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Cebus_imitator-1.0

Organism name:
Cebus imitator (Panamanian white-faced capuchin)
Isolate:
Cc_AM_T3
Sex:
male
BioSample:
SAMN04522148
BioProject:
PRJNA298580
Submitter:
McDonnell Genome Institute - Washington University School of Medicine
Date:
2016/04/04
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_001604975.1 (latest)
RefSeq assembly accession:
GCF_001604975.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
LVWQ01
Assembly method:
AllPaths-LG v. October 2015
Genome coverage:
81x
Sequencing technology:
Illumina

IDs: 716501 [UID] 3160568 [GenBank] 3333648 [RefSeq]

See Genome Information for Cebus imitator

History (Show revision history)

Comment

Cebus capucinus imitator (white-faced capuchin) Sequence Assembly Release Notes Background: Native to the forests of Central America and the extreme northwestern portion of South America, the white-faced (or white-headed) capuchin, Cebus capucinus, is a highly omnivorous and extractive forager ... that is important to rainforest ecology for its role in dispersing seeds and pollen. Among the most intelligent monkeys, capuchins have been trained to assist paraplegic persons and have been the subject of many studies on behavior and intelligence. Recent research has documented a rich repertoire of group-specific social conventions in Cebus capucinus. It is a medium-sized monkey, weighing up to 3.9 kg (8.6 lb) with a mostly black body color, but a pinkish face and white fur on much of the front part of the body. 
 The Cebus capucinus imitator DNA for shotgun sequencing is derived from an adult male (id no. Cc_AM_T3) that was killed by a vehicle in Costa Rica. Samples were transported to the laboratory of Dr. Amanda Melin at Washington University in St Louis, MO under CITES export permit 2015-CR1258/SJ (no. S 1320).
 Total sequence genome input coverage on the Illumina HiSeq 2500 instrument was approx. 81x (50x fragments, 26x 3kbs, and 5x 8kbs) using a genome size estimate of 3.0Gb. The combined sequence reads were assembled using ALLPATHS-LG software (Gnerre et al. 2011). This 1.0 version has been cleaned of contaminating contigs, and contigs 200bp and less were removed. The assembly is made up of a total of 7156 scaffolds (including single contig scaffolds) with an N50 scaffold length of 5.1Mb (N50 contig length was 41kb). The total assembled bases is almost 2.72Gb. 
 This work was supported by Washington University in St. Louis and The Eppley Foundation to Dr. Amanda Melin and the Grant-in-Aid for Scientific Research (A) (15H02421) from Japan Society for the Promotion of Science (JSPS) to Dr. Shoji Kawamura.
 Cebus capucinus imitator 1.0 Sequence and Assembly Credits: DNA Source Contact: Dr. Amanda Melin at Washington University in St. Louis, St Louis, MO. DNA source - Dr. Amanda Melin at Washington University in St Louis, St. Louis MO. Genome Sequence - McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO. Sequence Assembly - McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO.
 Citation upon use of this assembly in a manuscript: It is requested that users of this Cebus capucinus imitator 1.0 sequence assembly acknowledge Dr. Amanda Melin at Washington University in St. Louis, Dr. Shoji Kawamura at University of Tokyo, and Dr. Wesley Warren, McDonnell Genome Institute, Washington University School of Medicine in any publications that result from use of this sequence assembly.
 Cebus capucinus imitator 1.0 assembly statistics: (scaffold = supercontig) A 200bp contig size cutoff was applied.
 *** Contiguity: Contig *** Total contig number: 140637 Total contig bases: 2610524060 bp Average contig length: 18562 bp Maximum contig length: 458127 bp N50 contig length: 41196 bp N50 contig number: 17654
 *** Contiguity: Supercontig *** Total supercontig number: 7156 Total supercontig bases: 2.71772 Gbp Average supercontig length: 364802 bp Maximum supercontig length: 20393540 bp N50 supercontig length: 5132539 bp N50 supercontig number: 147
 *** Scaffold Distribution *** Scaffolds > 1M: 590 Scaffold 250K--1M: 277 Scaffold 100K--250K: 122 Scaffold 10--100K: 381 Scaffold 5--10K: 281 Scaffold 2--5K: 1510 Scaffold 0--2K: 3995  more

Global statistics

Total sequence length2,717,703,182
Total ungapped length2,610,518,382
Gaps between scaffolds0
Number of scaffolds7,156
Scaffold N505,274,112
Scaffold L50149
Number of contigs140,597
Contig N5041,196
Contig L5017,654
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)140,597

Supplemental Content

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Global assembly definition

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Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced2,717,703,1827,1562,610,518,3825,274,112133,4410
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