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Transcriptome of tung tree mature seeds with an emphasis on lipid metabolism genes

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Abstract

Tung oil, the major product of tung tree (Vernicia fordii) seeds, is one of the highest quality oils for industrial applications and has been considered for the production of biodiesel. Considering the poor agronomical traits of this crop, efforts have been made to breed tung trees for a higher fruit yield and oil property modification for biodiesel use or to engineer plants to produce a higher tung oil yield. However, these efforts have been hampered by a lack of molecular information, as there is no available genome and identified and characterized transcripts of this tree are scarce. Furthermore, there are still many knowledge gaps regarding tung oil biosynthesis. To provide a comprehensive and accurate foundation for molecular studies of tung tree, we present here a reference transcriptome dataset of mature tung seeds. A set of 43,081,927 reads were assembled into 47,585 unigenes. A homology search using blastx against the GenBank nonredundant protein database and the Swiss-Prot database resulted in the annotation of 96 and 81 % of these unigenes, respectively. We also systematically arranged a series of unigenes potentially associated with oil biosynthesis and degradation and examined the expression profile of a subset of those genes in samples from five different stages of seed development, providing a valuable source of genes and transcriptional information related to these pathways. This study represents the first large-scale transcriptome annotation of tung tree and will be useful in tung breeding for oil properties and other agronomical traits.

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Acknowledgments

This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) grant number 559636/2009-1, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Fundação de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS), Financiadora de Projetos (FINEP), Embrapa, Petrobrás, and Ministério de Ciência e Tecnologia (MCT).

Data Archiving Statement

The RNA-Seq data and the transcriptome of tung tree seeds are currently been submitted to GenBank as Gene Expression Omnibus (GEO) data libraries. The accession numbers will be supplied once available.

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Authors and Affiliations

  1. Centro de Biotecnologia, PPGBCM, Laboratório de Genomas e População de Plantas, prédio 43431, Universidade Federal do Rio Grande do Sul-UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, Rio Grande do Sul, Brazil

    Vanessa Galli & Rogério Margis

  2. Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA, P.O. Box 403, CEP 96010-971, Pelotas, Rio de Grande do Sul, Brazil

    Vanessa Galli, Rafael S. Messias & Sérgio D. A. Silva

  3. PPGGBM, Universidade Federal do Rio Grande do Sul-UFRGS, P.O. Box 15005, CEP 91501-970, Porto Alegre, Rio Grande do Sul, Brazil

    Frank Guzman, Ana P. Körbes, Márcia Margis-Pinheiro & Rogério Margis

Authors
  1. Vanessa Galli
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  2. Frank Guzman
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  3. Rafael S. Messias
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  4. Ana P. Körbes
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  5. Sérgio D. A. Silva
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  6. Márcia Margis-Pinheiro
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  7. Rogério Margis
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Correspondence to Rogério Margis.

Additional information

Communicated by J. F. D. Dean

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Figure S1

The five stages of fruit development used to obtain seeds for RT-qPCR analysis. S1: 20 days after flower opening (DAF); S2: 35 DAF; S3: 50 DAF; S4: 80 DAF; S5: 100 DAF. (GIF 21 kb)

High Resolution Image (TIFF 662 kb)

Figure S2

Distribution of tung contigs in metabolic pathways. The graphic representation of assigned metabolic pathways was obtained with the IPATH2 software (http://pathways.embl.de/ipath2) using the Blastall annotation. (PDF 402 kb)

Table S1

Primers used for RT-qPCR analysis. (XLSX 9 kb)

Table S2

Annotation of tung contigs according to the alignment against the GenBank non-redundant protein database (NR). The tung transcriptome contigs were utilized for homology searches against non-redundant sequences from NCBI (http://www.ncbi.nlm.nih.gov/) by applying the BLASTX program (e-value<1e-6). The bit score and e-value of the alignment, nucleotide and protein accession number, length, coding sequence (CDS) structure, and species with homologous sequences are presented. (XLSX 4555 kb)

Table S3

Annotation of tung contigs according to the alignment against the Swiss-Prot database. Contigs of the tung transcriptome were utilized for homology searches against protein sequences from the Swiss-Prot database (http://www.expasy.ch/sprot/) by applying the BLASTX program (e-value<1e-6). The bit score and e-value of the alignment, nucleotide and protein accession number, length, and species with homologous sequences are presented. (XLSX 3638 kb)

Table S4

KEGG annotation for tung contigs. KEGG pathway annotations were performed using the Blastall software against the KEGG databases (http://www.genome.jp/kegg/). (XLSX 1013 kb)

Table S5

The 50 most highly expressed contigs in tung seeds. The number of reads was calculated based on the alignment of the reads from RNA-Seq against the contigs. (XLSX 11 kb)

Table S6

Contigs related to oil biosynthesis in mature tung seeds. The BLASTX annotation against the Swiss-Prot and non-redundant sequence databases were used to search for sequences involved in oil biosynthesis. (XLSX 95 kb)

Table S7

Contigs related to oil breakdown in tung seeds. The BLASTX annotation against the Swiss-Prot and non-redundant sequence databases were used to search for sequences involved in oil breakdown. (XLSX 42 kb)

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Galli, V., Guzman, F., Messias, R.S. et al. Transcriptome of tung tree mature seeds with an emphasis on lipid metabolism genes. Tree Genetics & Genomes 10, 1353–1367 (2014). https://doi.org/10.1007/s11295-014-0765-6

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  • DOI: https://doi.org/10.1007/s11295-014-0765-6

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