PXD008508

PXD008508 is an original dataset announced via ProteomeXchange.

Title	Proteogenomic refinement of the Neomegalonema perideroedes genome annotation
Description	Neomegalonema perideroedes (formerly Meganema perideroedes) str. G1 is the type strain and only described isolate of the genus Neomegalonema (formerly Meganema). N. perideroedes is distinguished by the ability to accumulate high amounts of polyhydroxyalkanoates and has been associated with bulking problems in wastewater treatment plants due to its filamentous morphology. In 2013, its genome was sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which aims to improve the sequencing coverage of the poorly represented regions of the bacterial and archaeal branches of the tree of life. As N. perideroedes str. G1 is relatively distantly related to well described species – being the only sequenced member of its proposed family - the in silico prediction of genes by nucleotide homology to reference genes might be less reliable. The aim of this study was to improve the genome annotation by usage of proteomic data. Besides the identification of novel and overlooked genes, the N-terminal cleavage pattern and the differences between databases were considered. Proteogenomic approaches, such as is described here, complements the GEBA initiative well - by providing important refinement of reference genome annotations.
HostingRepository	PRIDE
AnnounceDate	2019-03-20
AnnouncementXML	Submission_2019-03-20_04:43:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Florian-Alexander Herbst
SpeciesList	scientific name: Meganema perideroedes; NCBI TaxID: 217219;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-20 01:05:58	ID requested
⏵ 1	2019-03-20 04:43:09	announced

Herbst FA, Gon, ç, alves SCL, Behr T, McIlroy SJ, Nielsen PH, Genome Annotation. Proteomics, 19(9):e1800330(2019) [pubmed]

curator keyword: Biological

submitter keyword: Meganema, wastewater treatment, bulking, PHA, proteogenomics

Per H. Nielsen
contact affiliation	Aalborg University Department of Chemistry and Bioscience 9220 Aalborg, Denmark
contact email	phn@bio.aau.dk
lab head
Florian-Alexander Herbst
contact affiliation	Aalborg University
contact email	fah@bio.aau.dk
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/2019/03/PXD008508

PRIDE project URI

• PRIDE
  1. PXD008508
     1. Label: PRIDE project
     2. Name: Proteogenomic refinement of the Neomegalonema perideroedes genome annotation