The complete chloroplast genome of Sesbania cannabina (Fabaceae) from China

Abstract

Sesbania cannabina (Retz.) Poir. (Fabaceae) is an annual herb, widely distributed in the tropical and subtropical regions. In this study, the complete chloroplast (cp) genome of S. cannabina was reported and phylogenetic analysis was conducted with Fabaceae species based on the cp genome sequences. The cp genome of S. cannabina is 156,894 bp in length, consisting of a pair of inverted repeats (IR, 25,465 bp), a small single-copy (SSC, 18,837bp) and a large single-copy (LSC, 87128 bp) region. It encodes 126 genes including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The Maximum Likelihood tree shows S. cannabina which is nested in Hologalegina clade of the subfamily Papilionoideae (Fabaceae).

Keywords:

• Sesbania cannabina
• Fabaceae
• chloroplast genome

The genus Sesbania Adanson (Fabaceae) is usually distributed in tropical and subtropical regions which included around 85 species (Farruggia et al. 2018). Most Sesbania species are quite unusual because they prefer the wetland habitats compared to the mostly dry-site inhabiting members of the legume family. Sesbania cannabina (Retz.) Poir (Fabaceae) is an annual herb with strong rhizomes, and it is a source of materials widely cultivated as a fiber plant, especially in India, and it is often used as manure. The sample in this study was collected from Guangzhou, China. The voucher specimen (Duan2019001) was deposited at the South China Botanical Garden (IBSC).

Total genomic DNA were extracted from leaf tissue samples preserved in silica gel using the CTAB method (Doyle 1987). Total genomic DNA sample was fragmented into around 500 bp in size. The libraries were prepared and sequenced on the Illumina Hiseq X-Ten plat-form (Illumina Inc., San Diego, CA) with 150 bp paired-end reads. The adapters of the raw data were removed by Trimmomatic (Bolger et al. 2014). SPAdes v. 3.11 (Bankevich et al. 2012) was applied for the complete chloroplast (cp) genome de novo assembly. The cp genome was annotated by Dual Organellar GenoMe Annotator (DOGMA) (Wyman et al. 2004). The cp genome of S. cannabina (GenBank accession no. MT120811) is 156, 894 bp in length, which included a large single-copy (LSC, 87,128 bp), a small single copy (SSC, 18,837 bp), and a pair of inverted repeats (IRs, 25,465 bp). Total 126 genes were annotated, including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall G/C content is 35.4%.

To understand the phylogenetic relationship of this newly sequenced S. cannabina with related genera, totally 18 chloroplast genomes downloaded from GenBank were applied to construct the systematic relationships. The download genomes accession numbers are shown in Figure 1. We used Geneious prime and Mauve plugin to adjust gene order and remove one copy of IR regions of chloroplast genomes, MAFFT v.7 (Katoh and Standley 2013) to align these 19 cp genomes, TrimAl (Capella-Gutiérrez et al., 2009) with parameter 0.75 to trim the alignment, and the program IQ-TREE v.1.4.2 (Nguyen et al. 2015) with 1000 bootstrap replicates to run a Maximum Likelihood (ML) tree. GenBank accession numbers are given in Figure 1. The ML tree (Figure 1) shows that the genus Sesbania has a close relationship with Robinia, and they belong to the clade of Hologalegina, which is congruent with the previous study (Farruggia et al., 2018).

Figure 1. Maximum-likelihood phylogenetic tree inferred from 19 chloroplast genomes of Fabaceae. The position of Sesbania cannabina is highlighted. The bootstrap values are shown above each node and the values of 100% are shown with asterisks. 

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This study was supported by the grants from the Natural Science Foundation of China (Grant no. 31600162), Science and Technology Key research and development project of Guangxi (Grant no. Guike AB18221054) and Strategic Priority Research Program of Chinese Academy of Sciences (Grant no. XDA13020603). The first author was sponsored by the China Scholarship Council (Grant no. 201806300089) and the International Association for Plant Taxonomy (IAPT) Research grant.