Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae

Yihui Wang; Yifei Xie; Jiayi Jin; Jinyue Li; Xiangdong Qiu; Yang Tong; Zhongyang Li; Zhixiang Zhang; Wenling Lai

doi:10.7717/peerj.15322

Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae

PeerJ. 2023 May 9:11:e15322. doi: 10.7717/peerj.15322. eCollection 2023.

Authors

Yihui Wang^#^{1

2}, Yifei Xie^#^{1

3}, Jiayi Jin¹, Jinyue Li⁴, Xiangdong Qiu¹, Yang Tong¹, Zhongyang Li^{1

3}, Zhixiang Zhang⁵, Wenling Lai^{1

3}

Affiliations

¹ School of Life Sciences, Gannan Normal University, Ganzhou, P.R. China.
² School of Landscape Architecture, Beijing Forestry University, Beijing, P.R. China.
³ Key Laboratory of Nanling Plant Resources Conservation and Utilization, Ganzhou, P.R. China.
⁴ Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna, P.R. China.
⁵ School of Ecology and Nature conservation, Beijing Forestry University, Beijing, P.R. China.

^# Contributed equally.

Abstract

Background: Elaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking.

Methods: To understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with Elaeocarpus japonicus and Sloanea sinensis (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software.

Results: The results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of Elaeocarpus, Sloanea, Crinodendron and Vallea lacked the rpl32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the ndhK gene in Elaeocarpus, Vallea stipularis, and Aristotelia fruticosa. The LSC region of the chloroplast genomes lacked the infA gene in genus Elaeocarpus and Crinodendron patagua. (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. Rps3 was detected in the neighboring regions of the LSC and IRb regions in Elaeocarpus. (d) Phylogenomic analysis revealed that the genus Elaeocarpus is closely related to Crinodendron patagua on an independent branch and Aristotelia fruticosa is closely related to Vallea stipularis, forming a clade with the genus Sloanea. Structural comparisons showed that Elaeocarpaceae diverged at 60 Mya, the genus Elaeocarpus diverged 53 Mya and that the genus Sloanea diverged 0.44 Mya. These results provide new insight into the evolution of the Elaeocarpaceae.

Keywords: Chloroplast genome; Divergence time; Elaeocarpus; Phylogenomic.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chloroplasts / genetics
Ecosystem
Elaeocarpaceae* / genetics
Genome, Chloroplast* / genetics
Phylogeny

Grants and funding

This work was supported by the National Natural Science Foundation of China (Grant numbers 31110103911, J1310002), and the Science and Technology Project in Jiangxi Province Department of Education (GJJ170839). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.