Cargando…

A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)

BACKGROUND: Pods of the vanilla orchid (Vanilla planifolia) accumulate large amounts of the flavor compound vanillin (3-methoxy, 4-hydroxy-benzaldehyde) as a glucoside during the later stages of their development. At earlier stages, the developing seeds within the pod synthesize a novel lignin polym...

Descripción completa

Detalles Bibliográficos
Autores principales: Rao, Xiaolan, Krom, Nick, Tang, Yuhong, Widiez, Thomas, Havkin-Frenkel, Daphna, Belanger, Faith C, Dixon, Richard A, Chen, Fang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233054/
https://www.ncbi.nlm.nih.gov/pubmed/25380694
http://dx.doi.org/10.1186/1471-2164-15-964
_version_ 1782344678958432256
author Rao, Xiaolan
Krom, Nick
Tang, Yuhong
Widiez, Thomas
Havkin-Frenkel, Daphna
Belanger, Faith C
Dixon, Richard A
Chen, Fang
author_facet Rao, Xiaolan
Krom, Nick
Tang, Yuhong
Widiez, Thomas
Havkin-Frenkel, Daphna
Belanger, Faith C
Dixon, Richard A
Chen, Fang
author_sort Rao, Xiaolan
collection PubMed
description BACKGROUND: Pods of the vanilla orchid (Vanilla planifolia) accumulate large amounts of the flavor compound vanillin (3-methoxy, 4-hydroxy-benzaldehyde) as a glucoside during the later stages of their development. At earlier stages, the developing seeds within the pod synthesize a novel lignin polymer, catechyl (C) lignin, in their coats. Genomic resources for determining the biosynthetic routes to these compounds and other flavor components in V. planifolia are currently limited. RESULTS: Using next-generation sequencing technologies, we have generated very large gene sequence datasets from vanilla pods at different times of development, and representing different tissue types, including the seeds, hairs, placental and mesocarp tissues. This developmental series was chosen as being the most informative for interrogation of pathways of vanillin and C-lignin biosynthesis in the pod and seed, respectively. The combined 454/Illumina RNA-seq platforms provide both deep sequence coverage and high quality de novo transcriptome assembly for this non-model crop species. CONCLUSIONS: The annotated sequence data provide a foundation for understanding multiple aspects of the biochemistry and development of the vanilla bean, as exemplified by the identification of candidate genes involved in lignin biosynthesis. Our transcriptome data indicate that C-lignin formation in the seed coat involves coordinate expression of monolignol biosynthetic genes with the exception of those encoding the caffeoyl coenzyme A 3-O-methyltransferase for conversion of caffeoyl to feruloyl moieties. This database provides a general resource for further studies on this important flavor species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-964) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4233054
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-42330542014-11-17 A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia) Rao, Xiaolan Krom, Nick Tang, Yuhong Widiez, Thomas Havkin-Frenkel, Daphna Belanger, Faith C Dixon, Richard A Chen, Fang BMC Genomics Research Article BACKGROUND: Pods of the vanilla orchid (Vanilla planifolia) accumulate large amounts of the flavor compound vanillin (3-methoxy, 4-hydroxy-benzaldehyde) as a glucoside during the later stages of their development. At earlier stages, the developing seeds within the pod synthesize a novel lignin polymer, catechyl (C) lignin, in their coats. Genomic resources for determining the biosynthetic routes to these compounds and other flavor components in V. planifolia are currently limited. RESULTS: Using next-generation sequencing technologies, we have generated very large gene sequence datasets from vanilla pods at different times of development, and representing different tissue types, including the seeds, hairs, placental and mesocarp tissues. This developmental series was chosen as being the most informative for interrogation of pathways of vanillin and C-lignin biosynthesis in the pod and seed, respectively. The combined 454/Illumina RNA-seq platforms provide both deep sequence coverage and high quality de novo transcriptome assembly for this non-model crop species. CONCLUSIONS: The annotated sequence data provide a foundation for understanding multiple aspects of the biochemistry and development of the vanilla bean, as exemplified by the identification of candidate genes involved in lignin biosynthesis. Our transcriptome data indicate that C-lignin formation in the seed coat involves coordinate expression of monolignol biosynthetic genes with the exception of those encoding the caffeoyl coenzyme A 3-O-methyltransferase for conversion of caffeoyl to feruloyl moieties. This database provides a general resource for further studies on this important flavor species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-964) contains supplementary material, which is available to authorized users. BioMed Central 2014-11-07 /pmc/articles/PMC4233054/ /pubmed/25380694 http://dx.doi.org/10.1186/1471-2164-15-964 Text en © Rao et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Rao, Xiaolan
Krom, Nick
Tang, Yuhong
Widiez, Thomas
Havkin-Frenkel, Daphna
Belanger, Faith C
Dixon, Richard A
Chen, Fang
A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)
title A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)
title_full A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)
title_fullStr A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)
title_full_unstemmed A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)
title_short A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia)
title_sort deep transcriptomic analysis of pod development in the vanilla orchid (vanilla planifolia)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233054/
https://www.ncbi.nlm.nih.gov/pubmed/25380694
http://dx.doi.org/10.1186/1471-2164-15-964
work_keys_str_mv AT raoxiaolan adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT kromnick adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT tangyuhong adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT widiezthomas adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT havkinfrenkeldaphna adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT belangerfaithc adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT dixonricharda adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT chenfang adeeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT raoxiaolan deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT kromnick deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT tangyuhong deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT widiezthomas deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT havkinfrenkeldaphna deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT belangerfaithc deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT dixonricharda deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia
AT chenfang deeptranscriptomicanalysisofpoddevelopmentinthevanillaorchidvanillaplanifolia