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 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.
Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA. Xiaolan.Rao@unt.edu.
Xiaolan
X
Rao
Nick
N
Krom
Yuhong
Y
Tang
Thomas
T
Widiez
Daphna
D
Havkin-Frenkel
Faith C
FC
Belanger
Richard A
RA
Dixon
Fang
F
Chen
D001547:Benzaldehydes / Q000378:metabolism; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D008031:Lignin / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D018547:Plant Stems / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012015:Reference Standards; D015203:Reproducibility of Results; D012639:Seeds / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D031669:Vanilla / Q000235:genetics* / Q000254:growth & development*
D001547:Benzaldehydes; D012333:RNA, Messenger; D008031:Lignin; C100058:vanillin