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Chrysemys_picta_bellii-3.0.3

Organism name:
Chrysemys picta bellii (western painted turtle)
Isolate:
RCT428
Sex:
female
BioSample:
SAMN02713681
BioProject:
PRJNA78657
Submitter:
Painted turtle genome sequencing consortium
Date:
2014/03/31
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000241765.2 (replaced)
RefSeq assembly accession:
GCF_000241765.3 (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:
AHGY02
Assembly method:
Newbler v. 2.6
Genome coverage:
15x
Sequencing technology:
Sanger; 454; Illumina

IDs: 138171 [UID] 986518 [GenBank] 1073638 [RefSeq]

See Genome Information for Chrysemys picta

There are 2 assemblies for this organism

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History (Show revision history)

Comment

Release Notes - Release 3.0.3
 The Chrysemys picta bellii, the painted turtle, whole genome shotgun library from primary donor-derived reads (Field number: RCT428 Locality: WA: Grant Co: small lake 1.3 miles south of Potholes Reservoir) were assembled using Newbler ... (version 2.6) using stringent parameters. After the assembly was complete, 15X of paired end sequencing data were generated on the Illumina platform and used for error correction in the reference assembly (see below). All scaffolds larger than 500 bases (81,642 scaffolds with a total size of 2618Mb, N50 scaffold size of 3.01Mb (N50 number is 248)) were retained for submission to the public databases.
 For error correction, the Illumina data were aligned against the assembly using bwa and processed using samtools and bcftools. Based on the paired end mapping data, all duplicately mapped reads were removed. One and two basepair indels were introduced into the reference for all cases where there were >=3 and <200 reads aligned (mapping quality >=40 and the indel was >=10 bases from the end of the alignment), and where all reads disagreed with the reference and agreed with one another. There were a total of 27,296 indels introduced into 24,712 contigs.

 We processed this submitted assembly using an unpublished program designed to close gaps, a program that functions the same as Image (Tsai, 2010), but has been modified to scale up for large genome gap closing. As Image, this program aligns Illumina reads at contig ends, performs local assembly of reads into new contigs, extends or merges reference contigs, and runs multiple iterations of the whole process to extend and merge more contigs. We performed three iterations of gap closing for the Chrysemys assembly. We aligned the gap closed assembly version 3.0.3 to the NCBI publicly available Pelodiscus sinensis and Chelonia mydas assemblies using NUCmer, part of the MUMmer 3.0 package (Kurtz 2004). In both cases we used Chrysemys as the query assembly and the other turtle as the reference. We obtained best one to one reciprocal matches by using the -r and -q options. This is a list of all NUCmer options used: minInd=40; c=400; l=10; g=500; rearrange=" -r -q -o 1 "
 When scaffolds were identically ordered/oriented by alignments to P. sinensis and to C. mydas scaffolds the order/orientation provided by the alignments was introduced into the C. picta assembly. When scaffolds were ordered/oriented by a C. mydas or P. sinensis alignment and had the support of at least one BAC end sequence pair or by alignment to the chicken genome (galGal4), lizard (anoCar2), or alligator (allMis1) they were also introduced into the assembly. Similarly when a scaffold merge was suggested by alignment to the chicken, lizard or alligator genome and supported by at least a single BAC end pair, the scaffolds were joined into a single ultrascaffold. Finally alignments to finished BAC clones were used to identify additional ordered/oriented scaffolds. Using these data, we created 100 new ultra-scaffolds containing 259 scaffolds spanning almost 941Mb of sequence. The final assembly had a scaffold N50 of 6.6Mb with an N50 scaffold count of 102 (contig N50 size of 21.3kb and N50 contig count of 29,025). The resulting assembly was labeled as release 3.0.4.

 BACs were mapped to the C. picta chromosomes by Nicole Valenzuela. The resulting maps provided only order for the BACs and did not provide orientation information unless there were BAC end pairs providing connectivity between neighboring scaffolds. Chromosomal AGPs were created and centromeres were positioned using the Valenzuela BAC maps that localized 461Mb to 18 chromosomes.
 Background information on the Chrysemys picta bellii genome sequencing project and the initial news release about the Chrysemys picta bellii assembly can be found on the Washington University School of Medicine website.
 Bulk downloads of the sequence and annotation data are available via GenBank, Ensembl, DDBJ and the UCSC Genome Browser. The complete set of sequence reads is available at the NCBI trace archive.

 Credits: Genome Sequence - Washington University School of Medicine Sequence Assembly and Chromosomal Sequence/AGP Construction - Washington University School of Medicine BAC Mapping - Nicole Valenzuela - Iowa State University
 DNA sources: WGS library; UC-Davis Shaffer lab; Female; Chrysemys picta bellii ; Field number: RCT428 (This will later have an MVZ number assigned) ; Locality: WA: Grant Co: small lake 1.3 miles south of potholes reservoir BAC Library VMRC CHY3; J. Froula JGI (from C. Amemiya Lab) Female; Strain MVZ #238119; Locality: WA: Grant Co: small lake 1.3 miles south of potholes reservoir
 Read Types: 11.3X 454 fragments 6.5X 454 3 Kb inserts 1.3X 454 8 Kb inserts 0.06X Sanger BAC-end sequences
 Funding for the sequence characterization of the Chrysemys picta bellii genome is being provided by the National Human Genome Research Institute (NHGRI), National In  more

Global statistics

Total sequence length2,365,766,571
Total ungapped length2,173,204,098
Gaps between scaffolds56
Number of scaffolds78,631
Scaffold N506,605,846
Scaffold L50102
Number of contigs262,326
Contig N5021,349
Contig L5029,024
Total number of chromosomes and plasmids19
Number of component sequences (WGS or clone)262,326

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_000241775.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM002655.1=NC_024218.10
Chromosome 2CM002656.1=NC_024219.10
Chromosome 3CM002657.1=NC_024220.10
Chromosome 4CM002658.1=NC_024221.10
Chromosome 5CM002659.1=NC_024222.10
Chromosome 6CM002660.1=NC_024223.10
Chromosome 7CM002661.1=NC_024224.10
Chromosome 8CM002662.1=NC_024225.10
Chromosome 10CM002663.1=NC_024226.10
Chromosome 11CM002664.1=NC_024227.10
Chromosome 13CM002665.1=NC_024228.10
Chromosome 15CM002666.1=NC_024229.10
Chromosome 17CM002667.1=NC_024230.10
Chromosome 19CM002668.1=NC_024231.10
Chromosome 21CM002669.1=NC_024232.10
Chromosome 22CM002670.1=NC_024233.10
Chromosome 24CM002671.1=NC_024234.10
Chromosome 25CM002672.1=NC_024235.10
unplacedn/an/an/a78,576

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All2,365,749,69678,6302,173,187,2236,605,846183,69556
Chromosome 177,392,008970,782,87524,943,3645,5649
Chromosome 268,452,538662,810,54718,838,7234,8116
Chromosome 375,876,001670,752,29717,920,5974,9586
Chromosome 449,328,617645,351,63213,829,3273,1416
Chromosome 54,924,45523,682,0152,284,6062643
Chromosome 662,603,786557,595,95616,360,0384,2455
Chromosome 77,275,58415,818,4256,275,5846091
Chromosome 851,558,079846,627,1936,919,9733,9888
Chromosome 107,267,47315,670,0196,267,4736021
Chromosome 114,997,86313,778,5363,997,8632831
Chromosome 131,215,3342109,641214,394333
Chromosome 1519,094,261117,219,12618,094,2611,1031
Chromosome 174,552,50713,325,8643,552,5073201
Chromosome 199,077,46117,607,2288,077,4614871
Chromosome 211,374,4231339,741374,423421
Chromosome 222,511,00411,411,8841,511,0041251
Chromosome 2413,185,004111,645,69612,185,0047861
Chromosome 251,060,959154,93860,95981
unplaced1,904,002,33978,5761,758,603,6105,566,888152,3260
MoleculeTotal
Length
Mitochondrion MT16,875
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