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 (Zingiberaceae). 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 a genome-wide association study 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.

References

[1] Yang X, Küenzi P, Plitzko I et al. Bicyclononane aldehydes and antiproliferative constituents from Amomum tsao-ko . Planta Med. 2009; 75: 543-6.

[2] Martin M . Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011; 17: 10-2.

[3] Chinese Pharmacopoeia Commission . Pharmacopoeia of the People’s Republic of China (Part I) . Beijing: Chinese Medicine and Technology Press, 2010, 249-50.

[4] Ren W, Liang P, Ma Y et al. Research progress of traditional Chinese medicine against COVID-19. Biomed Pharmacother. 2021; 137: 111310.

[5] Ai ZZ, Zhou S, Li W et al. "Fei Yan no. 1" as a combined treatment for COVID-19: an efficacy and potential mechanistic study. Front Pharmacol. 2020; 11: 581277.

[6] Barbosa GB, Jayasinghe NS, Natera SHA et al. From common to rare Zingiberaceae plants - a metabolomics study using GC-MS. Phytochemistry. 2017; 140: 141-50.

[7] Zhang W, Chen JW, Shen Y et al. Extraction and determination of essential oil in different cultivars of Amomum tsao-ko . Adv Mater Res-Switz. 2012; 549: 474-7.

[8] Yang Z, Hu Y, Nong P et al. Investigation of Amomum tsao-ko planting area and climate factors analysis of ecological suitability of Amomum tsao-ko in Yunnan . Chin J Agric Resour Reg Plan. 2017; 38: 178-86.

[9] Jiang T, Liu G, Shen S et al. Present states and prospect of Amomum tsao-ko Crevost et Lemaire processing industry . Farm Prod Process. 2016; 19: 48-51.

[10] Wang JJ, Li Y, Lu Q et al. Drying temperature affects essential oil yield and composition of black cardamom (Amomum tsao-ko) . Ind Crop Prod. 2021; 168: 113580.

[11] Sim S, Tan SK, Kohlenberg B et al. Amomum tsao-ko-Chinese black cardamom: detailed oil composition and comparison with two other cardamom species . Nat Prod Commun. 2019; 14: 1934578X1985767.

[12] Feng X, Jiang ZT, Wang Y et al. Composition comparison of essential oils extracted by hydrodistillation and microwave-assisted hydrodistillation from Amomum tsao-ko in China. J Essent Oil Bear Plants. 2010; 13: 286-91.

[13] Degenhardt J, Kollner TG, Gershenzon J . Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants. Phytochemistry. 2009; 70: 1621-37.

[14] Starkenmann C, Mayenzet F, Brauchli R et al. Structure elucidation of a pungent compound in black cardamom: Amomum tsao-ko Crevost et Lemarié (Zingiberaceae) . J Agric Food Chem. 2007; 55: 10902-7.

[15] Nagegowda DA . Plant volatile terpenoid metabolism: biosynthetic genes, transcriptional regulation and subcellular compartmentation. FEBS Lett. 2010; 584: 2965-73.

[16] Wang H, Ma D, Yang J et al. An integrative volatile terpenoid profiling and transcriptomics analysis for gene mining and functional characterization of AvBPPS and AvPS involved in the monoterpenoid biosynthesis in Amomum villosum . Front Plant Sci. 2018; 9: 846.

[17] Song X, Wang J, Li N et al. Deciphering the high-quality genome sequence of coriander that causes controversial feelings. Plant Biotechnol J. 2020; 18: 1444-56.

[18] Zhao C, Yu Z, Silva JAT et al. Functional characterization of a Dendrobium officinale geraniol synthase DoGES1 involved in floral scent formation. Int J Mol Sci. 2020; 21: 7005.

[19] Zhao H, Li M, Zhao Y et al. A comparison of two monoterpenoid synthases reveals molecular mechanisms associated with the difference of bioactive monoterpenoids between Amomum villosum and Amomum longiligulare . Front Plant Sci. 2021; 12: 695551.

[20] Mans D, Djotaroeno M, Friperson P et al. Phytochemical and pharmacological support for the traditional uses of Zingiberacea species in Suriname - a review of the literature. Pharmacogn J. 2019; 11: 1511-25.

[21] Bora PK, Saikia J, Kemprai P et al. Evaluation of postharvest drying, key odorants, and phytotoxins in plai (Zingiber montanum) essential oil . J Agric Food Chem. 2021; 69: 5500-9.

[22] Zhou K, Yang S, Li S-M . Naturally occurring prenylated chalones from plants: structural diversity, distribution, activities and biosynthesis. Nat Prod Rep. 2021; 38: 2236-60.

[23] Li HL, Wu L, Dong Z et al. Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway . Hortic Res. 2021; 8: 189.

[24] Cheng SP, Jia KH, Liu H et al. Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. Hortic Res. 2021; 8: 188.

[25] Chakraborty A, Mahajan S, Jaiswal SK et al. Genome sequencing of turmeric provides evolutionary insights into its medicinal properties. Commun Biol. 2021; 4: 1193.

[26] Chen ZY, Chen SZ, Hwang SF . Preliminary report of chromosome number on Chinese Zingiberaceae. Guihaia. 1982; 2: 153-7.

[27] Aubourg S, Lecharny A, Bohlmann J . Genomic analysis of the terpenoid synthase (AtTPS) gene family of Arabidopsis thaliana . Mol Gen Genomics. 2002; 267: 730-45.

[28] Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011; 27: 2987-93.

[29] Li H, Handsaker B, Wysoker A et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25: 2078-9.

[30] Duarte FJ, Santos AG . Enantioselective organocatalytic intramolecular Diels-Alder reactions: a computational study. J Org Chem. 2012; 77: 3252-61.

[31] Hong B-C, Tseng H-C, Chen S-H . Synthesis of aromatic aldehydes by organocatalytic [4+2] and [3+3] cycloaddition of α, β-unsaturated aldehydes . Tetrahedron. 2007; 63: 2840-50.

[32] Wojcik AM, Wojcikowska B, Gaj MD . Current perspectives on the auxin-mediated genetic network that controls the induction of somatic embryogenesis in plants. Int J Mol Sci. 2020; 21: 1333.

[33] Yang Z, Xie C, Huang Y et al. Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage. PeerJ. 2021; 9: e11465.

[34] Liu G, Jin M, Cai C et al. Soil microbial community structure and physicochemical properties in Amomum tsaoko-based agroforestry systems in the Gaoligong mountains, Southwest China. Sustainability. 2019; 11: 546.

[35] Duan SZ, Zhu K, Li W et al. Phenotype diversity analysis of Amomum tsao-ko in Lvchun county of Yunnan province. ACSR Adv Comput. 2016; 63: 176-9.

[36] Zhang W, Lu B, Meng H et al. Phenotypic diversity analysis of the fruit of Amomum tsao-ko Crevost et Lemarie, an important medicinal plant in Yunnan, China. Genet Resour Crop Evol. 2019; 66: 1145-54.

[37] Ma M, Wang T, Lu B . Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers. Genet Resour Crop Evol. 2021; 68: 2655-67.

[38] Lu B, Ma M, Zhang W et al. Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing. Mol Biol Rep. 2021; 48: 1943-9.

[39] Yang YW, Yang ZY, Yan MR et al. Isolation and characterization of microsatellite markers for Amomum tsaoko (Zingiberaceae), an economically important plant in China. Genet Mol Res. 2014; 13: 8220-4.

[40] Elshamy AI, Mohamed TA, Essa AF et al. Recent advances in Kaempferia phytochemistry and biological activity: a comprehensive review. Nutrients. 2019; 11: 2396.

[41] You MK, Lee YJ, Kim JK et al. The organ-specific differential roles of rice DXS and DXR, the first two enzymes of the MEP pathway, in carotenoid metabolism in Oryza sativa leaves and seeds. BMC Plant Biol. 2020; 20: 167.

[42] Saladie M, Wright LP, Garcia-Mas J et al. The 2-C-methylerythritol 4-phosphate pathway in melon is regulated by specialized isoforms for the first and last steps. J Exp Bot. 2014; 65: 5077-92.

[43] Chappell J, Wolf F, Proulx J et al. Is the reaction catalyzed by 3-hydroxy-3-methylglutaryl coenzyme A reductase a rate-limiting step for isoprenoid biosynthesis in plants? Plant Physiol. 1995; 109: 1337-43.

[44] Liao P, Lung SC, Chan WL et al. Overexpression of HMG-CoA synthase promotes Arabidopsis root growth and adversely affects glucosinolate biosynthesis. J Exp Bot. 2020; 71: 272-89.

[45] Chen YC, Li Z, Zhao YX et al. The Litsea genome and the evolution of the laurel family. Nat Commun. 2020; 11: 1675.

[46] Picaud S, Olsson ME, Brodelius M et al. Cloning, expression, purification and characterization of recombinant (+)-germacrene D synthase from Zingiber officinale . Arch Biochem Biophys. 2006; 452: 17-28.

[47] Yue Y, Yu R, Fan Y . Characterization of two monoterpene synthases involved in floral scent formation in Hedychium coronarium . Planta. 2014; 240: 745-62.

[48] Yu F, Okamto S, Nakasone K et al. Molecular cloning and functional characterization of α-humulene synthase, a possible key enzyme of zerumbone biosynthesis in shampoo ginger (Zingiber zerumbet Smith) . Planta. 2008; 227: 1291-9.

[49] Yang Y, Yan RW, Cai XQ et al. Chemical composition and antimicrobial activity of the essential oil of Amomum tsao-ko . J Sci Food Agric. 2008; 88: 2111-6.

[50] Hu Z, Bai JW, Yang W et al. Identification of the key odorants in fresh Amomum tsaoko fruit. Food Sci. 2020; 41: 173-8.

[51] Hong SS, Lee JH, Choi YH et al. Amotsaokonal A-C, benzaldehyde and cycloterpenal from Amomum tsao-ko . Tetrahedron Lett. 2015; 56: 6681-4.

[52] He X, Chen JJ, Huang XY et al. The antidiabetic potency of Amomum tsao-ko and its active flavanols, as PTP1B selective and α-glucosidase dual inhibitors . Ind Crop Prod. 2021; 160: 112908.

[53] He X, Wang HM, Geng CA et al. Amomutsaokols A-K, diarylheptanoids from Amomum tsao-ko and their α-glucosidase inhibitory activity . Phytochemistry. 2020; 177: 112418.

[54] Moon SS, Lee JY, Cho SC . Isotsaokoin, an antifungal agent from Amomum tsao-ko . J Nat Prod. 2004; 67: 889-91.

[55] Walker BJ, Abeel T, Shea T et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9: e112963.

[56] Simao FA, Waterouse RM, Loannidis P et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31: 3210-2.

[57] Langmead B, Salzberg SL . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9: 357-9.

[58] Servant N, Varoquaux N, Lajoie BR et al. HiC-pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015; 16: 259.

[59] Burton JN, Adey A, Patwardhan RP et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol. 2013; 31: 1119-25.

[60] Gary B. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27: 573-80.

[61] Stanke M, Waack S . Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003; 19 Suppl 2: ii215-5.

[62] She R, Chu JSC, Wang K et al. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 2009; 19: 143-9.

[63] Birney E, Clamp M, Durbin R . GeneWise and genomewise. Genome Res. 2004; 14: 988-95.

[64] Trapnell C, Roberts A, Goff L et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7: 562-78.

[65] Haas BJ, Salzberg SL, Zhu W et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 2008; 9: R7.

[66] Wu CH, Apweiler R, Bairoch A et al. The universal protein resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 2006; 34: D187-91.

[67] Quevillon E, Silventoinen V, Pillai S et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005; 33: W116-20.

[68] Katoh K, Standley DM . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30: 772-80.

[69] Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30: 1312-3.

[70] Nguyen LT, Schmidt HA, von Haeseler A et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32: 268-74.

[71] Yang Z . PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007; 24: 1586-91.

[72] Tang H, Bowers JE, Wang X et al. Synteny and collinearity in plant genomes. Science. 2008; 320: 486-8.

[73] Wang D, Zhang Y, Zhang Z et al. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 2010; 8: 77-80.

[74] Kim D, Langmead B, Salzberg SL . HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12: 357-60.

[75] Liao Y, Smyth GK, Shi W . FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014; 30: 923- 30.

[76] Love MI, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15: 550.

[77] Yu G, Wang LG, Han Y et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16: 284-7.

[78] Tsugawa H, Cajka T, Kind T et al. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods. 2015; 12: 523-6.