Chromosome-level genome assembly of Amomum tsao-ko provides insights into the biosynthesis of flavor compounds

Abstract

Amomum tsao-ko is an economically important spice plant in the ginger family (Zingiberaceous). The dried ripe fruit has been widely used as spice and medicine in Southeast Asia due to its distinct flavor metabolites. However, there is little genomic information available to understand the biosynthesis of its characteristic flavor compounds. Here, we present a high-quality chromosome-level genome of A. tsao-ko with a total length of 2.08 Gb assembled into 24 chromosomes. Potential relationships between genetic variation and chemical constituents were analyzed by genome-wide association study (GWAS) of 119 representative A. tsao-ko specimens in China. Metabolome and transcriptome correlation analysis of different plant organs and fruit developmental stages revealed the proposed biosynthesis of the characteristic bicyclononane aldehydes and aromatic metabolites in A. tsao-ko fruit. Transcription factors of 20 families may be involved in the regulatory network of terpenoids. This study provides genomic and chemical insights into the biosynthesis of characteristic aroma and flavor constituents, which can be used to improve the quality of A. tsao-ko as food and medicine.

Metabolomics and Transcriptomics Reveal that Diarylheptanoids Vary in Amomum tsao-ko Fruit Development

“…This finding is different from our previous study in that the content and numbers of volatile metabolites of A. tsao-ko fruit changed significantly during fruit ripening …”

“…As previously reported, total RNA was extracted and purified using a TRIzol reagent (Invitrogen). Libraries with insert sizes ranging from 200 to 500 bp were produced and sequenced by Illumina NovaSeq 6000.…”

“…Our previous investigation on the high quality of the chromosome-level genome of A. tsao-ko provides insights into the biosynthesis of important metabolites . The aim of this study is to investigate the characteristic diarylheptanoids and the possible biosynthesis pathway in edible A.…”

“…Our previous investigation on the high quality of the chromosome-level genome of A. tsao-ko provides insights into the biosynthesis of important metabolites. 31 The aim of this study is to investigate the characteristic diarylheptanoids and the possible biosynthesis pathway in edible A. tsao-ko fruit. Based on the integrated metabolomics and transcriptomic analysis of the developmental stage of A. tsao-ko fruit, our findings provide a scientific basis for the deep exploitation and utilization of edible and medicinal plant resources.…”

Chromosome-level genome and multi-omics analyses provide insights into the geo-herbalism properties of Alpinia oxyphylla

“…Currently, numerous species have seen completed molecular markers, gene mining and cloning, and the functional identification of important agronomic traits, marking the onset of the post-genome era. However, research on Zingiberaceae is still in its nascent stages, with only a few genomes having been sequenced, including those of Amomum tsao-ko ( Li et al., 2022 ), Zingiber officinale ( Cheng et al., 2021b ; Li et al., 2021a ), Wurfbainia villosa ( Yang et al., 2022 ), Curcuma alismatifolia ( Liao et al., 2022 ), Curcuma longa ( Chakraborty et al., 2021 ), and Alpinia nigra ( Ranavat et al., 2021 ). It is worth noting that the genomes of Curcuma longa and Alpinia nigra are only a sketch, meaning that the whole-genome information of genus Alpinia has yet to be revealed or reported.…”