Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae

Abstract

Chinese mahogany (Toona sinensis) is a woody plant that is widely cultivated in China and Malaysia. Toona sinensis is important economically, including as a nutritious food source, as material for traditional Chinese medicine and as a high‐quality hardwood. However, the absence of a reference genome has hindered in‐depth molecular and evolutionary studies of this plant. In this study, we report a high‐quality T. sinensis genome assembly, with scaffolds anchored to 28 chromosomes and a total assembled length of 596 Mb (contig N50 = 1.5 Mb and scaffold N50 = 21.5 Mb). A total of 34,345 genes were predicted in the genome after homology‐based and de novo annotation analyses. Evolutionary analysis showed that the genomes of T. sinensis and Populus trichocarpa diverged ~99.1–103.1 million years ago, and the T. sinensis genome underwent a recent genome‐wide duplication event at ~7.8 million years and one more ancient whole genome duplication event at ~71.5 million years. These results provide a high‐quality chromosome‐level reference genome for T. sinensis and confirm its evolutionary position at the genomic level. Such information will offer genomic resources to study the molecular mechanism of terpenoid biosynthesis and the formation of flavour compounds, which will further facilitate its molecular breeding. As the first chromosome‐level genome assembled in the family Meliaceae, it will provide unique insights into the evolution of members of the Meliaceae.

Genomic Analysis Based on Chromosome-Level Genome Assembly Reveals an Expansion of Terpene Biosynthesis of Azadirachta indica

“…TPS-a and -b subfamilies were the main subfamilies in A. indica , approximately 37.5 and 32.5% of the total AziTPS genes in phylogenetic analysis. This is in accordance with other plant species, including tea, grape, and Chinese mahogany ( Chen et al, 2011 ; Zhou et al, 2020 ; Ji et al, 2021 ). Furthermore, we identified putative A. indica -specific TPSs using phylogenetic analysis and a cutoff of 55% identity, which indicates separate subfamily assignment ( Liu et al, 2018 ; Tu et al, 2020 ).…”

“…This may also explain the fact that A. indica had more expanded gene families than C. sinensis . Our result is in agreement with the research of Chinese mahogany, which indicated that a recent WGD occurred in Toona sinensis ( Ji et al, 2021 ). The occurrence of recent WGD mixed with gene duplications has been reported in Papaver somniferum L. genome ( Guo et al, 2018 ).…”

“…70 TPS genes were identified in A. indica , which is much more than that of the other 13 species. This is consistent with the result of Chinese mahogany ( T. sinensis ), the first chromosome-level genome assembly of the Meliaceae family ( Ji et al, 2021 ). Furthermore, TPS genes have also been reported to be abundant in other angiosperms that are rich in terpenoids.…”

“…Phylogenetic analysis was performed using 403 TPSs (the remaining TPS genes were too short for meaningful alignment) from A. indica and other 13 plants, including six reported TPS genes belonged to TPS- a, b, c, e, f, and g subfamilies, respectively ( Supplementary Table 11 ). As shown in Figure 5B , the topology of six subfamilies is similar to that of the previous papers ( Kumar et al, 2018b ; Zhou et al, 2020 ; Ji et al, 2021 ). Among the 40 AziTPS used in phylogenetic analysis, 15, 13, 4, 3, 1, and 4 AziTPS genes fell in TPS- a, b, c, e, f, and g subfamilies, respectively.…”

Research Advances in Toona sinensis, a Traditional Chinese Medicinal Plant and Popular Vegetable in China

“…A total of 126 genes, including 82 protein-coding genes, 36 tRNA genes, and eight rRNA genes, were identified [118]. Ji et al (2021) reported a high-quality T. sinensis genome assembly with scaffolds anchored to 28 chromosomes, an assembled length of 596 Mb, and a total of 34,345 genes predicted in the genome after homology-based and de novo annotation analyses [119].…”