Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

Abstract

Background Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance. Findings We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs. Conclusions Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.

A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds

“…The STAG algorithm (Emms and Kelly, 2018) implemented in Orthofinder was used to estimate the species tree. Chia and other nine genomes were used for the construction of orthologous groups, including Arabidopsis thaliana (version Araport11) (Cheng et al, 2017), Solanum lycopersicum (version ITAG4.0) (Hosmani et al, 2019), Antirrhinum majus (version IGDBV1) (Li et al, 2019), Tectona grandis (Zhao et al, 2019), Callicarpa americana (Hamilton et al, 2020), Jacaranda mimosifolia (Wang et al, 2021), Salvia bowleyana (Zheng et al, 2021), Salvia miltiorrhiza (version 1.0) (Song et al, 2020), and Salvia splendens (version SspV2) (Jia et al, 2021). Gene family size expansion and contraction analysis was performed by CAFE5 (version 5.0.0) (Mendes et al, 2020).…”

The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants

“…Both Saoff5g02841 and Saoff7g00522 encode ent-CPP synthase of the GA biosynthetic pathway. Furthermore, two enzymes (Saoff2g04399 and Saoff1g04999) belong to a distinct group of class II diTPSs and the former is 74.9% identical to (À)-kolavenyl diphosphate synthase (SdKPS) involved in neo-clerodane diterpenoid biosynthesis in S. divinorum (Chen et al, 2017) and Callicarpa americana (Hamilton et al, 2020). The 14 diTPS genes reside on five chromosomes, with half on chromosome 1 (Figure S3A).…”

Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (Callicarpa americana)

“…While, the number of type II genes in C. americana (46) was higher than that in O. tenuiflorum (43) but lower than S. indicum (62). The genome size of C. americana was 506.1 Mb [ 4 ], compared to the genome size of S. indicum 337 Mb [ 34 ] and 612 Mb estimated genome size for O. tenuiflorum [ 37 ]. When compared to the large soybean genome (1115 M) [ 34 , 38 ], which also has 269 MADS box genes, and Camelina sativa estimated the genome size of 785 Mb [ 39 ], which has 384 MADS box genes.…”

“…Callicarpa is a representative from the early-diverging mint lineage, and thus, it has an important phylogenetic position to study the evolution of key gene families, such as the MADS-box genes. Recently, the full genome sequence of C. americana has been published [4], providing Plants 2021, 10, 1805 2 of 18 the opportunity to conduct a comprehensive analysis of the C. americana MADS-box gene family. However, the identity and function of MADS-box genes in this species have not been reported in detail.…”