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

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• 作者：Xiaolan Rao (8)
  Nick Krom (9)
  Yuhong Tang (9)
  Thomas Widiez (10) (11)
  Daphna Havkin-Frenkel (11)
  Faith C Belanger (11)
  Richard A Dixon (8)
  Fang Chen (8)
  
  8. Department of Biological Sciences ; University of North Texas ; 1155 Union Circle #305220 ; Denton ; TX ; 76203 ; USA
  9. Samuel Roberts Noble Foundation ; 2510 Sam Noble Parkway ; Ardmore ; OK ; 73402 ; USA
  10. Unit茅 Reproduction et D茅veloppement des Plantes ; INRA (UMR879)/CNRS (UMR5667)/Universit茅 de Lyon and Ecole Normale Sup茅rieure de Lyon ; 69364 ; Lyon ; France
  11. Department of Plant Biology and Pathology ; Rutgers ; The State University of New Jersey ; 59 Dudley Road ; New Brunswick ; NJ ; 08901 ; USA
  
• 关键词：Vanilla ; Vanilla planifolia ; Transcriptome ; RNA sequencing ; Lignin ; Vanillin
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：2,574 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

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.