PXD017093

PXD017093 is an original dataset announced via ProteomeXchange.

Title	A Spirodela polyrhiza genome and proteome reveal conserved chromosomal structure and translation favoring energy production
Description	Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. We generated a highly contiguous, chromosome-scale assembly of Spirodela polyrhiza line Sp7498 using Oxford Nanopore plus Hi-C scaffolding (Sp7498_HiC) that is highly syntenic with a related line (Sp9509). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations in a recent PacBio assembly of Sp7498, highlighting the necessity of orthogonal long-range scaffolding techniques like Hi-C and BioNano optical mapping. Proteome analysis of Sp7498 verified the expression of nearly 2,250 proteins and revealed a high level of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome, demonstrates that duckweed is a model for genomics- and proteomics-based education.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:00:34.864.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fionn McLoughlin
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-14 07:52:12	ID requested
1	2022-10-26 08:48:06	announced
⏵ 2	2023-11-14 08:00:38	announced	2023-11-14: Updated project metadata.

Harkess A, McLoughlin F, Bilkey N, Elliott K, Emenecker R, Mattoon E, Miller K, Czymmek K, Vierstra RD, Meyers BC, Michael TP, Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production. J Exp Bot, 72(7):2491-2500(2021) [pubmed]

submitter keyword: Arabidopsis,Spyrodela, proteome composition

Alex Harkess
contact affiliation	Auburn University, Alabama
contact email	AHarkess@danforthcenter.org
lab head
Fionn McLoughlin
contact affiliation	Washington University in Saint Louis
contact email	fmcloughlin@wustl.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017093
     1. Label: PRIDE project
     2. Name: A Spirodela polyrhiza genome and proteome reveal conserved chromosomal structure and translation favoring energy production