The Acer truncatum genome provides insights into nervonic acid biosynthesis

Abstract

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent wholegenome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.

Transcriptome Analysis of Acer truncatum Seeds Reveals Candidate Genes Related to Oil Biosynthesis and Fatty Acid Metabolism

“…DYNAMIC CHANGES IN GENE EXPRESSION DURING SEED DEVELOPMENT. A. truncatum is an important woody tree species that produces seeds with high levels of UFAs (Ma et al, 2020). Studying the key stages of seed development and the molecular mechanism of oil synthesis is a critical step in improving the quantity and quality of A. truncatum seed oil.…”

“…Total RNA was extracted from developing seeds at 70, 85, 100, 115, 145, and 180 DAF from three plants (three biological repeats) using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer's instructions. cDNA library construction and normalization were performed using the methods previously described by Ma et al (2020). The 18 cDNA libraries were sequenced on an Illumina HiSeq X10 (Illumina, San Diego, CA) and 150-bp paired-end reads were generated.…”

“…The 18 cDNA libraries were sequenced on an Illumina HiSeq X10 (Illumina, San Diego, CA) and 150-bp paired-end reads were generated. The paired-end reads that remained after quality control (low-quality reads containing >10% unknown bases or 50% low-quality bases) were mapped to our A. truncatum reference genome (Ma et al, 2020) using HISTA2 version 2.0.4 (Kim et al, 2015).…”

“…The average ratio of clean reads to raw reads was 97.27%. The clean reads were mapped to the A. truncatum genome we sequenced previously (Ma et al, 2020), with an average mapping percentage of 90.39% per sample. Overall, 73.71% to 84.08% of the reads were uniquely matched, whereas 6.80% to 12.83% of reads mapped to multiple positions (Supplemental Table 2).…”

“…Acer truncatum is a versatile oil-producing woody tree. It is well-known for its colorful leaves and high value as an ornamental, medicinal, and oil plant (Ma et al, 2005(Ma et al, , 2020Yang et al, 2017). In 2011, the seed oil was approved as a New Resource Food by the National Health and Family Planning Commission of the People's Republic of China, with potentially important implications for the fields of food and medicine.…”