Comparative chloroplast genome analyses provide insights into evolutionary history of Rhizophoraceae mangroves

Ying Zhang; Yuchen Yang; Meng He; Ziqi Wei; Xi Qin; Yuanhao Wu; Qingxing Jiang; Yufeng Xiao; Yong Yang; Wei Wang; Xiang Jin

doi:10.7717/peerj.16400

Comparative chloroplast genome analyses provide insights into evolutionary history of Rhizophoraceae mangroves

PeerJ. 2023 Nov 17:11:e16400. doi: 10.7717/peerj.16400. eCollection 2023.

Authors

Ying Zhang^#^{1

2

3}, Yuchen Yang^#⁴, Meng He⁵, Ziqi Wei⁵, Xi Qin⁵, Yuanhao Wu⁵, Qingxing Jiang⁵, Yufeng Xiao⁵, Yong Yang⁵, Wei Wang², Xiang Jin^{2

5}

Affiliations

¹ Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, Hainan, China.
² Qiongtai Normal University, Research Center for Wild Animal and Plant Resource Protection and Utilization, Haikou, Hainan, China.
³ Lingnan Normal University, Life Science and Technology School, Zhanjiang, Guangdong, China.
⁴ State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, Guangdong, China.
⁵ Hainan Normal University, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Haikou, Hainan, China.

^# Contributed equally.

Abstract

Background: The Rhizophoraceae family comprises crucial mangrove plants that inhabit intertidal environments. In China, eight Rhizophoraceae mangrove species exist. Although complete chloroplast (Cp) genomes of four Rhizophoraceae mangrove plants have been reported, the Cp genomes of the remaining four species remain unclear, impeding a comprehensive understanding of the evolutionary history of this family.

Methods: Illumina high-throughput sequencing was employed to obtain the DNA sequences of Rhizophoraceae species. Cp genomes were assembled by NOVOPlasty and annotated using CpGAVAS software. Phylogenetic and divergence time analyses were conducted using MEGA and BEAST 2 software.

Results: Four novel Cp genomes of Rhizophoraceae mangrove species (Bruguiera sexangula, Bruguiera gymnorrhiza, Bruguiera × rhynchopetala and Rhizophora apiculata) were successfully assembled. The four Cp genomes ranged in length from 163,310 to 164,560 bp, with gene numbers varying from 124 to 128. The average nucleotide diversity (Pi) value of the eight Rhizophoraceae Cp genomes was 0.00596. Phylogenetic trees constructed based on the complete Cp genomes supported the monophyletic origin of Rhizophoraceae. Divergence time estimation based on the Cp genomes of representative species from Malpighiales showed that the origin of Rhizophoraceae occurred at approximately 58.54-50.02 million years ago (Mya). The divergence time within the genus Rhizophora (∼4.51 Mya) was much earlier than the divergence time within the genus Bruguiera (∼1.41 Mya), suggesting recent speciation processes in these genera. Our data provides new insights into phylogenetic relationship and evolutionary history of Rhizophoraceae mangrove plants.

Keywords: Chloroplast genome; Divergence time; Mangroves; Organellar phylogenomics; Rhizophoraceae.

MeSH terms

Base Sequence
Chloroplasts
Genome, Chloroplast*
Phylogeny
Rhizophoraceae* / genetics

Grants and funding

This work was supported by project of Technical Innovation Special Project of Hainan Scientific Research Institutes (Grant No. JCYJ-2021-10, KYYS-2021-13); the Foundation for Academician Innovation Platform of Hainan Province (Grant No. YSPTZX2020023, YSPTZX2022011); Undergraduates Training Program for Innovation and Entrepreneurship of Hainan Province; BGCI Franklinia TC project (Grant No. GTC/2022/023). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.