Tung Tree(Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production

Tung tree(Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further wholegenome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites;17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.

Transcriptomic Analysis of Differentially Expressed Genes and Alternative Splicing Events Associated with Crassulacean Acid Metabolism in Orchids

Phalaenopsis equestris is an obligate crassulacean acid metabolism(CAM) plant with high ornamental and economic value. CAM photosynthesis is associated with drought tolerance and efficient water utilization, which enhances the survival rate of CAM plants in arid environments.The identification and analysis of CAM-related genes will be helpful to improve our understanding of the regulatory mechanisms of CAM metabolism. In this study, we analyzed RNA-Seq data to identify differentially expressed genes(DEGs) between circadian day and night in P.equestris leaves then performed GO and KEGG functional enrichment analysis. The pathways that were significantly enriched among these DEGs included carbon fixation, circadian clock regulation, glucose metabolism, photosynthesis, and plant hormone signaling. We also used Pac Bio long-read Iso-Seq technology, which identified many alternative splicing events for key genes in CAM-related pathways, including carbon fixation, circadian clock regulation, and stomatal movement. These findings suggested that alternative splicing events might be involved in CAM metabolism. Many unknown or uncharacterized genes were also found to be potentially involved in CAM metabolism. For example, the Peq000162 gene encodes a protein belonging to the Ldp A(light-dependent period) iron-sulfur protein family, and it was found to generate many alternatively spliced products. These findings shed light on CAM metabolic mechanisms in P. equestris along with the molecular functions of key CAM genes. Ultimately, the information may help enhance crop yield and drought tolerance through the introduction of CAM features into C3 crops.