Research Article | Volume 12, Issue 2, March, 2024

The de novo genome assembly of lemon grass to identify the genes in essential oil production

Navajeet Chakravartty Nageswara Rao Reddy Neelapu   

Open Access   

Published:  Feb 20, 2024

DOI: 10.7324/JABB.2024.125317
Abstract

Lemon grass (Cymbopogon citratus L.) is a member of the Poaceae family and is famous for its culinary, cultural, cosmetic, and medicinal properties. Therefore, the present study aims to assemble the genome of the lemon grass and provide a valuable resource for mining biochemical pathways. The raw genome data is retrieved from NCBI and cleaned with AdapterRemoval version 2.3.2 for high-quality clean data. The genome size was estimated using Jellyfish 2.2.10 and GenomeScope version 1.0. MaSurCa version 3.3.2. was used to generate genome assembly. BUSCO version 4.1.2. is used to assess the completeness and quality of genome assembly. This analysis resulted in a draft nuclear genome of 364,442,032 bps with 127,303 scaffolds. RepeatModeler version 2.0.1., AUGUSTUS version 3.3.2., and tRNAscan-SE version 2.0.6. are used to identify repeats, genes, and tRNA genes, respectively. This study identified 41.66% repeats, 41,775 genes, and 681 tRNAs. UniProt protein database, OrthoFinder version 2.2.7, InterproScan, Plant metabolic network analysis, and Gene Ontology categorization annotate the genome functionally. GetOrganelle version 1.6.4., is used to generate the mitochondrial and chloroplast genome assembly of 367,579 bps and 139,690 bps. CPGAVAS2 version 1 and AGORA version 1 annotate the genome of chloroplast and mitochondria, respectively. The genes and pathways (photosynthesis, glycolysis, pyruvate, terpenoid backbone synthesis, and tricarboxylic acid cycle) associated with essential oil production are identified and mapped. Thus, this study reports the draft nuclear and organelle genome assembly; and genes and pathways participating in the biosynthesis of essential oil production in C. citratus L.


Keyword:     Chloroplast genome Cymbopogon citratus Genome assembly Lemon grass Mitochondrial genome Nuclear genome


Citation:

Chakravartty N, Neelapu NRR. The de novo genome assembly of lemon grass to identify the genes in essential oil production. J App Biol Biotech. 2024;12(2):100-149. http://doi.org/10.7324/JABB.2024.125317  

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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ARTICLE HIGHLIGHTS

  1. The nuclear genome size is predicted to be 454,049,232 bps for lemon grass. The de-novo assembly generated 127,303 scaffolds, with an assembly size of 364,442,032 bps. The genome assembly of lemon grass was complete by 60.9%.

  2. A complete circular chloroplast genome of 139,690 bps was generated and annotated without any gap for lemon grass.

  3. A complete circular mitochondrial genome of 367,579 bps was generated and annotated without any gap for lemon grass.

  4. The genes and pathways (photosynthesis, glycolysis, pyruvate, terpenoid backbone synthesis, and tricarboxylic acid cycle) associated with essential oil production are identified and mapped.


1. INTRODUCTION

The essential oil-producing plants are primarily distributed across the plant kingdom and cover many families, including Lamiaceae (mint, basil, lavender), Rosaceae (roses), and Poaceae (aromatic grasses) [1]. The genus Cymbopogon of the Poaceae family is well known for its aromatic properties and consists of approximately 180 species distributed worldwide [2], of which 45 species are reported in India [3]. These fragrant grasses consist of a differential blend of several terpenoid constituents and are significant reserves of monoterpene-rich essential oils [4]. The major components reported in the essential oil of lemon grass are monoterpene alcohols, aldehydes, and acetates [5]. The monoterpene alcohols like geraniol (GOL) and citronellol (COL) are previously reported [5]. The aldehydes include geranial (GAL), neral (NAL), and citronellal (CAL) [5]. Acetates include citronellyl acetate and geranyl acetate [5].

Essential oils are significant in food flavors, cosmetics, oral healthcare products, fragrances, insect repellents, and aromatherapy. For instance, citral is a raw material for perfumery, confectionery, Vitamin A, and ionones [6]. Likewise, alcohol COL, a raw material for producing rose oxide, and its aldehyde CAL are used to manufacture flavor and fragrance agents [7]. In addition, essential oils and their constituents from aromatic grasses possess potent pharmacological activities like cytotoxic, anti-inflammatory, antifungal, and antioxidant [8]. Besides oil production, citronella grass is a flavoring agent for culinary purposes. Thus, there is a need to understand the genomic architecture of this highly significant species with relevance to essential oils.

Currently, 911 genes and 1,769 protein sequences are available at NCBI for the genus Cymbopogon [9], whereas 128 genes and 347 protein sequences are available at NCBI for Cymbopogon citratus L. [10]. The non-availability of high-quality genome sequence assembly for the species C. citratus is a bottleneck in understanding the genomic architecture of the species. The whole-genome sequencing (WGS) is a precise method for analyzing entire genomes [11]. The rapidly reducing sequencing costs and the ability to produce large volumes of data with today’s high throughput sequencers have made WGS a powerful tool for genomics research [11,12]. The raw genome sequence data of C. citratus is available at NCBI (BioProject ID: PRJNA610008) [13]. Thus, the present study aims to report the draft genome assembly of lemon grass with genes, repeats, and functional relevance; genes associated with metabolites and secondary metabolites; genes related to culinary properties in lemon grass; and genes and pathways associated with essential oil production in lemon grass.


2. MATERIALS AND METHODS

The genome of C. citratus was assembled and annotated with the modified protocol of Chakravartty and Neelapu [14].

2.1. Assembly and Annotation of the Nuclear Genome in Lemon Grass

2.1.1. Genome sample and assembly

The raw genome sequence data of C. citratus was downloaded from NCBI (BioProject ID: PRJNA610008), evaluated, and checked. AdapterRemoval version 2.3.2 was employed to remove contaminated adapter sequences and bases of low-quality (with Q30) from reads to provide high-quality clean data [15]. The de novo assembly is generated based on high-quality clean data. Jellyfish 2.2.10 [16] and GenomeScope version 1.0 [17] are employed to estimate the genome size, and MaSurCa version 3.3.2 [18] generated de novo assembly. BUSCO version 4.1.2 [19] is used to check the de novo assembly and was considered for downstream analysis to check the completeness and quality of the genome assembly. The plant dataset viridiplantae_odb10 is provided as a model for BUSCO version 4.1.2 [19].

2.1.2. Genome annotation and analysis

RepeatModeler version 2.0.1 [20] and RepeatMasker version 4.0.9 [21] are employed to identify repeats and mask the genome. AUGUSTUS version 3.3.2 [22] predicts genes with Arabidopsis as the model, and tRNAscan-SE version 2.0.6 [23] recognizes tRNAs. OrthoFinder version 2.2.7 [24] is employed to carry out orthologous analysis. The orthologous analysis was performed for predicted protein sequences of C. citratus by considering protein sequences of eight model species, i.e., Aegilops tauschii, Arabidopsis thaliana, Dichanthelium oligosanthes, Oryza sativa, Setaria italica, Sorghum bicolor, Triticum aestivum, and Zea mays. UniProt protein database [25] is employed to process functional annotation of the predicted genes based on homology. The top hits in the homology search are assigned to the genes in the functional annotation [25]. MISA version 2.1 [26] is utilized to predict simple sequence repeats markers, and primer3 version 2.5.0 [27] is employed to design primers.

2.1.3. Identifying genes and pathways associated with metabolites, secondary metabolites, and culinary properties in lemon grass

Mapman [28] and KEGG [29] predicted genes and pathways associated with the metabolism of essential oils in lemon grass. The orthologous analysis is carried out between C. citratus, and four culinary herbs Ocimum basilicum L., Origanum majorana L., Origanum vulgare L, and Rosmarinus officinalis L, to predict genes associated with the culinary properties in lemon grass. OrthoFinder version 2.2.7 [24] is employed to carry out orthologous analysis.

2.2. Assembly and Annotation of Organelle Genome in Lemon Grass

GetOrganelle version 1.6.4 [30] generated the mitochondria and chloroplast assembly. CPGAVAS2 version 1 [31] annotated the chloroplast genome, whereas AGORA version 1 [32] annotated the mitochondrial genome considering Y08501.2 as a model.


3. RESULTS AND DISCUSSION

3.1. Draft Genome (Nuclear and Organelle) Assembly of Lemon Grass

The whole-genome sequence data of 28.96 GBs from NCBI Bio project PRJNA610008 is retrieved. There were 194,645,804 reads, 44.237% of G.C. content, and 94.72% data ≥Q30 with read length 2 × 150bp. The adapter removal and quality trimming resulted in 194,640,684 reads, 44.23% of G.C. content, and 94.8% data ≥Q30. The genome size of 454,049,232 bps is predicted for lemon grass [Supplementary Figure 1]. The de-novo assembly generated 127,303 scaffolds, with an assembly size of 364,442,032 bps. The longest scaffold is 67,673 bps, and the shortest scaffold is 301 bps. Table 1 presents the genome estimation summary of lemon grass. The assembled genome’s G.C. content and scaffold length distribution are calculated and shown in Supplementary Figures 2 and 3, respectively. The G.C. content of the assembled genome is ~43.86%. The evaluation of the genome using BUSCO version 4.1.2., predicted that the genome assembly of lemon grass was complete by 60.9% [Table 1 and Supplementary Table 1].

Table 1: The summary of genome assembly, BUSCO score parameters, repeats, gene prediction, and annotation on lemon grass

S. No.StatisticsCount
Genome Assembly Statistics
1Number of scaffolds127303
2Total size of scaffolds364442032
3Longest scaffold67673
4Shortest scaffold301
5Number of scaffolds >1K nt97384
6Percentage of scaffolds >1K nt76.5
7Number of scaffolds >10K nt4251
8Percentage of scaffolds >10K nt3.3
9Mean scaffold size2863
10Median scaffold size1864
11N50 scaffold length4347
12L50 scaffold count23781
13scaffold %A28
14scaffold %C21.91
15scaffold %G21.95
16scaffold %T28.11
17scaffold %N0.03
BUSCO Statistics
1Complete BUSCOs (C)60.90%
2Complete and single-copy BUSCOs (S)58.80%
3Complete and duplicated BUSCOs (D)2.10%
4Fragmented BUSCOs (F)21.40%
5Missing BUSCOs (M)17.7%
6Total BUSCO groups searched100.00%
Repeat Statistics
1SINEs665
2LINEs26231
3LTR elements51540
4DNA elements12288
5Unclassified366513
6Small RNA355
7Satellites229
8Simple repeats63921
9Low complexity7157
Gene prediction and annotation
1Number of CDS predicted41,775
2Number of CDS got annotated with UniProt protein db34,239
3Number of CDS got annotated with INTERPRO34,348
4Number of CDS got annotated with the plant metabolic network8,550

The repeat analysis predicted that 41.66% of the genome contains repetitive elements. Table 1 and Supplementary Table 2 provides the repeat classification. The repeat classification revealed 0.02% of SINEs, 3.64% of LINEs, 9.98% of LTR elements, 1.49% of DNA elements, and unclassified repeats of 25.41%. The analysis revealed 50779, 10874, 11942, 1515, 461, 451, and 4784 mono-nucleotide repeats, di-nucleotide repeats, tri-nucleotide repeats, tetra-nucleotide repeats, penta-nucleotide repeats, hexa-nucleotide repeats, and complex type repeats, respectively [Supplementary Table 3]. Out of the simple repeats predicted, the primers were designed successfully for 47,048 mono-nucleotides, 9321 di-nucleotides, 10,901 tri-nucleotides, 1378 tetra-nucleotides, 414 penta-nucleotides, 385 hexa-nucleotides and 4241 complex type repeats [Supplementary Table 3]. The tRNAs identified in the assembly of lemon grass are 681.

The gene prediction based on AUGUSTUS version 3.3.2 revealed 41,775 genes. Nearly 34,239 were annotated based on best hits with the UniProt protein database [Table 1]. InterproScan was used to annotate genes resulting in the annotation of 34,348 genes. The KEGG analysis predicted many significant pathways in lemon grass. The Gene Ontology categorization identified 1745 genes associated with biological processes, 484 genes related to cellular components, and 1373 genes linked with molecular function [Supplementary Figures 4-6]. The Mapman analysis identified 43.09% of genes having a significant role in metabolic pathways [Supplementary Figure 7]. Plant metabolic network analysis identified 8550 genes associated with metabolic pathways. A linear tree presents phylogenetic relationships of nine species based on the maximum likelihood method [24,33]. It is viewed in Figtree [34] to understand the phylogenetic relationship between the models and C. citratus, as shown in Supplementary Figure 8. The linear tree showed that lemon grass is close to S. bicolor, followed by Z. mays, S. italica, and D. oligosanthes. The orthologous study considered 562,517 genes, and nearly 447,596 (79.57%) genes are in orthogroups. The number of orthogroups identified in this study is 26,100, and Supplementary Table 4 presents the orthologous summary.

A complete circular chloroplast genome of 139,690 bps was generated and annotated without any gap [Supplementary Figure 9]. A complete circular mitochondrial genome of 367,579 bps was generated and annotated without any gap [Supplementary Figure 10]. A. thaliana ecotype Col-0 mitochondrion, complete genome (Y08501.2) was used as a reference for genome annotation in the mitochondria.

3.2. The Genes Associated with Metabolites and Secondary Metabolites in Lemon Grass

The study identified genes associated with metabolites and secondary metabolites of lemon grass. Metabolites and secondary metabolites are essential for producing essential oils in lemon grass. Table 2 summarizes lemon grass’s KO ID, gene count, and metabolic pathways [Figure 1 and Supplementary Figures 11-33]. The number of genes identified in purine metabolism, cysteine and methionine metabolism, glycerophospholipid metabolism, pyruvate metabolism, starch and sucrose metabolism, and pyrimidine metabolism is 43, 43, 35, 32, 31, and 30, respectively. Similarly, this study identifies fifteen genes in sulfur metabolism, sphingolipid, alpha-Linolenic acid, phenylalanine, tryptophan, and Beta-alanine.

Table 2: The genes identified and associated with the metabolism of lemon grass

 S. No. KO IDMetabolic pathwaysNumber of genes
1230Purine metabolism43
2270Cysteine and methionine metabolism43
3564Glycerophospholipid metabolism35
4620Pyruvate metabolism32
5500Starch and sucrose metabolism31
6240Pyrimidine metabolism30
7260Glycine, serine, and threonine metabolism29
8630Glyoxylate and dicarboxylate metabolism28
9561Glycerolipid metabolism27
10250Alanine, aspartate and glutamate metabolism27
11562Inositol phosphate metabolism23
12330Arginine and proline metabolism22
13480Glutathione metabolism20
1453Ascorbate and aldarate metabolism19
15350Tyrosine metabolism18
1651Fructose and mannose metabolism17
1752Galactose metabolism16
18680Methane metabolism16
19920Sulfur metabolism15
20600Sphingolipid metabolism15
21592alpha-Linolenic acid metabolism15
22380Tryptophan metabolism15
23410beta-Alanine metabolism15
24790Folate biosynthesis15
25950Isoquinoline alkaloid biosynthesis8
26941Flavonoid biosynthesis13
27940Phenylpropanoid biosynthesis15
28904Diterpenoid biosynthesis9
29906Carotenoid biosynthesis15
30900Terpenoid backbone biosynthesis28
31130Ubiquinone and other terpenoid-quinone biosynthesis20
Figure 1: The genes associated with metabolites of the pyruvate metabolism. This figure shows genes associated with metabolites of the pyruvate metabolism, and the genes are highlighted in the pathway. These genes are mapped onto the pathway and was retrieved from KAAS.



[Click here to view]

Table 2 summarizes genes associated with secondary metabolites [Figure 2 and Supplementary Figures 34-39]. The number of genes identified in folate biosynthesis, isoquinoline alkaloid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, diterpenoid biosynthesis, carotenoid biosynthesis, terpenoid backbone biosynthesis, and ubiquinone and other terpenoid-quinone biosynthesis are 15, 8, 13, 15, 9, 15, 28, and 20 respectively.

Figure 2: The genes associated with metabolites of the terpenoid backbone synthesis. This figure shows genes associated with metabolites of the terpenoid backbone synthesis, and the genes are highlighted in the pathway. These genes are mapped onto the pathway and was retrieved from KAAS.



[Click here to view]

3.3. The Genes Associated with Culinary Properties in Lemon Grass

The orthologous analysis between C. citratus and four culinary herbs, O. basilicum L., O. majorana L., O. vulgare L., and R. officinalis L. identified the genes associated with culinary properties in lemon grass. Nearly 5442, 219, 9943, and 558 protein sequences are available for O. basilicum L., O. majorana L., O. vulgare L., and R. officinalis L. at NCBI. The orthologous study identified 7775 orthogroups; out of them, 74.8% of genes were present in the orthogroup. The Venn analysis revealed 19 orthogroups that are common between all the five culinary herbs, and Table 3 presents the orthologous summary. A linear tree shows the phylogenetic relationship of the five species based on the maximum likelihood method [27,33]. It is viewed in Figtree [34] to understand the phylogenetic relationship between the models and C. citratus, as shown in Supplementary Figure 40. The analysis also helped to identify genes associated with culinary properties in lemon grass, paving the way to culinary genomics.

Table 3: Orthologous analysis between five culinary herbs

S. No.Summary of Orthogroups and GenesCounts

Cymbopogon citratusOcimum basilicumOriganum majoranaOriganum vulgareRosmarinus officinalis
1Number of genes4177554422199943558
2Number of genes in orthogroups3256733481826679544
3Number of unassigned genes9208209437326414
4Percentage of genes in orthogroups7861.583.167.297.5
5Percentage of unassigned genes2238.516.932.82.5
6Number of orthogroups containing species58091849942306110
7Percentage of orthogroups containing species74.723.81.229.71.4
8Number of species-specific orthogroups488035008584
9Number of genes in species-specific orthogroups2856411220287326
10Percentage of genes in species-specific orthogroups68.420.6028.94.7

3.4. The Genes and Pathways Associated with Essential oil Production in Lemon Grass

The lemon grass essential oil is a mixture of cyclic and acyclic monoterpenes (GAL, NAL, and CAL). Figure 3 shows the biosynthesis of essential oil in lemon grass, the role of different cellular organelles, and crosstalk with other metabolic processes [35]. Like most other plants, the lemongrass chloroplast produces glucose through photosynthesis. The present study identified and mapped the genes participating in the photosynthesis pathway of lemon grass [Table 4 and Figure 4]. The glucose undergoes glycolysis in the cytoplasm, yielding pyruvate, a two-carbon compound. The present study identified and mapped the genes participating in the pathway’s glycolysis and pyruvate of lemon grass [Table 4, Figures 1 and 5]. Lemongrass uses pyruvate as a substrate for the biosynthesis of isopentenyl diphosphate (IPP) units, either through the cytoplasmic mevalonate (MVA) pathway or plastidic methylerythritol phosphate (MEP) pathway in their young and rapidly growing leaves [35]. MVA Pathway (MVA pathway) is a multi-step (three-step) process that starts with two acetyl-CoA molecules and forms IPP units [36]. MVA-independent Pathway (MEP Pathway) is a multi-step (seven-step) process that begins with glyceraldehyde 3-phosphate and forms IPP [36].

Table 4: The genes associated with pathways of essential oil production identified in lemon grass.

S. No.Gene IDKO IDGene NameAnnotation of the gene
Photosynthesis (map00195)
 1G867.t1K02695psaHphotosystem I subunit VI
 2G2701.t1K08902psb27photosystem II Psb27 protein
 3G3233.t1K02638petEPlastocyanin
 4G3376.t1K02692psaDphotosystem I subunit II
 5G3404.t1K02115ATPF1, atpGF-type H+-transporting ATPase subunit gamma
 6G3831.t1K03542psbSphotosystem II 22kDa protein
 7G6122.t1K02699psaLphotosystem I subunit XI
 8G6505.t1K02717psbPphotosystem II oxygen-evolving enhancer protein 2
 9G7149.t1K08903psb28photosystem II 13kDa protein
 10G9610.t1K02701psaNphotosystem I subunit PsaN
 11G12274.t1K02690psaBphotosystem I P700 chlorophyll a apoprotein A2
 12G14580.t1K02639petFFerredoxin
 13G16158.t1K02721psbWphotosystem II PsbW protein
 14G17949.t1K08901psbQphotosystem II oxygen-evolving enhancer protein 3
 15G19732.t1K02636petCcytochrome b6-f complex iron-sulfur subunit [EC: 7.1.1.6]
 16G20807.t1K02693psaEphotosystem I subunit IV
 17G23499.t1K02641petHferredoxin--NADP+reductase [EC: 1.18.1.2]
 18G25025.t1K03541psbRphotosystem II 10kDa protein
 19G26577.t1K02109ATPF0, atpFF-type H+-transporting ATPase subunit b
 20G27268.t1K02113ATPF1, atpHF-type H+-transporting ATPase subunit delta
 21G28907.t1K02694psaFphotosystem I subunit III
 22G30260.t1K02716psbOphotosystem II oxygen-evolving enhancer protein 1
 23G36823.t1K08905psaGphotosystem I subunit V
 24G37457.t1K02723psbYphotosystem II PsbY protein
Glycolysis/Gluconeogenesis (map00010)
 25G762.t1K03841FBP, fbpfructose-1,6-bisphosphatase I [EC: 3.1.3.11]
 26G1358.t1K00382DLD, lpd, pdhDdihydrolipoamide dehydrogenase [EC: 1.8.1.4]
 27G2227.t1K15633gpmI2,3-bisphosphoglycerate-independent phosphoglycerate mutase [EC: 5.4.2.12]
 28G3925.t1K00134GAPDH, gapAglyceraldehyde 3-phosphate dehydrogenase (phosphorylating) [EC: 1.2.1.12]
 29G4309.t1K01006ppdKpyruvate, orthophosphate dikinase [EC: 2.7.9.1]
 30G6749.t1K00128ALDHaldehyde dehydrogenase (NAD+) [EC: 1.2.1.3]
 31G7450.t1K00895pfp, PFPdiphosphate-dependent phosphofructokinase [EC: 2.7.1.90]
 32G9335.t1K01810GPI, pgiglucose-6-phosphate isomerase [EC: 5.3.1.9]
 33G9705.t1K01610E4.1.1.49, pckAphosphoenolpyruvate carboxykinase (ATP) [EC: 4.1.1.49]
 34G10700.t1K01785galM, GALMaldose 1-epimerase [EC: 5.1.3.3]
 35G11810.t1K00873PK, pykpyruvate kinase [EC: 2.7.1.40]
 36G12188.t1K01835Pgmphosphoglucomutase [EC: 5.4.2.2]
 37G12423.t1K01568PDC, pdcpyruvate decarboxylase [EC: 4.1.1.1]
 38G12843.t1K00844HKhexokinase [EC: 2.7.1.1]
 39G13296.t1K01689ENO, enoenolase [EC: 4.2.1.11]
 40G14904.t1K01785galM, GALMaldose 1-epimerase [EC: 5.1.3.3]
 41G16892.t1K00002AKR1A1, adhalcohol dehydrogenase (NADP+) [EC: 1.1.1.2]
 42G17507.t1K00627DLAT, aceF, pdhCpyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC: 2.3.1.12]
 43G18230.t1K00131gapNglyceraldehyde-3-phosphate dehydrogenase (NADP+) [EC: 1.2.1.9]
 44G18839.t1K00927PGK, pgkphosphoglycerate kinase [EC: 2.7.2.3]
 45G20474.t1K01623ALDOfructose-bisphosphate aldolase, class I [EC: 4.1.2.13]
 46G22816.t1K01834PGAM, gpmA2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC: 5.4.2.11]
 47G24955.t1K00016LDH, ldhL-lactate dehydrogenase [EC: 1.1.1.27]
 48G26444.t1K01792E5.1.3.15glucose-6-phosphate 1-epimerase [EC: 5.1.3.15]
 49G30535.t1K01895ACSS1_2, acsacetyl-CoA synthetase [EC: 6.2.1.1]
 50G34419.t1K01803TPI, tpiAtriosephosphate isomerase (TIM) [EC: 5.3.1.1]
 51G34750.t1K03103MINPP1multiple inositol-polyphosphate phosphatase/2,3-bisphosphoglycerate 3-phosphatase [EC: 3.1.3.62 3.1.3.80]
Pyruvate metabolism (map00620)
 52G1358.t1K00382DLD, lpd, pdhDdihydrolipoamide dehydrogenase [EC: 1.8.1.4]
 53G1431.t1K01759GLO1, gloAlactoylglutathione lyase [EC: 4.4.1.5]
 54G2339.t1K00627DLAT, aceF, pdhCpyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC: 2.3.1.12]
 55G3152.t1K00626ACAT, atoBacetyl-CoA C-acetyltransferase [EC: 2.3.1.9]
 56G4066.t1K00029E1.1.1.40, maeBmalate dehydrogenase (oxaloacetate-decarboxylating)(NADP+) [EC: 1.1.1.40]
 57G4673.t1K01759GLO1, gloAlactoylglutathione lyase [EC: 4.4.1.5]
 58G4880.t1K00873PK, pykpyruvate kinase [EC: 2.7.1.40]
 59G6227.t1K11262ACACAacetyl-CoA carboxylase/biotin carboxylase 1 [EC: 6.4.1.2 6.3.4.14 2.1.3.15]
 60G6396.t1K01512acyPacylphosphatase [EC: 3.6.1.7]
 61G7753.t1K01069gloB, gloC, HAGHhydroxyacylglutathione hydrolase [EC: 3.1.2.6]
 62G8777.t1K01595Ppcphosphoenolpyruvate carboxylase [EC: 4.1.1.31]
 63G9662.t1K01638aceB, glcBmalate synthase [EC: 2.3.3.9]
 64G13833.t1K01895ACSS1_2, acsacetyl-CoA synthetase [EC: 6.2.1.1]
 65G17101.t1K01649leuA, IMS2-isopropylmalate synthase [EC: 2.3.3.13]
 66G17414.t1K00028E1.1.1.39malate dehydrogenase (decarboxylating) [EC: 1.1.1.39]
 67G18607.t1K00382DLD, lpd, pdhDdihydrolipoamide dehydrogenase [EC: 1.8.1.4]
 68G18719.t1K00051E1.1.1.82malate dehydrogenase (NADP+) [EC: 1.1.1.82]
 69G24955.t1K00016LDH, ldhL-lactate dehydrogenase [EC: 1.1.1.27]
 70G31224.t1K00025MDH1malate dehydrogenase [EC: 1.1.1.37]
 71G32233.t1K00102LDHD, dldD-lactate dehydrogenase (cytochrome) [EC: 1.1.2.4]
 72G35811.t1K01595Ppcphosphoenolpyruvate carboxylase [EC: 4.1.1.31]
 73G9705.t1K01610E4.1.1.49, pckAphosphoenolpyruvate carboxykinase (ATP) [EC: 4.1.1.49]
Terpenoid backbone biosynthesis (map00900)
 74G1288.t1K15889PCMEprenylcysteine alpha-carboxyl methylesterase [EC: 3.1.1.-]
 75G1832.t1K10960chlP, bchPgeranylgeranyl diphosphate/geranylgeranyl-bacteriochlorophyllide a reductase [EC: 1.3.1.83 1.3.1.111]
 76G2230.t1K00787FDPSfarnesyl diphosphate synthase [EC: 2.5.1.1 2.5.1.10]
 77G2323.t1K00869MVK, mvaK1mevalonate kinase [EC: 2.7.1.36]
 78G3152.t1K00626ACAT, atoBacetyl-CoA C-acetyltransferase [EC: 2.3.1.9]
 79G6541.t1K06981ipkisopentenyl phosphate kinase [EC: 2.7.4.26]
 80G8703.t1K05954FNTBprotein farnesyltransferase subunit beta [EC: 2.5.1.58]
 81G8827.t1K01823idi, IDIisopentenyl-diphosphate Delta-isomerase [EC: 5.3.3.2]
 82G9071.t1K00099dxr1-deoxy-D-xylulose-5-phosphate reductoisomerase [EC: 1.1.1.267]
 83G9850.t1K15891FLDHNAD+-dependent farnesol dehydrogenase [EC: 1.1.1.354]
 84G10131.t1K01641HMGCShydroxymethylglutaryl-CoA synthase [EC: 2.3.3.10]
 85G10476.t1K01662dxs1-deoxy-D-xylulose-5-phosphate synthase [EC: 2.2.1.7]
 86G10495.t1K11778DHDDS, RER2, SRT1ditrans, polycis-polyprenyl diphosphate synthase [EC: 2.5.1.87]
 87G10803.t1K05356SPS, sdsall-trans-nonaprenyl-diphosphate synthase [EC: 2.5.1.84 2.5.1.85]
 88G11653.t1K00991ispD2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [EC: 2.7.7.60]
 89G11679.t1K00919ispE4-diphosphocytidyl-2-C-methyl-D-erythritol kinase [EC: 2.7.1.148]
 90G13764.t1K00938E2.7.4.2, mvaK2phosphomevalonate kinase [EC: 2.7.4.2]
 91G14936.t1K06013STE24STE24 endopeptidase [EC: 3.4.24.84]
 92G15260.t1K01770ispF2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [EC: 4.6.1.12]
 93G23454.t1K13789GGPS1geranylgeranyl diphosphate synthase, type III [EC: 2.5.1.1 2.5.1.10 2.5.1.29]
 94G27299.t1K00021HMGCRhydroxymethylglutaryl-CoA reductase (NADPH) [EC: 1.1.1.34]
 95G29757.t1K08658RCE1, FACE2prenyl protein peptidase [EC: 3.4.22.-]
 96G38362.t1K01597MVD, mvaDdiphosphomevalonate decarboxylase [EC: 4.1.1.33]
 97G39569.t1K05906PCYOX1, FCLYprenylcysteine oxidase/farnesylcysteine lyase [EC: 1.8.3.5 1.8.3.6]
Citrate cycle (TCA cycle) (map00020)
 98G115.t1K01647CS, gltAcitrate synthase [EC: 2.3.3.1]
 99G777.t1K01899LSC1succinyl-CoA synthetase alpha subunit [EC: 6.2.1.4 6.2.1.5]
 100G1358.t1K00382DLD, lpd, pdhDdihydrolipoamide dehydrogenase [EC: 1.8.1.4]
 101G1497.t1K00234SDHA, SDH1succinate dehydrogenase (ubiquinone) flavoprotein subunit [EC: 1.3.5.1]
 102G2517.t1K01647CS, gltAcitrate synthase [EC: 2.3.3.1]
 103G7103.t1K00164OGDH, sucA2-oxoglutarate dehydrogenase E1 component [EC: 1.2.4.2]
 104G9705.t1K01610E4.1.1.49, pckAphosphoenolpyruvate carboxykinase (ATP) [EC: 4.1.1.49]
 105G11248.t1K01648ACLYATP citrate (pro-S)-lyase [EC: 2.3.3.8]
 106G13750.t1K00658DLST, sucB2-oxoglutarate dehydrogenase E2 component (dihydrolipoamide succinyltransferase) [EC: 2.3.1.61]
 107G15077.t1K01681ACO, acnAaconitate hydratase [EC: 4.2.1.3]
 108G17507.t1K00627DLAT, aceF, pdhCpyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [EC: 2.3.1.12]
 109G18607.t1K00382DLD, lpd, pdhDdihydrolipoamide dehydrogenase [EC: 1.8.1.4]
 110G23327.t1K00161aceEpyruvate dehydrogenase E1 component [EC: 1.2.4.1]
 111G28266.t1K00031IDH1, IDH2, icdisocitrate dehydrogenase [EC: 1.1.1.42]
 112G28544.t1K00030IDH3isocitrate dehydrogenase (NAD+) [EC: 1.1.1.41]
 113G39479.t1K01681ACO, acnAaconitate hydratase [EC: 4.2.1.3]
Figure 3: The summary of the pathway for biosynthesis of essential oil in lemon grass. The figure summarizes the pathway for the biosynthesis of lemon grass essential oil, its crosstalk with other metabolic processes, and the role of different organelles.



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Figure 4: The genes associated with metabolites of the photosynthetic pathway. This figure shows genes associated with metabolites of the photosynthetic pathway, and the genes are highlighted in the pathway. These genes are mapped onto the pathway and was retrieved from KAAS.



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Figure 5: The genes associated with metabolites of the glycolysis pathway. This figure shows genes associated with metabolites of the glycolytic pathway, and the genes are highlighted in the pathway. These genes are mapped onto the pathway and was retrieved from KAAS.



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The present study identified and mapped the genes in lemon grass’s terpenoid backbone synthesis pathway [Table 4 and Figure 2]. This pathway shows the information on terpenoid backbone synthesis, MVA, and MEP pathways. Alternatively, Mitochondria can import pyruvate and yield citrate through the tricarboxylic acid (TCA) cycle [35]. The present study identified and mapped the genes participating in the pathway TCA cycle of lemon grass [Table 4 and Figure 6]. The citrate can transform into Acetyl-CoA and join the MVA pathway to yield IPP units. The geranyl diphosphate (GPP) mediated step produces GOL from IPP in lemongrass plastids [34] [Table 4 and Figure 2].

Figure 6: The genes associated with metabolites of the TCA cycle. This figure shows genes associated with metabolites of the TCA cycle; the genes are highlighted in the pathway. These genes are mapped onto the pathway and was retrieved from KAAS.



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IPP and dimethylallyl diphosphate (DMAPP) units are condensed to form GPP. IPP is converted to GPP by GPP synthase or GPS (E.C. 2.5.1.1) through the MVA and MEP pathways. GOL is a precursor for essential oil biosynthesis in lemongrass and yields all the major components through multiple reversible and irreversible reactions [35].

The number of genes identified in terpene synthesis is 34, and Supplementary Table 5 presents the detailed table. The number of genes identified in MEP and mevalonic acid (MVA) is 37. Supplementary Table 6 shows the detailed table. The genes identified in the metabolic pathways of MEP and MVA, can further be validated in the wet laboratory study.


4. CONCLUSION

The biosynthesis of essential oil starts with glucose production through photosynthesis. Glucose undergoes glycolysis in the cytoplasm, yielding pyruvate. Pyruvate is a substrate for the biosynthesis of IPP through the MVA or MEP pathways. The IPP and DMAPP units are condensed, forming GPP by GPP synthase leading to GOL. GOL is the precursor for essential oil (GAL, NAL, and CAL) biosynthesis through multiple reversible and irreversible reactions. This study presents the draft de-novo assembly (scaffold-level assembly with gaps) and annotation of C. citratus as a valuable resource for the scientific community. This study also identified and mapped genes participating in pathways of photosynthesis, glycolysis, pyruvate, terpenoid backbone synthesis, and TCA cycle, which are associated with essential oil production in lemon grass. Future studies include validating the genes identified in terpene synthesis, MEP and MVA through wet laboratory studies. This study will help in understanding the biosynthesis of essential oil production.


5. ACKNOWLEDGMENT

NC and NNNR are grateful to the management of GITAM (Deemed to be University) for providing the necessary facilities to carry out the research work and extending constant support. The authors are grateful to Dr. Stacy Pirro, Iridian Genomes Inc, USA, for allowing us to use their public data sets for whole-genome or organelle assembly and/or annotation; and submit genome assemblies to NCBI GenBank as Third-Party Annotation (TPA).


6. AUTHORS’ CONTRIBUTIONS

All authors made substantial contributions to the conception and design, acquisition of data, or analysis and interpretation of data; took part in drafting the article or revising it critically for important intellectual content; agreed to submit to the current journal; gave final approval of the version to be published; and agreed to be accountable for all aspects of the work. All the authors are eligible to be an author as per the International Committee of Medical Journal Editors (ICMJE) requirements/guidelines.


7. FUNDING

There is no funding to report.


8. CONFLICTS OF INTEREST

The authors report no financial or any other conflicts of interest in this work.


9. ETHICAL APPROVALS

This study does not involve experiments on animals or human subjects.


10. DATA AVAILABILITY

The assembled nuclear genome, mitochondrial genome, and chloroplast genome of lemon grass (C. citratus L.) were deposited to NCBI Genome as TPA (Third Party Annotation) submission with accession numbers DXKC00000000, BK059359, and BK059356 respectively. The supplementary files generated in this study and the nuclear and organelle genome annotations were deposited to Harvard dataverse (https://doi.org/10.7910/DVN/ZTM70X).


11. PUBLISHER’S NOTE

This journal remains neutral with regard to jurisdictional claims in published institutional affiliation.

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SUPPLEMENTARY MATERIALS

Supplementary Figure 1: The K-mer histogram for estimation of genome size in lemon grass. The figure shows K-mers frequency in lemon grass’s genome, which is predicted using Jellyfish and visualized using GenomeScope. A graph was plotted with K-mer frequency on the X-axis and the coverage on the Y-axis. The predicted genome size of lemon grass is 454,049,232 bp.



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Supplementary Figure 2: The distribution of G.C. percentage in the assembled genome of lemon grass. The figure shows the distribution of G.C. percentage in the assembled genome of lemon grass. A graph was plotted with the G.C. percentage range (G.C. %) on the X-axis and the number of scaffolds (contigs) on the Y-axis. The G.C. percentage in the assembled genome of lemon grass is ~ 43.86%.



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Supplementary Figure 3: The cumulative length distribution of the assembled genome in lemon grass. The figure shows the distribution of scaffold length distribution in the assembled genome of lemon grass. A graph was plotted with the scaffold length range on the X-axis and the number of scaffolds on the Y-axis.



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Supplementary Figure 4: The gene ontologies related to biological process observed in lemon grass. The figure shows gene ontologies related to biological processes observed in lemon grass. A graph with gene ontologies of biological processes on the X-axis and the number of genes on the Y-axis is plotted.



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Supplementary Figure 5: The gene ontologies related to cellular components observed in lemon grass. The figure shows gene ontologies related to cellular components observed in lemon grass. A graph with gene ontologies of cellular components on the X-axis and the number of genes on the Y-axis is plotted.



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Supplementary Figure 6: The gene ontologies related to molecular function observed in lemon grass. The figure shows gene ontologies related to molecular functions observed in lemon grass. A graph with gene ontologies of molecular functions on the X-axis and a number of genes on the Y-axis is plotted.



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Supplementary Figure 7: The pathway summary predicted with Mapman. This figure shows thirty-four metabolic categories along with the participating percentage of genes having a significant role in the metabolic pathways of lemon grass. Mapman analysis identified 43.09% of genes having a significant role in metabolic pathways.



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Supplementary Figure 8: The linear tree generated between model plants and Cymbopogon citratus. This figure shows the linear tree generated based on orthology between Aegilops tauschii, Arabidopsis thaliana, Dichanthelium oligosanthes, Oryza sativa, Setaria italica, Sorghum bicolor, Triticum aestivu, Zea mays. The orthology data was generated using OrthoFinder version 2.3.11 for the above species. The orthology data was used to construct a linear tree based on the maximum likelihood method, and the tree was viewed in FigTree version 1.4.4.



[Click here to view]
Supplementary Figure 9: The chloroplast genome and annotation of lemon grass. This figure shows a circular chloroplast genome of 139,690 bps generated without gaps using GetOrganelle version 1.6.4. This figure also shows chloroplast genome annotation predicted using CPGAVAS2 version 1.



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Supplementary Figure 10: The mitochondrial genome and annotation of lemon grass. This figure shows a circular mitochondrial genome of 367,579 bps generated without any gap using GetOrganelle version 1.6.4. This figure also shows mitochondrial genome annotation predicted using AGORA version 1.



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Supplementary Figure 11: The genes associated with metabolites of purine metabolism. This figure shows 43 genes associated with metabolites of purine metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 12: The genes associated with metabolites of cysteine and methionine metabolism. This figure shows 43 genes associated with cysteine and methionine metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 13: The genes associated with metabolites of glycerophospholipid metabolism. This figure shows 35 genes associated with glycerophospholipid metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 14: The genes associated with metabolites of starch and sucrose metabolism. This figure shows 31 genes associated with starch and sucrose metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 15: The genes associated with metabolites of pyrimidine metabolism. This figure shows 30 genes associated with pyrimidine metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 16: The genes associated with metabolites of glycine, serine, and threonine metabolism. This figure shows 29 genes associated with glycine, serine, and threonine metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 17: The genes associated with metabolites of glyoxylate and dicarboxylate metabolism. This figure shows 28 genes associated with glyoxylate and dicarboxylate metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 18: The genes associated with metabolites of glycerolipid metabolism. This figure shows 29 genes associated with glycerolipid metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 19: The genes associated with metabolites of alanine, aspartate and glutamate metabolism. This figure shows 27 genes associated with alanine, aspartate, and glutamate metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 20: The genes associated with metabolites of inositol phosphate metabolism. This figure shows 23 genes associated with inositol phosphate metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 21: The genes associated with metabolites of arginine and proline metabolism. This figure shows 22 genes associated with arginine and proline metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 22: The genes associated with metabolites of glutathione metabolism. This figure shows 20 genes associated with glutathione metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 23: The genes associated with metabolites of ascorbate and aldarate metabolism. This figure shows 19 genes associated with ascorbate and aldarate metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 24: The genes associated with metabolites of tyrosine metabolism. This figure shows 18 genes associated with tyrosine metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 25: The genes associated with metabolites of fructose and mannose metabolism. This figure shows 17 genes associated with fructose and mannose metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 26: The genes associated with metabolites of tryptophan metabolism. This figure shows 15 genes associated with tryptophan metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 27: The genes associated with metabolites of beta-alanine metabolism. This figure shows 15 genes associated with beta-alanine metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 28: The genes associated with alpha-linolenic acid metabolism metabolites. This figure shows 15 genes associated with alpha-linolenic acid metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 29: The genes associated with metabolites of sphingolipid metabolism. This figure shows 15 genes associated with sphingolipid metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 30: The genes associated with metabolites of sulfur metabolism. This figure shows 15 genes associated with sulfur metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 31: The genes associated with metabolites of methane metabolism. This figure shows 16 genes associated with methane metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 32: The genes associated with metabolites of galactose metabolism. This figure shows 16 genes associated with galactose metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 33: The genes associated with metabolites of ubiquinone and other terpenoid-quinone biosynthesis metabolism. This figure shows 20 genes associated with ubiquinone and other terpenoid-quinone biosynthesis metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 34: The genes associated with metabolites of carotenoid biosynthesis metabolism. This figure shows 15 genes associated with carotenoid biosynthesis metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 35: The genes associated with metabolites of diterpenoid biosynthesis metabolism. This figure shows nine genes associated with diterpenoid biosynthesis metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 36: The genes associated with metabolites of phenylpropanoid biosynthesis metabolism. This figure shows 15 genes associated with phenylpropanoid biosynthesis metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 37: The genes associated with metabolites of flavonoid biosynthesis metabolism. This figure shows 13 genes associated with flavonoid biosynthesis metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 38: The genes associated with metabolites of folate metabolism. This figure shows 15 genes associated with folate metabolism, and the genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 39: The genes associated with metabolites of isoquinoline alkaloid biosynthesis metabolism. This figure shows eight genes associated with isoquinoline alkaloid biosynthesis metabolism. The genes were highlighted in the pathway. These genes are mapped onto the pathway and were retrieved from KAAS.



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Supplementary Figure 40: The phylogenetic tree between five economically important culinary herbs. This figure shows a phylogenetic relationship between Cymbopogon citratus and four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.). The orthology data was generated using OrthoFinder version 2.3.11 for the above species. The orthology data was used to construct a linear tree based on maximum likelihood method and the tree was viewed in FigTree version 1.4.4.



[Click here to view]

Supplementary Table 1: The summary of BUSCO score parameters to evaluate the completeness of lemon grass.

S. NoBUSCO StatisticsCountPercentage
1Complete BUSCOs (C)25960.90%
2Complete and single-copy BUSCOs (S)25058.80%
3Complete and duplicated BUSCOs (D)92.10%
4Fragmented BUSCOs (F)9121.40%
5Missing BUSCOs (M)7517.7%
6Total BUSCO groups searched425100.00%

Supplementary Table 2: The summary of repeats predicted in the genome of lemon grass.

S.No.Type of repeatsNumber of repeatsLength of repeatsElements occupied(%)
1SINEs66572070 bp0.02%
2LINEs2623113279888 bp3.64%
3LTR elements5154036376114 bp9.98%
4DNA elements122885427562 bp1.49%
5Unclassified36651392614638 bp25.41%
6Total interspersed repeats147770272 bp40.55%
7Small RNA35580194 bp0.02%
8Satellites229159256 bp0.04%
9Simple repeats639212647666 bp0.73%
10Low complexity7157352141 bp0.10%

Supplementary Table 3: The summary of primers designed successfully for SSRs repeats in lemon grass

S. No.Type of simple repeatsCount of simple repeatCount of primers designed
1Mononucleotides (p1)50,77947,048
2Dinucleotides (p2)10,8749,321
3trinucleotides (p3)11,94210,901
4Tetranucleotides (p4)1,5151,378
5Pentanucleotides (p5)461414
6Hexanucleotides (p6)451385
7Complex type of repeats ( c)4,7844,241

Supplementary Table 4: The summary of orthogroups and genes in lemon grass as revealed by the orthologous analysis

S.No.Summary of orthogroups and genesCounts
1Number of genes562517
2Number of genes in orthogroups447596
3Number of unassigned genes114921
4Percentage of genes in orthogroups79.6
5Percentage of unassigned genes20.4
6Number of orthogroups26100
7Number of species-specific orthogroups714
8Number of genes in species-specific orthogroups4138
9Percentage of genes in species-specific orthogroups0.7
10Mean orthogroup size17.1
11Median orthogroup size13
12G50 (assigned genes)26
13G50 (all genes)20
14O50 (assigned genes)4770
15O50 (all genes)7256
16Number of orthogroups with all species present7898
17Number of single-copy orthogroups8

Supplementary Table 5: Identification of genes from lemon grass taking part in terpene synthases

S. No.GeneIDAnnotationGeneID_shortGene nameTPS familySwiss Prot EntrySwissProt gene namesGene ID in lemongrass
1AT2G24210.1terpene synthase 10AT2G24210TPS10TPSbQ9ZUH4TPS10 At2g24210 F27D4.12g38217.t1
2AT3G25810.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G25810TPS24TPSbQ9LRZ6TPS24 At3g25810 K13N2.7g34393.t1
3AT3G25820.1terpene synthase-like sequence-1,8-cineoleAT3G25820TPS27; TPS-CIN1TPSbP0DI76TPS27 TPS-CIN1 At3g25820 K13N2.19g34393.t1
4AT3G25830.1terpene synthase-like sequence-1,8-cineoleAT3G25830TPS23; TPS-CIN2TPSbP0DI77TPS23 TPS-CIN2 At3g25830 K9I22.3g34393.t1
5AT4G16730.1terpene synthase 02AT4G16730TPS02TPSbP0CJ42TPS02 At4g16730 dl4390w FCAALL.15g32271.t1
6AT4G16740.1terpene synthase 03AT4G16740TPS03TPSbA4FVP2TPS03 At4g16740 dl4395w FCAALL.18g34393.t1
7AT5G23960.1terpene synthase 21AT5G23960TPS21; PUP8TPSaQ84UU4TPS21 PUP8 At5g23960 MZF18.16g3033.t1
8AT4G02780.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT4G02780TPS31; TPSGA1; GA1; CPS; CPS1TPScQ38802GA1 ABC33 CPS CPS1 TPSGA1 At4g02780 T5J8.9g17067.t1
9AT1G79460.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT1G79460TPS32; TPSGA2; GA2; KS; KS1TPSe/fQ9SAK2GA2 KS KS1 TPSGA2 At1g79460 T8K14.12g12107.t1
10AT1G61120.1terpene synthase 04AT1G61120TPS04; GES; LISTPSe/fQ93YV0GES LIS TPS04 At1g61120 F11P17.15g12107.t1
11AT1G61680.1terpene synthase 14AT1G61680TPS14TPSgQ84UV0TPS14 At1g61680 T13M11.3g9415.t1
12AT1G66020.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT1G66020TPS26TPSaQ9C8E3TPS26 At1g66020 F15E12.3g3033.t1
13AT3G29190.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G29190TPS15TPSaQ9LS76TPS15 At3g29190 MXO21.3g3033.t1
14AT4G20200.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT4G20200TPS07TPSaO65434TPS07 At4g20200 F1C12.120g3033.t1
15AT4G20210.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT4G20210TPS08TPSaO65435TPS08 At4g20210 F1C12.130g3033.t1
16AT4G20230.2terpenoid synthase superfamily proteinAT4G20230TPS09TPSaQ8L7G4TPS09 At4g20230 F1C12.150g3033.t1
17AT1G31950.3Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT1G31950TPS29TPSaQ9C6W6TPS29 At1g31950 F5M6.5 T12O21.14g3033.t1
18AT3G14520.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G14520TPS18TPSaQ9LUE2TPS18 At3g14520 MIE1.2g3033.t1
19AT3G14540.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G14540TPS19TPSaQ9LUE0TPS19 At3g14540 MIE1.4g3033.t1
20AT4G13280.2terpenoid synthase 12AT4G13280TPS12TPSaQ9T0J9TPS12 At4g13280 T9E8.20g3033.t1
21AT4G13300.1terpenoid synthase 13AT4G13300TPS13TPSaQ9T0K1TPS13 At4g13300 T9E8.40g3033.t1
22AT5G44630.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT5G44630TPS11; BSTPSaQ4KSH9BS TPS11 At5g44630 K15C23.7g3033.t1
23AT1G48800.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT1G48800TPS28TPSaQ9C748TPS28 At1g48800 F11I4_3g3033.t1
25AT1G70080.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT1G70080TPS06TPSaQ84UU9TPS06 At1g70080 F20P5.19g3033.t1
26AT5G48110.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT5G48110TPS20TPSaQ9FI27TPS20 At5g48110 MDN11.20g3033.t1
27AT2G37140.1Terpenoid synthases superfamily proteinAT2G37140pseudo-C(TPSa)Q1PEW2At2g37140g26763.t1
28AT4G15870.1terpene synthase 1AT4G15870TPS01; TC1; TS1TPSaO23651TPS01 TC1 TS1 At4g15870 dl3975c FCAALL.405g3033.t1
29AT1G33750.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT1G33750TPS22TPSaQ9LQ27TPS22 At1g33750 F14M2.13g3033.t1
30AT2G23230.2Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT2G23230TPS05TPSaO22184TPS05 At2g23230 T20D16.14g3033.t1
31AT3G14490.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G14490TPS17TPSaQ9LRR2TPS17 At3g14490 MOA2.12g3033.t1
32AT3G29110.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G29110TPS16TPSaQ9LVP7TPS16 At3g29110 MXE2.1g3033.t1
33AT3G29410.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G29410TPS25TPSaQ9LIA1TPS25 At3g29410 MUO10.2g3033.t1
34AT3G32030.1Terpenoid cyclases/Protein prenyltransferases superfamily proteinAT3G32030TPS30TPSaQ9LH31TPS30 At3g32030 T8O3.12g3033.t1

Supplementary Table 6: Identification of methylerythritol phosphate (MEP) and mevalonic acid (MVA) genes in lemon grass

S. No.Gene ID from LemongrassUniprot ID Uniprot EntryAnnotation
1g38362.t1F4JCU3MVD2_ARATHDiphosphomevalonate decarboxylase MVD2, peroxisomal OS=Arabidopsis thaliana OX=3702 GN=MVD2 PE=1 SV=1
2g8212.t1F4K0E8ISPG_ARATH4 hydroxy 3 methylbut 2 en 1 yl diphosphate synthase (ferredoxin), chloroplastic OS=Arabidopsis thaliana OX=3702 GN=ISPG PE=1 SV=1
3g38362.t1O23722MVD1_ARATHDiphosphomevalonate decarboxylase MVD1, peroxisomal OS=Arabidopsis thaliana OX=3702 GN=MVD1 PE=1 SV=1
4g11679.t1O81014ISPE_ARATH4 diphosphocytidyl 2 C methyl D erythritol kinase, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=ISPE PE=2 SV=1
5g33940.t1P14891HMDH1_ARATH3 hydroxy 3 methylglutaryl coenzyme A reductase 1 OS=Arabidopsis thaliana OX=3702 GN=HMG1 PE=1 SV=1
6g23454.t1P34802GGPP1_ARATHHeterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=GGPPS1 PE=1 SV=2
7g33940.t1P43256HMDH2_ARATH3 hydroxy 3 methylglutaryl coenzyme A reductase 2 OS=Arabidopsis thaliana OX=3702 GN=HMG2 PE=2 SV=1
8g4041.t1P46086KIME_ARATHMevalonate kinase OS=Arabidopsis thaliana OX=3702 GN=At5g27450 PE=2 SV=1
9g10131.t1P54873HMCS_ARATHHydroxymethylglutaryl CoA synthase OS=Arabidopsis thaliana OX=3702 GN=HMGS PE=1 SV=2
10g11653.t1P69834ISPD_ARATH2 C methyl D erythritol 4 phosphate cytidylyltransferase, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=ISPD PE=1 SV=1
11g2230.t1Q09152FPPS1_ARATHFarnesyl pyrophosphate synthase 1, mitochondrial OS=Arabidopsis thaliana OX=3702 GN=FPS1 PE=2 SV=2
12g10476.t1Q38854DXS_ARATH1 deoxy D xylulose 5 phosphate synthase, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=DXS PE=1 SV=2
13g8827.t1Q38929IDI1_ARATHIsopentenyl diphosphate Delta isomerase I, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=IPP1 PE=1 SV=3
14g9222.t1Q39108GGR_ARATHHeterodimeric geranylgeranyl pyrophosphate synthase small subunit, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=GGR PE=1 SV=2
15g8827.t1Q42553IDI2_ARATHIsopentenyl diphosphate Delta isomerase II, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=IPP2 PE=1 SV=1
16g2230.t1Q43315FPPS2_ARATHFarnesyl pyrophosphate synthase 2 OS=Arabidopsis thaliana OX=3702 GN=FPS2 PE=2 SV=1
17g3152.t1Q8S4Y1THIC1_ARATHAcetyl CoA acetyltransferase, cytosolic 1 OS=Arabidopsis thaliana OX=3702 GN=AAT1 PE=1 SV=1
18g36791.t1Q94B35ISPH_ARATH4 hydroxy 3 methylbut 2 enyl diphosphate reductase, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=ISPH PE=1 SV=1
19g13764.t1Q9C6T1PMK_ARATHPhosphomevalonate kinase, peroxisomal OS=Arabidopsis thaliana OX=3702 GN=PMK PE=1 SV=1
20g15260.t1Q9CAK8ISPF_ARATH2 C methyl D erythritol 2,4 cyclodiphosphate synthase, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=ISPF PE=1 SV=1
21g3152.t1Q9FIK7THIC2_ARATHProbable acetyl CoA acetyltransferase, cytosolic 2 OS=Arabidopsis thaliana OX=3702 GN=At5g47720 PE=2 SV=1
22g9071.t1Q9XFS9DXR_ARATH1 deoxy D xylulose 5 phosphate reductoisomerase, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=DXR PE=2 SV=2
23g8827.t1A0A178ULI3A0A178ULI3_ARATHIsopentenyl diphosphate Delta isomerase OS=Arabidopsis thaliana OX=3702 GN=At5g16440 PE=3 SV=1
24g3152.t1A0A178UN67A0A178UN67_ARATHAACT1 OS=Arabidopsis thaliana OX=3702 GN=At5g47720 PE=3 SV=1
25g8827.t1A0A1I9LM15A0A1I9LM15_ARATHIsopentenyl diphosphate Delta isomerase OS=Arabidopsis thaliana OX=3702 GN=IPP2 PE=1 SV=1
26g38362.t1A0A1I9LME2A0A1I9LME2_ARATHDiphosphomevalonate decarboxylase OS=Arabidopsis thaliana OX=3702 GN=At3g54250 PE=1 SV=1
27g2230.t1A0A1P8B4W4A0A1P8B4W4_ARATHFarnesyl diphosphate synthase 2 OS=Arabidopsis thaliana OX=3702 GN=FPS2 PE=1 SV=1
28g22151.t1A0A2H1ZEF4A0A2H1ZEF4_ARATH2 C methyl D erythritol 2,4 cyclodiphosphate synthase OS=Arabidopsis thaliana OX=3702 GN=ISPF PE=1 SV=1
29g3152.t1A0A5S9YC31A0A5S9YC31_ARATHUncharacterized protein OS=Arabidopsis thaliana OX=3702 GN=At5g48230 PE=3 SV=1
30g33940.t1A0A654ER34A0A654ER34_ARATH3 hydroxy 3 methylglutaryl coenzyme A reductase OS=Arabidopsis thaliana OX=3702 GN=At1g76490 PE=3 SV=1
31g8212.t1B3H725B3H725_ARATH4 hydroxy 3 methylbut 2 enyl diphosphate synthase OS=Arabidopsis thaliana OX=3702 GN=HDS PE=1 SV=1
32g27299.t1C0Z3D4C0Z3D4_ARATHHydroxymethylglutaryl CoA reductase (NADPH) OS=Arabidopsis thaliana OX=3702 GN=At1g76490 PE=2 SV=1
33g2230.t1F4JNF1F4JNF1_ARATHFarnesyl diphosphate synthase 2 OS=Arabidopsis thaliana OX=3702 GN=FPS2 PE=1 SV=1
34g3152.t1F4JYM8F4JYM8_ARATHThiolase family protein OS=Arabidopsis thaliana OX=3702 GN=AACT1 PE=1 SV=1
35g9071.t1F4K7T6F4K7T6_ARATH1 deoxy D xylulose 5 phosphate reductoisomerase OS=Arabidopsis thaliana OX=3702 GN=DXR PE=1 SV=1
36g19714.t1Q67XB6Q67XB6_ARATHUncharacterized protein At1g31910 OS=Arabidopsis thaliana OX=3702 GN=At1g31910 PE=2 SV=1
37g23015.t1Q944G7Q944G7_ARATH1 deoxy D xylulose 5 phosphate synthase OS=Arabidopsis thaliana OX=3702 GN=At4g15560 PE=2 SV=1
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