The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms

Authors: LI, ZE - Central South University Of Forestry And Technology; LONG, HONGXU - Central South University Of Forestry And Technology; ZHANG, LIN - Central South University; LIU, ZHIMING - Central South University; Cao, Heping; SHI, MINGWANG - Henan Institute Of Science And Technology; TAN, XIAOFENG - Central South University Of Forestry And Technology

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2017
Publication Date: 5/12/2017
Citation: Li, Z., Long, H., Zhang, L., Liu, Z., Cao, H., Shi, M., Tan, X. 2017. The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms. Scientific Reports. 7(1):1869. https://doi.org/10.1038/s41598-017-02076-6.
DOI: https://doi.org/10.1038/s41598-017-02076-6

Interpretive Summary: Tung tree (Vernicia fordii) belongs to the family Euphorbiaceae of woody angiosperms. It is a native tree species being cultivated for more than 1,000 years in China. Tung tree grows fast, blossoms and yields fruits in three years due to high efficiency of photosynthesis. Tung oil extracted from seed kernels is of high value because it contains 80% of eleostearic acid. Tung oil possesses excellent features such as fast drying, excellent adhesion, resisting to acid & alkali, frost crack and many chemical treatments. Unlike other drying oils, it does not darken with age. These properties underlie the value of tung oil as a drying ingredient in paints, varnishes, and other coatings and finishes. In recent years, the rapid growth of the population and economic development creates severe energy crisis and ecological environment problems. However, recent research has shown that tung oil can be used as a raw material for producing biodiesel, and therefore tung tree would be one of the most promising biomass species to resolve energy shortage problem. One approach to improving tung oil production would be to engineer chloroplasts with more efficient photosynthesis in tung tree leaves. Sequencing the complete chloroplast genome would facilitate the chloroplast transformation technique because the transformation of chloroplast genome has many advantages over nuclear transformation including a high level of transgene expression, lack of gene silencing or positional effect and transgene containment. We present the first complete nucleotide sequence of tung tree cp genome using PacBio RS II sequencing platforms. The tung tree chloroplast genome (161,524 bp) was fully characterized and compared to other chloroplast genomes of related species. We identified a pair of inverted repeat regions, one large single copy region and one small single copy region. The tung tree cp genome coded for 114 unique genes including 82 protein-coding genes, 28 transfer RNAs and four ribosomal RNAs. The data presented in this paper will be very valuable for further studies of phylogenetics and evolution as well as tree improvement by genetic engineering via chloroplast transformation of this important woody oil tree.

Technical Abstract: Tung tree (Vernicia fordii) is an economically important plant widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized the complete chloroplast genome. The chloroplast genome was 161,524 bp in length and contained a pair of inverted repeat (IR) regions (26,819 bp), one large single copy region (89,130 bp), and one small single copy (SSC) region (18,756 bp). The genome coded for 114 unique genes, including 82 protein-coding genes, 28 transfer RNAs, and four ribosomal RNAs. Eighty-one simple sequence repeats with more than 10 repeated motifs were identified in the tung tree chloroplast genome. Eight-five single nucleotide polymorphisms (SNPs) and 82 indels were found in V. fordii by comparing its sequences with those of J. carcass; whereas 86 SNPs and 81 indels were found in V. fordii by comparing with M. esculenta. The tung tree chloroplast genome showed an extreme expansion at the IR/SSC boundary owing to the integration of an additional rps19 gene in the IRb region. Phylogenetic analysis demonstrated that V. fordii was a basal member of the Malpighiales and closer to Jatropha carcas in the Euphorbiaceae and that there is a sister relationship between Malpighiales and Rosales.