Complete chloroplast genome sequence and phylogenetic analysis of Mallotus paniculatus (Lam.) Müll. Arg. (Euphorbiaceae)

Abstract Mallotus paniculatus (Lam.) Müll. Arg. 1865 (Euphorbiaceae) is a shrub or small tree with medicinal properties that is distributed across Southeast Asia. In this study, we sequenced the complete chloroplast genome of M. paniculatus to study phylogenetic relationships within the family Euphorbiaceae Juss. The complete chloroplast genome of M. paniculatus was 164,455 bp in length, with an overall GC content of 35.3%. It was found to consist of a long single copy region of 89,021 bp, a small single copy region of 18,524 bp, and a pair of inverted repeats of 28,455 bp. Results indicated that the chloroplast genome contains a total of 131 genes, including 78 protein-coding genes, 37 tRNA genes, eight rRNA genes, and eight pseudogenes. The phylogenetic tree showed that M. paniculatus is closely related to Mallotus japonicus and Mallotus peltatus.

Mallotus paniculatus (Lam.) M€ ull. Arg. is a shrub or small tree belonging to the spurge family (Euphorbiaceae Juss.), which was first described by Lamarck in 1865 (Lamarck 1865). It is primarily distributed in the Chinese provinces of Yunnan, Guizhou, Guangxi, Guangdong, Hainan, Fujian, and Taiwan, where it grows in thickets at altitudes of 50-1300 m above sea level. In traditional medicine, the leaves and roots of M. paniculatus are often used as a drug and have a slightly bitter, astringent, and flat taste (Qiu 1996). The leaves are used for heat-clearance, damp-elimination, and detoxification, as well as to relieve pain and stop bleeding, whereas the roots have anti-inflammatory and astringent properties (Rivi ere et al. 2010;Wang et al. 2013;Zhu and Ma 2014). In Guangxi province, the plant is used to treat dysentery, otitis media, and other ailments. Previous studies on this species have focused on its chemical composition, morphological characteristics, and biological activities. However, no studies on the molecular biological properties of M. paniculatus have been published. Here, we studied the sequence of the chloroplast genome of M. paniculatus and revealed the phylogenetic relationship between this plant and other species of the Euphorbiaceae family.
Fresh leaves of M. paniculatus were collected in the city of Fangchenggang, Guangxi,China. (107.98 E,22.15 N). The specimens were identified by Nong Zhou (erhaizn@126.com) and deposited into the herbarium of the Chongqing Three Gorges University (https://www.sanxiau.edu.cn) under the voucher number ZN20210315. Total genomic DNA was extracted using the improved CTAB method (Doyle 1987;Yang et al. 2014) and sequenced with the Illumina HiSeq 2500 platform (Novogene, Tianjin, China). High-throughput sequencing generated approximately 5.3 Gb of raw data. The default settings of the Trimmomatic software (v. 0.32) were used to screen the original data (Bolger et al. 2014). Then, the obtained clean reads were assembled into circular contigs using the GetOrganelle toolkit (Jin et al. 2020) with Mallotus peltatus (NC_047284) as the reference. Finally, the cpDNA was annotated using the Dual Organellar Genome Annotator GeSeq (Tillich et al. 2017) and CpGAVAS2 (Shi et al. 2019). The chloroplast genome was submitted to GenBank (accession number: MZ597547).
The total length of the chloroplast genome was 164,455 bp, and the total GC content was 35.3%. The chloroplast genome of M. paniculatus showed a typical quadripartite structure, including a pair of inverted repeats of 28,455 bp each, separated by a small single copy region of 18,524 bp and a long single copy region of 89,021 bp. The sequence of the chloroplast genome revealed a total of 131 genes, including 78 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Further, we identified a total of eight pseudogenes (rps16, rbcL, petB, ndhF, ndhD, ndhG, and a pair of reverse repeats of ycf1).
To study their phylogenetic relationships, the chloroplast genome sequences of 26 Euphorbiaceae species and two Daphniphyllaceae species were downloaded from the GenBank database. Sequence alignment was performed using MAFFT (v. 7.427) (Katoh and Standley 2013). A maximum-likelihood phylogenetic tree was constructed using RAxML (Stamatakis 2014), with 1000 bootstrap replicates, and by applying the GTRGAMMAI model. The maximum likelihood phylogenetic tree showed that among the species analyzed, M. japonicus and M. peltatus were the closest relatives of M. paniculatus (Figure 1). This study provides a scientific basis to exploit these resources and a foundation for further phylogenetic analyses of M. paniculatus.

Ethics statement
Mallotus paniculatus (Lam.) M€ ull. Arg. is not a protected plant, and our research did not damage any of the M. paniculatus population. Therefore, no special permission was needed.