Abstract
Spondias dulcis is a deciduous tree in the family Anacardiaceae. The species originates in South America and now is widely cultivated in tropical areas due to its edible fruits. In this study, we find that the length of the complete plastome of S. dulcis is 162,256 bp. It includes 35 tRNA genes and eight rRNA genes, 86 protein-coding genes and totally 130 genes. The complete plastome of S. dulcis includes a small single-copy (SSC) region of 18,459 bp, a large single-copy (LSC) region of 89,353 bp, and two inverted repeats (IRs) regions of 27,222 bp. The total G/C content of S. dulcis is 37.7%. It shows that S. dulcis is closely related to S. mombin within Anacardiaceae. It will contribute to the conservation genetics of S. dulcis and the phylogenetic studies in Anacardiaceae.
Keywords: Tropical fruits, genetics, Hainan, breeding, systematics, plastome
Introduction
Spondias dulcis Parkinson (1773) is a deciduous tree in the family Anacardiaceae (Buerki et al. 2010). The species originates in South America and is now widely cultivated in tropical areas (Buerki et al. 2010), partly because its fruits can be eaten. The species is called alien olive due to the fruits looking like olive. Here, we report the complete plastome of Spondias dulcis, which is expected to improve the quality of relevant collections and phylogenetic investigation of Anacardiaceae.
In this study, S. dulcis Parkinson was sampled from the city of Qionghai in Hainan, China (110.46°E,19.35°N). The tree of Spondias dulcis is 14 meters high and 16 cm in diameter at breast height. A voucher specimen (voucher code: D.-J. Chen, X.-R. Ke, A20, HUTB) and associated DNA were deposited in the Herbarium of Hainan University, Hainan province, China (code of herbarium: HUTB). The experiment was carried out as reported by Zhu et al. (2018). Cleaned sequencing data was assembled with GetOrganelle v1.7.5.0 (Santos and Almeida 2019). The plastome was annotated using the plastome of Spondias bahiensis P. Carvalho, Van den Berg and M. Machado (NC_030526.1) as a reference using Geneious v2021.1.1 (Biomatters Ltd, Auckland, New Zealand).
In this study, we find that the length of the complete plastome of S. dulcis is 162,256 bp. It includes 35 tRNA genes and eight rRNA genes, 86 protein-coding genes, and totally 130 genes. The complete plastome of Spondias dulcis includes a small single-copy (SSC) region of 18,459 bp, a large single-copy (LSC) region of 89,353 bp and two inverted repeats (IRs) regions of 27,222 bp. Eighteen protein-coding genes are duplicated in the IR. Seven tRNA are duplicated in the IR. 5S rRNA, 16S rRNA, 4.5S rRNA, and 23S rRNA are duplicated in the IR. The overall G/C content in the plastome is 37.7%, of which the corresponding value for the LSC, SSC, and IR regions are 35.7%, 32.2%, and 42.7%, respectively.
Based on existing data of related taxa from NCBI, we reconstructed a phylogenetic tree with RAxML with 1000 bootstraps with CIPRES (http://www.phylo.org/portal2/login!input.action). We found that Spondias dulcis is more closely related to Spondias mombin than other species in this genus in this study (Figure 1). Most nodes in the plastome maximum-likelihood (ML) tree of Anacardiaceae were highly supported. Furthermore, the plastid sequence of S. dulcis will promote relevant conservation and phylogenetic investigation of Anacardiaceae. Notably, Spondiadoideae was not supported as monophyletic as reported in previous studies (e.g. Pell et al. 2011; Weeks et al. 2014; Sun et al. 2016). Chen et al. (2016) found that Spondias, Dracontomelon, and Buchanania are in the same clade and sister to the rest of the family with moderate support, however, Muellner-Riehl et al. (2016) found that Spondias is closer to Dracontomelon than other genera within Anacardiaceae. Therefore, our study would bring great benefits to deepen the understanding complex relationships of plants such as those in Anacardiaceae.
Figure 1.
The maximum likelihood phylogeny obtained from 13 complete plastid sequences by RAxML. Support values are shown with bootstrap values at the nodes.
Funding Statement
This study is funded by the Hainan Province Science and Technology Special Fund [ZDYF2022XDNY190] and Hainan Provincial Natural Science Foundation of China [421RC486]. The funding information are inner funding of Hainan province.
Ethics statement
The study was approved by the institutional review board of Hainan University, Haikou, China. The collection of plant materials was conducted in accordance with guidelines provided by the Hainan University and Hainan province regulations. Field studies complied with Hainan province legislation.
Author contributions
Hua-Feng Wang designed the project. Xu-Long Yang and Xin-Xin Xu analyzed and interpreted the data; Xu-Long Yang and Xin-Xin Xu drafted the manuscript. Hua-Feng Wang revised it critically for intellectual content. All authors approved the final version of the manuscript.
Disclosure statement
No potential conflict of interest is reported by the author(s).
Data availability statement
The results of the genome sequence data are publicly available in NCBI GenBank (https://www.ncbi.nlm.nih.gov/) with registration number MZ929415.1. The associated BioProject, SRA and Bio-Sample numbers are PRJNA748537, SRR15651129 and SAMN20858429 respectively. A specimen was deposited at Hainan University (https://ha.hainanu.edu.cn/home2020/) under the voucher number D.-J. Chen, X.-R. Ke, A20.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The results of the genome sequence data are publicly available in NCBI GenBank (https://www.ncbi.nlm.nih.gov/) with registration number MZ929415.1. The associated BioProject, SRA and Bio-Sample numbers are PRJNA748537, SRR15651129 and SAMN20858429 respectively. A specimen was deposited at Hainan University (https://ha.hainanu.edu.cn/home2020/) under the voucher number D.-J. Chen, X.-R. Ke, A20.