PXD016522

PXD016522 is an original dataset announced via ProteomeXchange.

Title	A draft genome sequence of the elusive giant squid, Architeuthis dux
Description	We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
HostingRepository	PRIDE
AnnounceDate	2019-12-16
AnnouncementXML	Submission_2020-01-17_06:28:48.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mohammad Rahman
SpeciesList	scientific name: Architeuthis dux; NCBI TaxID: 256136;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-29 02:37:54	ID requested
1	2019-12-16 01:59:00	announced
⏵ 2	2020-01-17 06:28:49	announced	2020-01-17: Updated publication reference for PubMed record(s): 31942620.

da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro  M, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Fraz, ã, o B, Petersen B, Pe, ñ, aloza F, Musacchia F, Alexander GC, Os, ó, rio H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP, A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1):(2020) [pubmed]

submitter keyword: Cephalopod, invertebrate, genome assembly

Rute R. da Fonseca
contact affiliation	Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
contact email	rfonseca@bio.ku.dk
lab head
Mohammad Rahman
contact affiliation	Bioinformatics Solutions Inc
contact email	zrahman@bioinfor.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/12/PXD016522

PRIDE project URI

• PRIDE
  1. PXD016522
     1. Label: PRIDE project
     2. Name: A draft genome sequence of the elusive giant squid, Architeuthis dux