Abstract
Mallotus peltatus is a tropical plant of the Euphorbiaceae family, which could be used as a beverage and medicine in Hainan, China. Here, we report and characterize the complete plastome of M. peltatus. The complete plastome is 163,304 bp in length and contains a typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,112 bp, a large single-copy (LSC) region of 89,886 bp and a small single-copy (SSC) region of 18,840 bp. The plastome contains 131 genes, consisting of 78 unique protein-coding genes, 30 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA), and eight pseudogenes. The overall A/T content in the plastome of M. peltatus is 64.02%. The complete plastome sequence of M. peltatus will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae.
Keywords: Mallotus peltatus, plastome, phylogeny, genome structure, Euphorbiaceae
Introduction
Mallotus peltatus (Geiseler) Müll.Arg. (Euphorbiaceae) is an evergreen shrub or small tree ranging from two to eight m tall (Li et al. 2008). M. peltatus is a native plant of Hainan Island in China, which is used as a beverage and medicine for local people (Yan et al. 2019). At present, the complete plastome information and systematic position of M. peltatus has been rarely studied and reported. Hence, the genetic and genomic information is essential needed to aid to its resource exploitation and conservation. Here, we report and characterize the complete plastome of M. peltatus (GenBank accession number: MN885802, this study) in an effort to benefit M. peltatus germplasm collection, conservation and future breeding.
In this study, M. peltatus was sampled from Baoting county in Hainan province of China (109.70° E, 18.63° N). A voucher specimen (Wang et al., GPSII-001) and its DNA was deposited in the Herbarium of the Institute of Tropical Agriculture and Forestry (code of herbarium: HUTB), Hainan University, Haikou, China.
The experiment is performed as reported in Zhu et al. (2018). Around six Gb clean data were assembled against the plastome of Ricinus communis (JF937588.1) (Rivarola et al. 2011) using MITO bim v1.8 (Le-Petit-Quevilly, France) (Hahn et al. 2013). The plastome was annotated using Geneious R8.0.2 (Biomatters Ltd., Auckland, New Zealand) against the plastome of R. communis (JF937588.1). The annotation was corrected with DOGMA (Wyman et al. 2004).
The plastome of M. peltatus is found to possess a total length 163,304 bp with the typical quadripartite structure of angiosperms, contains two Inverted Repeats (IRs) of 27,112 bp, a Large Single-Copy (LSC) region of 89,886 bp and a Small Single-Copy (SSC) region of 18,840 bp. The plastozme contains 131 genes, consisting of 78 unique protein-coding genes (seven of which are duplicated in the IR), 30 unique tRNA genes (seven of which are duplicated in the IR) and four unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). Among these genes, there are eight pseudogenes. The overall A/T content in the plastome of M. peltatus is 64.02%, which the corresponding value of the LSC, SSC and IR region were 66.30%, 70.40% and 57.80%, respectively.
We used RAxML (Stamatakis 2006) with 1,000 bootstraps under the GTRGAMMAI substitution model to reconstruct a maximum likelihood (ML) phylogeny of seven published complete plastomes of Euphorbiaceae, using Glochidion chodoense (Phyllanthaceae, Malpighiales) and Linum usitatissimum (Linaceae, Malpighiales) as outgroups. The phylogenetic analysis indicates that M. peltatus is closer to R. communis than other species in this study (Figure 1). Most nodes in the plastome ML trees were highly supported. With the complete plastome sequence of M. peltatus plastome , its resource exploitation and conservation project can be better proceeded, and phylogenetic studies of Euphorbiaceae can be explored more sufficiently.
Figure 1.
The best ML phylogeny recovered from 10 complete plastome sequences by RAxML. Accession numbers: Mallotus peltatus (GenBank accession number, MN885802, this study), Manihot esculenta NC_010433.1, Hevea brasiliensis NC_015308.1, Ricinus communis NC_016736.1, Croton tiglium NC_040113.1, Jatropha curcas NC_012224.1, Euphorbia tirucalli NC_042193.1, Euphorbia esula NC_033910.1, Glochidion chodoense NC_042906.1, Linum usitatissimum NC_036356.1.
Funding Statement
This study was funded by National Natural Scientific Foundation of China [31660055, 31560108 and 31660074] and by startup fund from Hainan University [kyqd1633 and kydq(zr)1840].
Disclosure statement
No potential conflict of interest was reported by the authors.
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