PXD019784-2

PXD019784 is an original dataset announced via ProteomeXchange.

Title	Hypoxis hemerocallidea (Afrtican potato) corm, leaf and flower transcriptomics and proteomics
Description	The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions, such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours amongst others. The metabolites of H. hemerocallidea have been identified in several studies. More recently, the terpenoids of the plant have been identified. However, the biochemical pathways and the enzymes involved in the production of metabolites have not been characterised. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated between the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues was sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase and cycloartenol synthase amongst others. Transcripts were also annotated to encode for the terpene phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:23:16.304.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Silviu Tomescu
SpeciesList	scientific name: Hypoxis hemerocallidea; NCBI TaxID: 862860;
ModificationList	alkylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-15 05:06:25	ID requested
1	2021-06-23 11:19:45	announced
⏵ 2	2024-10-22 05:23:16	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: transcriptome, secondary metabolism, terpene biosynthesis., differential expression, proteome,African potato

Karl Rumbold
contact affiliation	Industrial Microbiology and Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, South Africa.
contact email	Karl.Rumbold@wits.ac.za
lab head
Silviu Tomescu
contact affiliation	Researcher
contact email	silviu.mihai.tomescu@gmail.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/2021/06/PXD019784

PRIDE project URI

• PRIDE
  1. PXD019784
     1. Label: PRIDE project
     2. Name: Hypoxis hemerocallidea (Afrtican potato) corm, leaf and flower transcriptomics and proteomics