The complete mitochondrial genome sequence of Senna occidentalis (Fabales: Fabaceae)

Abstract

Senna occidentalis (family: Fabaceae) is an annual herbaceous plant native to the Americans. The complete mitochondrial genome sequence of S. occidentalis is 447,106 bp long and contains 53 annotated genes, including 33 protein-coding genes, 17 tRNA genes, and 3 rRNA genes. Phylogenetic analysis of the mitochondrial genome confirmed divergence of S. occidentalis (subfamily: Caesalpinioideae) from the related subfamily Faboideae.

Keywords:

• Fabaceae family
• mitochondrial genome
• Senna occidentalis

The genus Senna of the Fabaceae family includes about 260 species in South America (Marazzi et al. 2006). Senna occidentalis (formerly Cassia occidentalis) tissues are used in many countries as anti-inflammatory, antiplatelet, muscle relaxant, antimalaria, and antihemolytic medicines (Neboh and Ufelle 2015). A sample for sequencing was obtained from the National Agrobiodiversity Center (voucher number: IT 175099; geographic coordinates: N 35° 49′ 19″, E 127° 8′ 56″) in Jeonju, Korea.

Whole genome sequencing was performed using the Illumina Genome Analyzer platform (HiSeq4000, Illumina, USA). Reads were assembled using CLC Genomics Workbench, version 4.6 (CLC Inc., Aarhus, Denmark). The resulting three contigs were joined using the mitochondrial sequence of Cicer arientinum (GenBank: EU835853) as a reference. The draft genome was confirmed by paired-end read mapping, and gene annotation was conducted using DOGMA (Wyman et al. 2004) and BLAST (https://blast.ncbi.nlm.nih.gov/).

The mitochondrial genome of S. occidentalis consists of a single circular chromosome 447,106 bp in length. The genome contains 53 annotated genes, including 33 protein-coding genes, 17 tRNA genes, and 3 rRNA genes. Among these, we identified 11 open reading frames corresponding to the nad1 and nad5 genes. Interestingly, the nad1 and nad5 splice sites are located near exons 1, 2, 3, 4, and 5. The complete mitochondrial genome of S. occidentalis was deposited into GenBank (accession number MF358694).

A phylogenetic tree of species in the Fabaceae family, including S. occidentalis, was constructed from mitochondrial sequences. Phylogenetic relationships were inferred from 16 common mitochondrial protein-coding genes. Genome alignments were performed using CLC Genomics Workbench, version 6.5 (CLC Inc., Aarhus, Denmark), and MEGA 7.0 (Kumar et al. 2016) was used for tree construction. Of the surveyed species, S. occidentalis was found to be most closely related to the last common ancestor of the Fabaceae family (Figure 1). Phylogenetic analysis also confirmed placement of S. occidentalis in the subfamily Caesalpinioideae, as it is clearly divergent from members of the Faboideae subfamily.

Figure 1. Phylogeny of S. occidentalis and seven related species based on mitochondrial genome sequences. The phylogenetic tree was constructed from the full mitochondrial genome sequences using maximum likelihood analysis with 1000 bootstrap replicates. Bootstrap values are displayed at each node.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was carried out with the support of the Cooperative Research Program for Agriculture Science and Technology Development (National Agricultural Genome Program, Project No. PJ013373), Rural Development Administration, Republic of Korea