De Novo Hybrid Assembled Draft Genome of Commiphora wightii (Arnott) Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis

Abstract

Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine–cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii.

A practical assembly guideline for genomes with various levels of heterozygosity

“…Consequently, more de novo genome assemblers for the HiFi reads were developed [ 18 , 19 ]. However, since HiFi sequencing is costlier than standard long-read sequencing, genome assembly using conventional long-read technology is preferred [ 20–22 ].…”