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Ornithorhynchus_anatinus-5.0.1

Organism name:
Ornithorhynchus anatinus (platypus)
Isolate:
Glennie
Sex:
female
BioSample:
SAMN02953646
BioProject:
PRJNA12885
Submitter:
Washington University (WashU)
Date:
2011/06/17
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
n/a
RefSeq assembly accession:
GCF_000002275.2 (latest)
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
AAPN01

IDs: 237598 [UID] 237598 [RefSeq]

See Genome Information for Ornithorhynchus anatinus

There are 3 assemblies for this organism

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History (Show revision history)

Comment

The platypus (Ornithorhynchus anatinus) genome of a female nicknamed "Glennie" (collected at the Upper Barnard River on Glen Rock Station, New South Wales) was sequenced to a total of 6x whole genome coverage. The sequencing strategy we utilized combined ... whole genome shotgun plasmid, fosmid end and BAC end sequences. The combined sequence reads were assembled using the PCAP software (Genome Res. 13(9):2164-70 2003) using stringent parameters. After initial assembly with the PCAP software, supercontigs (ordered/oriented contigs; contigs are contiguous sequences not interrupted by gaps) were linked to the physical map (Washington University Genome Sequencing Center) using BAC end sequences and in silico digests of the sequence itself. The physical map, then, was used to organize the supercontigs into "ultracontigs" (ordered/oriented supercontigs). With the exception of those supercontigs with alignments at >95% identity to a platypus EST (Washington University Genome Sequencing Center), supercontigs smaller than 2kb were removed from the data set prior to submission if they were >97% identical over >97% of their length to other ultracontigs larger than 2kb or if they were deemed to be >95% repetitive (based on analysis using RECON (Bao and Eddy, 2002) for repeat identification). Further, singleton contigs (those not part of a supercontig or ultracontig) smaller than 500bp that did not have an alignment of >95% identity to a platypus EST were not submitted.

 The assembly is composed of 205,534 supercontigs (of those, using the physical map 4,197 supercontigs have been organized into 689 ultracontigs) covering 1.84 Gb of actual sequence (without including estimated gap sizes) or almost 2.0Gb including gap sizes. Of the 1.84Gb, 437Mb (1507 supercontigs organized into 145 ultracontigs) have been anchored and ordered along platypus chromosomes using the physical map in combination with FISH data. The N50 statistic is defined as the length L such that 50% of all nucleotides are contained in contigs of size at least L. At the super/ultracontig level, the N50 number is 298 and the N50 size is 967kb.

 Future improvements to the platypus sequence assembly will be dependent on the availability of funding and improvements to existing assembler software. Funding for the sequencing of the platypus genome was provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

 Bulk downloads of the sequence and annotation data are available via the Ensembl, UCSC and NCBI Genome Browser FTP server or the Downloads pages. The complete set of sequence reads is available at the NCBI Trace Archive.

 Credits:
 DNA - Frank Grutzner, Jennifer Graves - Australian National University, The University of Adelaide
 BAC library - Pieter DeJong - Children's Hospital Oakland Research Institute (CHORI)
 cDNA tissue sources - Tim Hore, Frank Grutzner - The University of Adelaide
 cDNA/EST sequencing - Washington University Genome Sequencing Center
 Plasmid/Fosmid libraries - Washington University Genome Sequencing Center
 FISH data - Australian National University, The University of Adelaide, and Washington University Genome Sequencing Center
 Physical Map - Washington University Genome Sequencing Center
 Genome Sequencing - Washington University Genome Sequencing Center
 Assembly and Assembly/Map Integration - Washington University Genome Sequencing Center  more

Global statistics

Total sequence length1,995,607,322
Total assembly gap length154,534,268
Gaps between scaffolds137
Number of scaffolds200,283
Scaffold N50958,970
Scaffold L50309
Number of contigs443,981
Contig N5011,554
Contig L5039,543
Total number of chromosomes and plasmids20
Number of component sequences (WGS or clone)443,962

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_000000135.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000409.1=NC_009094.10
Chromosome 2CM000410.1=NC_009095.10
Chromosome 3CM000411.1=NC_009096.10
Chromosome 4CM000412.1=NC_009097.10
Chromosome 5CM000413.1=NC_009098.10
Chromosome 6CM000414.1=NC_009099.10
Chromosome 7CM000415.1=NC_009100.10
Chromosome 10CM000416.1=NC_009103.10
Chromosome 11CM000417.1=NC_009104.10
Chromosome 12CM000418.1=NC_009105.10
Chromosome 14CM000419.1=NC_009107.10
Chromosome 15CM000420.1=NC_009108.10
Chromosome 17CM000421.1=NC_009110.10
Chromosome 18CM000422.1=NC_009111.10
Chromosome 20CM000423.1=NC_009112.10
Chromosome X1CM000424.1=NC_009114.10
Chromosome X2CM000425.1=NC_009115.10
Chromosome X3CM000426.1=NC_009116.10
Chromosome X5CM000427.1=NC_009118.10
unplacedn/an/an/a200,134

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All1,995,590,303200,2821,841,056,035958,970243,698137
Chromosome 147,594,2831744,495,2182,621,8865,16216
Chromosome 254,797,3172450,937,3332,706,9606,29223
Chromosome 359,581,9531955,747,4074,172,6306,07818
Chromosome 458,987,2622055,333,8352,790,9336,09219
Chromosome 524,609,2201122,748,9862,699,7452,82310
Chromosome 616,302,927415,300,8528,507,2591,6713
Chromosome 740,039,0881037,712,7458,575,5643,8489
Chromosome 1011,243,762210,685,6199,212,7941,1011
Chromosome 116,809,22426,328,3254,696,2727802
Chromosome 1215,872,666315,077,73710,839,6411,4452
Chromosome 142,696,12212,492,0282,686,1222911
Chromosome 153,786,88023,543,3193,775,7944322
Chromosome 171,399,46911,274,2071,389,4692071
Chromosome 186,611,29016,313,9386,601,2905381
Chromosome 201,816,41211,654,0321,806,4122601
Chromosome X145,541,5511742,769,5303,972,2634,46116
Chromosome X25,652,50115,467,2395,642,5014311
Chromosome X35,951,35815,823,8775,941,3583671
Chromosome X527,786,7391125,785,2624,663,8842,80710
unplaced1,558,510,279200,1341,431,564,546118,863198,6120
MoleculeTotal
Length
Mitochondrion MT17,019
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