Labrador retriever
Isolate:
SID07034
Sex:
male
BioSample:
SAMN14478636
BioProject:
PRJNA615959
Submitter:
The Roslin Institute
Date:
2020/09/03
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_014441545.1 (latest)
RefSeq assembly accession:
GCF_014441545.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
JAAUVH01
Assembly method:
nuclear: FALCON-Unzip v. 1.2.4; Bionano Solve v. 3.3; Dovetail HiRise v. 2.1.6-072ca03871cc; Racon v. 1.3.2; PBJelly v. PBSuite 15.8.24; mito: Flye v. 2.7b-b1526
Expected final version:
yes
Genome coverage:
56.5x
Sequencing technology:
PacBio Sequel; Illumina

IDs: 8030911 [UID] 21981068 [GenBank] 23482308 [RefSeq]

See Genome Information for Canis lupus

There are 19 assemblies for this organism

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History (Show revision history)

Comment

The DNA used in the Labrador assembly was derived from a male Labrador retriever. DNA long reads were generated by Novogene using a Pacific Biosciences (PacBio) Sequel instrument. Eighteen SMRT cells yielded 135 subreads (56.5x estimated raw coverage, N50 ... average=19,332). The long read data were processed at The Roslin Institute (University of Edinburgh, UK). Contig level assembly was generated using Falcon-unzip capturing the 2.4 Gbp long genome in 1,439 contigs (with contig N50 of 9Mbp). Scaffolding was done, first, using optical mapping data produced on a Bionano Saphyr instrument, University of Nottingham Deep Seq) using Bionano Solve software. This was followed by scaffolding based on proximity ligation method. The Hi-C library was created using Dovetail's Hi-C library preparation kit. Refining the scaffolds were done using Dovetail HiRise pipeline. Error correction was done using the PacBio long-read data with Racon, followed by polishing with Pilon using an Illumina short read library generated from the same dog. Gap filling was done using PBJelly with the PacBio long-read dataset.
The mitochondrial (MT) sequence was assembled from filtered, MT specific, PacBio long-read data using the Flye assembler and was error corrected with Illumina short-read data with Pilon.
Funding sources: The Dogs Trust (Experienced Investigator award to Jeffrey Schoenebeck, Emily Clark, and Alan Archibald), BBSRC ISP1 (BBS/E/D/10002070), BBSRC Responsive Mode (BB/S02008X/ Alan Archibald).
Long read DNA sequencing: Novogene, HK
Short read DNA sequencing: Novogene, HK; Edinburgh Genomics (University of Edinburgh, UK)
Optical Mapping: Deep Seq, University of Nottingham, UK
Proximity ligation-based scaffolding: Dovetail Genomics, Scotts Valley, CA 95066, United States
Sequence assembly and data integration - The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK  more

Global statistics

Total sequence length2,396,858,295
Total ungapped length2,384,195,665
Gaps between scaffolds0
Number of scaffolds376
Scaffold N5064,037,277
Scaffold L5015
Number of contigs951
Contig N5012,024,593
Contig L5054
Total number of chromosomes and plasmids40
Number of component sequences (WGS or clone)376

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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
Assembly Unit: Primary Assembly (GCF_014441875.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM025100.1=NC_051805.10
Chromosome 2CM025101.1=NC_051806.10
Chromosome 3CM025102.1=NC_051807.10
Chromosome 4CM025103.1=NC_051808.10
Chromosome 5CM025104.1=NC_051809.10
Chromosome 6CM025105.1=NC_051810.10
Chromosome 7CM025106.1=NC_051811.10
Chromosome 8CM025107.1=NC_051812.10
Chromosome 9CM025108.1=NC_051813.10
Chromosome 10CM025109.1=NC_051814.10
Chromosome 11CM025110.1=NC_051815.10
Chromosome 12CM025111.1=NC_051816.10
Chromosome 13CM025112.1=NC_051817.10
Chromosome 14CM025113.1=NC_051818.10
Chromosome 15CM025114.1=NC_051819.10
Chromosome 16CM025115.1=NC_051820.10
Chromosome 17CM025116.1=NC_051821.10
Chromosome 18CM025117.1=NC_051822.10
Chromosome 19CM025118.1=NC_051823.10
Chromosome 20CM025119.1=NC_051824.10
Chromosome 21CM025120.1=NC_051825.10
Chromosome 22CM025121.1=NC_051826.10
Chromosome 23CM025122.1=NC_051827.10
Chromosome 24CM025123.1=NC_051828.10
Chromosome 25CM025124.1=NC_051829.10
Chromosome 26CM025125.1=NC_051830.10
Chromosome 27CM025126.1=NC_051831.10
Chromosome 28CM025127.1=NC_051832.10
Chromosome 29CM025128.1=NC_051833.10
Chromosome 30CM025129.1=NC_051834.10
Chromosome 31CM025130.1=NC_051835.10
Chromosome 32CM025131.1=NC_051836.10
Chromosome 33CM025132.1=NC_051837.10
Chromosome 34CM025133.1=NC_051838.10
Chromosome 35CM025134.1=NC_051839.10
Chromosome 36CM025135.1=NC_051840.10
Chromosome 37CM025136.1=NC_051841.10
Chromosome 38CM025137.1=NC_051842.10
Chromosome XCM025138.1=NC_051843.10
Chromosome YCM025139.1=NC_051844.12
unplacedn/an/an/a334

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,396,858,2953762,384,195,66564,037,2775750
Chromosome 1Assembled molecule123,313,9391123,307,686123,313,939120
Chromosome 2Assembled molecule86,187,811185,957,69886,187,811220
Chromosome 3Assembled molecule92,870,237192,870,10092,870,237110
Chromosome 4Assembled molecule89,007,665189,007,53989,007,66590
Chromosome 5Assembled molecule89,573,405189,515,37689,573,405100
Chromosome 6Assembled molecule78,268,176178,204,52278,268,176140
Chromosome 7Assembled molecule81,039,452181,039,34281,039,45270
Chromosome 8Assembled molecule75,260,524173,921,39675,260,52450
Chromosome 9Assembled molecule62,002,293161,929,63362,002,293130
Chromosome 10Assembled molecule70,361,000170,359,14170,361,00050
Chromosome 11Assembled molecule75,541,347175,386,81475,541,347180
Chromosome 12Assembled molecule73,497,294173,497,10473,497,294130
Chromosome 13Assembled molecule64,037,277163,838,30564,037,27790
Chromosome 14Assembled molecule61,043,064161,042,99061,043,06450
Chromosome 15Assembled molecule65,200,600165,194,53765,200,600140
Chromosome 16Assembled molecule62,021,213161,696,56362,021,213220
Chromosome 17Assembled molecule65,471,548165,440,19165,471,548210
Chromosome 18Assembled molecule56,883,407156,594,49156,883,407180
Chromosome 19Assembled molecule55,265,241155,256,70855,265,241100
Chromosome 20Assembled molecule58,896,461158,896,35758,896,46180
Chromosome 21Assembled molecule52,140,716151,922,88352,140,716100
Chromosome 22Assembled molecule62,106,979162,084,72762,106,979130
Chromosome 23Assembled molecule53,282,923153,282,75953,282,92350
Chromosome 24Assembled molecule48,838,997148,802,61748,838,99790
Chromosome 25Assembled molecule51,941,001151,924,58351,941,00140
Chromosome 26Assembled molecule40,674,351139,293,70040,674,351150
Chromosome 27Assembled molecule46,248,802146,247,08046,248,80260
Chromosome 28Assembled molecule41,862,212141,862,03441,862,21270
Chromosome 29Assembled molecule42,049,852142,046,80542,049,85250
Chromosome 30Assembled molecule40,414,903140,411,01040,414,90330
Chromosome 31Assembled molecule39,518,933139,518,89739,518,93330
Chromosome 32Assembled molecule39,023,732139,023,68339,023,73240
Chromosome 33Assembled molecule31,649,084131,647,25031,649,08430
Chromosome 34Assembled molecule42,263,871142,257,75042,263,87150
Chromosome 35Assembled molecule26,942,268126,942,19126,942,26850
Chromosome 36Assembled molecule31,065,185131,065,12431,065,18540
Chromosome 37Assembled molecule30,932,408130,932,34530,932,40830
Chromosome 38Assembled molecule24,102,048124,101,99724,102,04830
Chromosome XAssembled molecule127,069,6191122,508,213127,069,6191770
Chromosome YAllAssembled moleculeUnlocalized scaffolds6,728,6063,937,6232,790,9833126,271,6573,937,4772,334,1803,937,6233,937,6231,569,52215510000
unplacedAssembled molecule32,259,85133429,091,867117,757300
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