The complete chloroplast genome of the Euphorbia maculata L. (Euphorbiaceae): characterization and phylogeny

Abstract

Euphorbia maculata is an important medicinal plants of the family Euphorbiaceae. The complete chloroplast genome reported here is 162,685 bp in length, including two inverted repeats (IRs) of 26,822 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 90,514 bp and 18,527 bp, respectively. The whole chloroplast genome of E. maculata contains 111 genes, including 77 protein-coding genes, 4 transfer RNA, and 30 ribosome RNA. Phylogenetic analysis indicated that E. maculata is closely related to E. milii and E. tirucalli.

Keywords:

• Euphorbia maculata
• chloroplast genome
• phylogenetic analysis

Euphorbia maculata L. (Spotted spurge) is a fast-growing annual weed native to eastern North America and spread to Asia, Africa and Europe (Wu et al. 1994). It functions as a pioneer species with a prostrate growth habit in ecological succession. The milky sap of the plant is an irritant for many people. Like many members of the family Euphorbiaceae, it has been widely used as a folk medicine, which can produce anti-inflammatory and cancer chemopreventive agents of triterpenoids (Yi et al. 2018). It is necessary to develop genomic resources for E. maculata to provide intragenic information for its utilization and chloroplast genomes are valuable sources (Dong et al. 2020; Sun et al. 2020).

The fresh leaves of E. maculata were collected from Luxi county, Hunan province, China (28°12’59”N, 110°13’11”E). Voucher specimens were deposited in Institute of Chinese Materia Medica (Specimen accession number: 430723LY0485), China Academy of Chinese Medical Sciences. Total genomic DNA was extracted with the modified cetyltrimethyl ammonium bromide (CTAB) method (Li et al. 2013). Paired-end libraries were prepared with the NEBNext Ultra DNA Library Prep Kit. The genome was sequenced using the HiSeq X Ten platform (Illumina, Santiago, CA, USA). All good quality paired reads were assembled using the Spades program to contigs (Bankevich et al. 2012). Chloroplast genome sequence contigs were selected by the program BLAST (Altschul et al. 1990) using E. milii (Genbank accession number: MN713924) as a reference and the selected contigs were assembled using Sequencher 4.10 (Gene Codes Corporation, Ann Arbor, MI USA, http://www.genecodes.com). Chloroplast genome annotation was performed with Plann (Huang and Cronk 2015) using the E. milii as reference sequence. The annotated sequence was submitted to the GenBank under the accession number MT830858.

The complete chloroplast genome reported here is 1,62,685 bp in length, including two inverted repeats (IRs) of 26,822 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 90,514 bp and 18,527 bp, respectively. The overall GC-content of the chloroplast genome was 35.4%. The chloroplast DNA of E. maculata comprised 111 distinct genes, including 77 protein-coding genes, 4 transfer RNA, and 30 ribosome RNA, but didn’t contain cemA and rpl22 these two protein-coding genes. In these genes, 17 harbored a single intron, while two (ycf3and clpP) contained double introns.

In order to confirm the phylogenetic relationships of E. maculata within the genus Euphorbia and other related groups, total 26 complete cp genomes were obtained from Genbank and the genus Aristolochia was taken as an outgroup. All chloroplast genome sequences were aligned using MAFFT (Katoh et al. 2019) and ambiguous alignment regions were trimmed by Gblocks (Castresana 2000). Phylogenetic analysis was conducted based on maximum-likelihood (ML) analyses using RAxML (Stamatakis 2014), under the GTR + G model with 1000 rapid bootstrap replicates. The phylogenetic tree showed that all species of Euphorbia form a monophyletic group with 100% support, and E. maculata is closely related to E. milii and E. tirucalli (Figure 1). The chloroplast genome of E. maculata provided a lot of genetic information for species conservation and identification of genus Euphorbia.

Figure 1. Phylogenetic tree reconstruction of 27 taxa using maximum likelihood (ML) methods in the chloroplast genome sequences. ML bootstrap support value presented at each node.

Disclosure statement

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

Data availability statement

The data that support the findings of this study are openly available in GenBank of NCBI https://www.ncbi.nlm.nih.gov/, reference number MT830858, raw data BioProject ID: PRJNA662166.

Additional information

Funding

This work was supported by the National Key Research and Development Program of China [No. 2019YFC1711400 & No. 2019YFC1711402], and the National Natural Science Foundation of China [No. 81891014].