Tung tree (Vernicia fordii) genome provides a resource for understanding genome evolution and improved oil production

Authors: ZHANG, LIN - Central South University Of Forestry And Technology; LIU, MEILAN - Central South University Of Forestry And Technology; LONG, HONGXU - Central South University Of Forestry And Technology; DONG, WEI - Fujian Agriculture And Forest University; PASHA, ASHER - University Of Toronto; ESTEBAN, ASHERK - University Of Toronto; LI, WENYING - Central South University Of Forestry And Technology; YANG, XIAOMING - Nanjing Forestry University; LI, ZE - Central South University Of Forestry And Technology; SONG, AIXIA - Fujian Agriculture And Forest University; RAN, DUO - Central South University Of Forestry And Technology; ZHAO, GUANG - Central South University Of Forestry And Technology; ZENG, YANLING - Central South University Of Forestry And Technology; CHEN, HAO - Central South University Of Forestry And Technology; ZOU, MING - Nextomics Biosciences Co, Ltd; LI, JINGJING - Nextomics Biosciences Co, Ltd; LIANG, FAN - Nextomics Biosciences Co, Ltd; XIE, MEILI - Chinese Academy Of Agricultural Sciences; HU, JIANG - Nextomics Biosciences Co, Ltd; WANG, DEPENG - Nextomics Biosciences Co, Ltd; Cao, Heping; PROVART, NICHOLAS - University Of Toronto; ZHANG, LIANGSHENG - Fujian Agriculture And Forest University; TAN, XIAOFENG - Central South University Of Forestry And Technology

Submitted to: Genomics, Proteomics and Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/29/2019
Publication Date: 5/6/2020
Citation: Zhang, L., Liu, M., Long, H., Dong, W., Pasha, A., Esteban, E., Li, W., Yang, X., Li, Z., Song, A., Ran, D., Zhao, G., Zeng, Y., Chen, H., Zou, M., Li, J., Liang, F., Xie, M., Hu, J., Wang, D., Cao, H., Provart, N.J., Zhang, L., Tan, X. 2020. Tung tree (Vernicia fordii) genome provides a resource for understanding genome evolution and improved oil production. Genomics, Proteomics and Bioinformatics. 17(6):558-575. https://doi.org/10.1016/j.gpb.2019.03.006.
DOI: https://doi.org/10.1016/j.gpb.2019.03.006

Interpretive Summary: Tung tree is a native woody oil plant in subtropical areas of China. Tung tree taxonomically belongs to the Euphorbiaceae family, along with several other economically important species including cassava, castor oil plant, rubber tree and physic nut. Tung trees have been planted for the production of tung oil or cultured as ornamental plants for more than 1000 years in China. Tung trees have been widely distributed in 16 Chinese provinces and many countries after they were introduced into America, Argentina, and Paraguay and other countries for plantation and tung oil production at the beginning of the 20th century. Tung seeds contain 50-60% tung oil. Tung oil has been widely used as a drying ingredient in paints, varnishes, coating and finishes since ancient times. Tung oil also can be used for synthesizing thermosetting polymers and resins with superior properties. As an oil crop, economic traits involved in fatty acid biosynthesis and oil accumulation are the targets of improved breeding efficiency for tung tree. However, identification of genes or gene families and marker loci associated with oil content, fatty acid composition, and fruit yield has been hampered due to a lack of genetic and genomic information. We report in this manuscript the sequencing and assembly of tung tree genome. We conducted evolutionary comparisons and comprehensive transcriptome analysis of genes involved in oil biosynthesis to elucidate the genetic characteristics of oil synthesis and genetic difference as compared to other plant species. We provided a more complete picture for oil biosynthesis pathways, evaluated developmental expression of key oil biosynthesis-related genes, and revealed gene co-expression networks involved in oil accumulation. The tung tree genome and transcriptome sequences and major genes identified in oil biosynthesis and disease-resistance should provide valuable resources for molecular breeding and genetic improvement.

Technical Abstract: Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil containing a high proportion (~80%) of eleostearic acid. Here we report a high-quality, chromosome-scale tung tree genome sequence of 1.12 Gb with 28,422 predicted genes and over 73% repeat sequences. Tung tree genome was assembled by combining illumine short reads, PacBio single-molecule real-time long reads and Hi-C sequencing data. Insertion time analysis revealed that the repeat-driven tung tree genome expansion might be due to long standing LTR retrotransposon bursts and lack of efficient DNA delete mechanisms. An electronic fluorescent pictographic (eFP) browser was generated based on genomic data and RNA-seq data from 17 various tissues and developmental stages. We identified 88 resistant nucleotide-binding sites (NBS)-encoding genes of which 17 genes may help the tung tree resist the Fusarium wilt shortly after infection. A total of 651 oil-related genes were identified and 88 of them were predicted to be directly involved in tung oil biosynthesis. We provided a more complete picture for oil biosynthesis pathways, evaluated developmental expression of key oil biosynthesis-related genes, and revealed gene co-expression networks involved in oil accumulation. The tung tree genome and transcriptome sequences and major genes identified in oil biosynthesis and disease-resistance should provide valuable resources for molecular breeding and genetic improvement.