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

Rao X, Krom N, Tang Y, Widiez T, Havkin-Frenkel D, Belanger FC, Dixon RA, Chen F - BMC Genomics (2014)

Bottom Line: 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.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.This database provides a general resource for further studies on this important flavor species.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA. Xiaolan.Rao@unt.edu.

ABSTRACT

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.

Show MeSH

Related in: MedlinePlus

Vanilla pod tissue samples for RNA isolation. (A) A six-week old vanilla pod cross section. The pods at earlier developmental stages were separated into three tissue samples (dark, light and seed). (B) A twelve-week old vanilla pod cross section. The pods at later developmental stages were separated into four tissue samples (mesocarp, placenta, hair cells, and seed).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4233054&req=5

Fig1: Vanilla pod tissue samples for RNA isolation. (A) A six-week old vanilla pod cross section. The pods at earlier developmental stages were separated into three tissue samples (dark, light and seed). (B) A twelve-week old vanilla pod cross section. The pods at later developmental stages were separated into four tissue samples (mesocarp, placenta, hair cells, and seed).

Mentions: To obtain an overview of V. planifolia gene expression profiles in different organs at different developmental stages, RNA was extracted and cDNA prepared from 26 different tissue samples. The tissue types within the pod are shown in FigureĀ 1, and the listing of all tissue samples given in Additional file 1. cDNA derived from RNA from the two biological replicates of each of the above tissue samples was sequenced by the Illumina platform, and a single pool of cDNA obtained by mixing all cDNA samples was sequenced using the Roche 454 platform. For the Illumina sequences, purity filtered reads ranged from 0.69 to 1.8 million reads per sample and the percentage of preserved reads ranged from 82.4% to 97.4%. Pooling of the Roche 454 sequencing runs resulted in 1,678,293 qualified reads with an average length of 397 bases after filtering and trimming (Additional file 2).Figure 1


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

Rao X, Krom N, Tang Y, Widiez T, Havkin-Frenkel D, Belanger FC, Dixon RA, Chen F - BMC Genomics (2014)

Vanilla pod tissue samples for RNA isolation. (A) A six-week old vanilla pod cross section. The pods at earlier developmental stages were separated into three tissue samples (dark, light and seed). (B) A twelve-week old vanilla pod cross section. The pods at later developmental stages were separated into four tissue samples (mesocarp, placenta, hair cells, and seed).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4233054&req=5

Fig1: Vanilla pod tissue samples for RNA isolation. (A) A six-week old vanilla pod cross section. The pods at earlier developmental stages were separated into three tissue samples (dark, light and seed). (B) A twelve-week old vanilla pod cross section. The pods at later developmental stages were separated into four tissue samples (mesocarp, placenta, hair cells, and seed).
Mentions: To obtain an overview of V. planifolia gene expression profiles in different organs at different developmental stages, RNA was extracted and cDNA prepared from 26 different tissue samples. The tissue types within the pod are shown in FigureĀ 1, and the listing of all tissue samples given in Additional file 1. cDNA derived from RNA from the two biological replicates of each of the above tissue samples was sequenced by the Illumina platform, and a single pool of cDNA obtained by mixing all cDNA samples was sequenced using the Roche 454 platform. For the Illumina sequences, purity filtered reads ranged from 0.69 to 1.8 million reads per sample and the percentage of preserved reads ranged from 82.4% to 97.4%. Pooling of the Roche 454 sequencing runs resulted in 1,678,293 qualified reads with an average length of 397 bases after filtering and trimming (Additional file 2).Figure 1

Bottom Line: 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.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.This database provides a general resource for further studies on this important flavor species.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA. Xiaolan.Rao@unt.edu.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus