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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.

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Tissue-specific gene expression heatmap. Transcripts with RPKM values at least three times as high in the indicated tissue than in any other tissues were selected and clustered using R with the package ‘rsgcc’. The color scale indicates the tissue specificity score associated with all transcripts preferentially expressed in the various tissues and organs. The tissue specificity score is 1, if the gene is only expressed in one tissue.
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Fig6: Tissue-specific gene expression heatmap. Transcripts with RPKM values at least three times as high in the indicated tissue than in any other tissues were selected and clustered using R with the package ‘rsgcc’. The color scale indicates the tissue specificity score associated with all transcripts preferentially expressed in the various tissues and organs. The tissue specificity score is 1, if the gene is only expressed in one tissue.

Mentions: Knowledge of genes that are expressed specifically in one organ or tissue, or genes that are expressed at substantially higher levels in some organs/tissues than in others can provide insights into specialized processes at work in these organs/tissues [20]. To detect genes with tissue-restricted expression, all transcripts were filtered to obtain those above 10 RPKM value in at least one tissue or organ, then further analysed in R with the package “rsgcc” [23], setting the parameter value as “0.75”, which means that the expression level of a gene must be at least 3 times higher in one tissue than in any other tissue. We found 590 genes that were exclusively expressed in 6 week seeds, and 83 genes exclusively expressed in 8 week seeds. Eighty seven genes were more highly expressed in leaf than in any other organ; 119 genes were more highly expressed in aerial roots; and 93 genes were more highly expressed in the 1 year old stem (Additional file 12). These data are summarized in the heatmap in Figure 6.Figure 6


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)

Tissue-specific gene expression heatmap. Transcripts with RPKM values at least three times as high in the indicated tissue than in any other tissues were selected and clustered using R with the package ‘rsgcc’. The color scale indicates the tissue specificity score associated with all transcripts preferentially expressed in the various tissues and organs. The tissue specificity score is 1, if the gene is only expressed in one tissue.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Tissue-specific gene expression heatmap. Transcripts with RPKM values at least three times as high in the indicated tissue than in any other tissues were selected and clustered using R with the package ‘rsgcc’. The color scale indicates the tissue specificity score associated with all transcripts preferentially expressed in the various tissues and organs. The tissue specificity score is 1, if the gene is only expressed in one tissue.
Mentions: Knowledge of genes that are expressed specifically in one organ or tissue, or genes that are expressed at substantially higher levels in some organs/tissues than in others can provide insights into specialized processes at work in these organs/tissues [20]. To detect genes with tissue-restricted expression, all transcripts were filtered to obtain those above 10 RPKM value in at least one tissue or organ, then further analysed in R with the package “rsgcc” [23], setting the parameter value as “0.75”, which means that the expression level of a gene must be at least 3 times higher in one tissue than in any other tissue. We found 590 genes that were exclusively expressed in 6 week seeds, and 83 genes exclusively expressed in 8 week seeds. Eighty seven genes were more highly expressed in leaf than in any other organ; 119 genes were more highly expressed in aerial roots; and 93 genes were more highly expressed in the 1 year old stem (Additional file 12). These data are summarized in the heatmap in Figure 6.Figure 6

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