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
Lignin biosynthesis pathway and lignin-related gene expression in the early stage seeds and stems. (A) A simplified lignin biosynthesis pathway. (B) The expression levels of PAL, 4CL, CCR, CAD, C4H and CCoAOMT were represented as RPKM values in the light and dark pod tissues, seeds at 6, 8 and 10 weeks, and in stems. Each color represents one contig annotated as the corresponding class of lignin-related gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Lignin biosynthesis pathway and lignin-related gene expression in the early stage seeds and stems. (A) A simplified lignin biosynthesis pathway. (B) The expression levels of PAL, 4CL, CCR, CAD, C4H and CCoAOMT were represented as RPKM values in the light and dark pod tissues, seeds at 6, 8 and 10 weeks, and in stems. Each color represents one contig annotated as the corresponding class of lignin-related gene.

Mentions: Lignin is a phenylpropanoid polymer commonly found in terrestrial plant secondary cell walls. Lignin is assembled by oxidative polymerization of three major monolignols, p-hydroxycinnamyl alcohol (H unit), coniferyl alcohol (guaiacyl or G unit) and sinapyl alcohol (S unit). However, during the early stages of seed development in V. planifolia, a newly discovered polymer (C-lignin) is deposited to high concentrations in the seed coat. This lignin is naturally synthesized from the unusual monolignol caffeyl alcohol, whereas lignin in the vegetative tissues of V. planifolia is of the normal guaiacyl/syringyl (G/S) type [5]. To address potential pathways of C-lignin biosynthesis, we used annotated lignin pathway genes in Arabidopsis as query sequences (Figure 7A), searched by BlastX with the threshold as E-value <1E-5, and searched against the NCBI NR, GO and KEGG databases with the annotation of lignin pathway. Finally, 233 Vanilla genes were identified as homologous to genes potentially involved in the monolignol pathway (Additional file 14). These included genes encoding phenylalanine ammonia-lyase (PAL; 35 contigs), coumaroyl shikimate 3′-hydroxylase (C3′H; 5 contigs), cinnamate 4-hydroxylase (C4H; 14 contigs), 4-coumarate: CoA ligase (4CL; 41 contigs), cinnamoyl CoA reductase (CCR; 26 contigs), hydroxycinnamoyl CoA:shikimate hydroxycinnamoyl transferase (HCT; 9 contigs), caffeoyl-CoA 3-O-methyltransferase (CCoAOMT; 7 contigs), caffeic acid 3-O-methyltransferase (COMT; 1 contigs; characterized in [28, 29]), and caffeoyl-CoA O-methyltransferase-like (named as OMT-4 and OMT-5; 8 contigs; characterized in [30]), cinnamyl alcohol dehydrogenase (CAD; 23 contigs), caffeoyl shikimate esterase (CSE; 64 contigs) [31].Figure 7


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)

Lignin biosynthesis pathway and lignin-related gene expression in the early stage seeds and stems. (A) A simplified lignin biosynthesis pathway. (B) The expression levels of PAL, 4CL, CCR, CAD, C4H and CCoAOMT were represented as RPKM values in the light and dark pod tissues, seeds at 6, 8 and 10 weeks, and in stems. Each color represents one contig annotated as the corresponding class of lignin-related gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Lignin biosynthesis pathway and lignin-related gene expression in the early stage seeds and stems. (A) A simplified lignin biosynthesis pathway. (B) The expression levels of PAL, 4CL, CCR, CAD, C4H and CCoAOMT were represented as RPKM values in the light and dark pod tissues, seeds at 6, 8 and 10 weeks, and in stems. Each color represents one contig annotated as the corresponding class of lignin-related gene.
Mentions: Lignin is a phenylpropanoid polymer commonly found in terrestrial plant secondary cell walls. Lignin is assembled by oxidative polymerization of three major monolignols, p-hydroxycinnamyl alcohol (H unit), coniferyl alcohol (guaiacyl or G unit) and sinapyl alcohol (S unit). However, during the early stages of seed development in V. planifolia, a newly discovered polymer (C-lignin) is deposited to high concentrations in the seed coat. This lignin is naturally synthesized from the unusual monolignol caffeyl alcohol, whereas lignin in the vegetative tissues of V. planifolia is of the normal guaiacyl/syringyl (G/S) type [5]. To address potential pathways of C-lignin biosynthesis, we used annotated lignin pathway genes in Arabidopsis as query sequences (Figure 7A), searched by BlastX with the threshold as E-value <1E-5, and searched against the NCBI NR, GO and KEGG databases with the annotation of lignin pathway. Finally, 233 Vanilla genes were identified as homologous to genes potentially involved in the monolignol pathway (Additional file 14). These included genes encoding phenylalanine ammonia-lyase (PAL; 35 contigs), coumaroyl shikimate 3′-hydroxylase (C3′H; 5 contigs), cinnamate 4-hydroxylase (C4H; 14 contigs), 4-coumarate: CoA ligase (4CL; 41 contigs), cinnamoyl CoA reductase (CCR; 26 contigs), hydroxycinnamoyl CoA:shikimate hydroxycinnamoyl transferase (HCT; 9 contigs), caffeoyl-CoA 3-O-methyltransferase (CCoAOMT; 7 contigs), caffeic acid 3-O-methyltransferase (COMT; 1 contigs; characterized in [28, 29]), and caffeoyl-CoA O-methyltransferase-like (named as OMT-4 and OMT-5; 8 contigs; characterized in [30]), cinnamyl alcohol dehydrogenase (CAD; 23 contigs), caffeoyl shikimate esterase (CSE; 64 contigs) [31].Figure 7

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