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

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. ARTICLE HIGHLIGHTS1. The nuclear genome size is predicted to be 454,049,232 bps for 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.