Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).

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. The metabolites contributing to the medicinal propert...

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Autores principales:	Mihai-Silviu Tomescu, Selisha Ann Sooklal, Thuto Ntsowe, Previn Naicker, Barbara Darnhofer, Robert Archer, Stoyan Stoychev, Dirk Swanevelder, Ruth Birner-Grünberger, Karl Rumbold
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/57f72680fb45434fbf63e10112158680
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spelling	oai:doaj.org-article:57f72680fb45434fbf63e101121586802021-12-02T20:09:05ZTranscriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).1932-620310.1371/journal.pone.0253741https://doaj.org/article/57f72680fb45434fbf63e101121586802021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253741https://doaj.org/toc/1932-6203The 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. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. 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 using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were 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. Annotations also revealed a transcript encoding the terpene synthase 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.Mihai-Silviu TomescuSelisha Ann SooklalThuto NtsowePrevin NaickerBarbara DarnhoferRobert ArcherStoyan StoychevDirk SwanevelderRuth Birner-GrünbergerKarl RumboldPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0253741 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mihai-Silviu Tomescu Selisha Ann Sooklal Thuto Ntsowe Previn Naicker Barbara Darnhofer Robert Archer Stoyan Stoychev Dirk Swanevelder Ruth Birner-Grünberger Karl Rumbold Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).
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. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. 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 using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were 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. Annotations also revealed a transcript encoding the terpene synthase 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.
format	article
author	Mihai-Silviu Tomescu Selisha Ann Sooklal Thuto Ntsowe Previn Naicker Barbara Darnhofer Robert Archer Stoyan Stoychev Dirk Swanevelder Ruth Birner-Grünberger Karl Rumbold
author_facet	Mihai-Silviu Tomescu Selisha Ann Sooklal Thuto Ntsowe Previn Naicker Barbara Darnhofer Robert Archer Stoyan Stoychev Dirk Swanevelder Ruth Birner-Grünberger Karl Rumbold
author_sort	Mihai-Silviu Tomescu
title	Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).
title_short	Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).
title_full	Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).
title_fullStr	Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).
title_full_unstemmed	Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).
title_sort	transcriptome and proteome of the corm, leaf and flower of hypoxis hemerocallidea (african potato).
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/57f72680fb45434fbf63e10112158680
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Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato).

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