The complete chloroplast genome of Ocimum basilicum L. var. basilicum (Lamiaceae) and its phylogenetic analysis

Abstract

Ocimum basilicum L. var. basilicum (Sweet Basil) is an aromatic herb belonging to the family Lamiaceae and is known for its medicinal uses. It is commonly used in traditional medicine for its therapeutic value, including anti-allergic, anti-inflammatory, antioxidant, antitumor, and antimicrobial properties. In this study, we generated the complete chloroplast genome sequence of O. basilicum var. basilicum using Illumina paired-end sequencing data. The chloroplast genome was 152,407 bp in length, containing a large single-copy (LSC) region of 83,409 bp and a small single-copy region (SSC) of 17,604 bp, separated by a pair of inverted repeats (IRs) of 25,697 bp. The genome contained 134 genes, including 89 protein-coding, 37 tRNA, and eight rRNA genes. Nine genes had one intron, two genes had two introns, and others did not have any intron. Overall GC content of the chloroplast genome was 38%, while that of LSC, SSC, and IR regions was 35.9%, 31.6%, and 43.1%, respectively. Phylogenetic analysis of the chloroplast genomes revealed that O. basilicum var. basilicum was closely related to Ocimum basilicum from the Ocimum species.

Keywords: Basilicum variety; Thiruneetru Pachilai; phylogenetic tree; plastid genome; sweet basil.

Figure 1.

The picture of the collected Ocimum basilicum var. basilicum sample. This image shows the whole plant (A), inflorescence (B), and herbarium specimen (C), which were recorded by the authors (Kirankumar S.I. and Raju Balaji).

Figure 2.

Circular map of the chloroplast genome of O. basilicum var. basilicum. From the center going outward, the first circle shows the distribution of the repeats connected with red (the forward direction) and green (the reverse direction) arcs. The second circle displays the tandem repeats marked with short bars. The third circle shows the LSC, SSC, IRa, and IRb regions. The fourth circle shows the percent of GC content. The next circle shows the genes having different colors based on the functional groups. The functional classification is shown at the bottom left. Genes inside the circle are transcribed in a clockwise direction, and those outside are in a counter-clockwise direction.

Figure 3.

Phylogenetic tree constructed by maximum-likelihood (ML) analysis based on complete chloroplast genome sequences, including O. basilicum var. basilicum (OQ706275.1) sequenced in this study. The numbers on the nodes indicate bootstrap values with 1000 replicates. The sequences used for tree construction are as follows: Ocimum basilicum (KY623639.1; Rabah et al. 2017), O. gratissimum (MW348919.1; Balaji et al. 2021), O. tenuiflorum subtype Rama (MW829604.1; Harini et al. 2021), O. tenuiflorum subtype Krishna (MW724787.1; Kavya et al. 2021), Platostoma chinense (MT328397.1), Pycnostachys reticulata (MT740257.1; Wu et al. 2021), Plectranthus barbatus (ON641315.1), Coleus hadiensis (OP611428.1), Hanceola exserta (MW238418.1; Zhu et al. 2023), Isodon serra (MT317099.1; Zhang et al. 2020), Siphocranion macranthum (MT473779.1; Zhao et al. 2021), Lycopus lucidus var. hirtus (MT980792.1; Wang et al. 2021), Lycopus europaeus (OM617843.1), Elsholtzia densa (MN793319.1; Fu et al. 2020), Elsholtzia densa var. ianthina (MT083931.1; Yang et al. 2020), Perilla frutescens var. hirtella (KT220692.1), P. frutescens var. frutescens (KT220689.1), P. frutescens var. crispa (KT220687.1), and Avicennia marina (CM032785.1; Natarajan et al. 2021).