Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights

Rui XU; Xinyue GUAN; Jing LIU; Xiujuan YIN; Liqiang WANG

doi:10.1007/s00343-026-6037-0

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Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights

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- Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights
- Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights
- 海洋湖沼学报(英文) 2026年页码：1-16
- Affiliations：
  
  College of Pharmacy, Heze University, Heze 274015, China
- Author bio：
  
  lys832000@163.com
- Funds：
- DOI：10.1007/s00343-026-6037-0
  中图分类号：
- 收稿：2026-01-26，
  
  录用：2026-03-25，
  
  网络首发：2026-10-19，
- Accepted：
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Rui XU, Xinyue GUAN, Jing LIU, 等. Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights[J/OL]. 海洋湖沼学报(英文), 2026,1-16.

XU Rui,GUAN Xinyue,LIU Jing,et al.Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights[J].Journal of Oceanology and Limnology,
Rui XU, Xinyue GUAN, Jing LIU, 等. Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights[J/OL]. 海洋湖沼学报(英文), 2026,1-16. DOI： 10.1007/s00343-026-6037-0.

XU Rui,GUAN Xinyue,LIU Jing,et al.Comprehensive analysis of chloroplast genomes from 15 mangrove species (Rhizophoraceae): codon usage, phylogenetic relationships, and evolutionary insights[J].Journal of Oceanology and Limnology, DOI：.

摘要

Abstract

Mangrove plants

serving as critical blue carbon ecosystems and biodiversity hotspots

play critical roles in coastal protection

water purification

and climate change mitigation. In this paper

we present the first comprehensive analysis of chloroplast genomes from 15 mangrove species within the Rhizophoraceae family

with particular emphasis on their codon usage bias (CUB)

phylogenetic connections

and evolutionary dynamics. The total GC contents of protein-coding genes (PCGs) span from 36.79% to 38.13%

with a distribution trend of 50%

-site GC (GC1)

-site GC (GC2)

total GC (GCall)

-site GC (GC3)

synonymous codon 3

GC (GC3s). The average values of effective number of codons (ENC) range from 46.43 to 47.18

reflecting a relatively weak CUB across the genomes. This bias is shaped by both mutational pressure and natural selection

with mutation exerting a more significant influence. We identified 13–19 optimal codons across these species

with ACU

AUU

CAA

CGU

GGU

GUA

UGC

and UUA being the most common optimal codons. Among all the genes analyzed

the

rps14

gene demonstrated the strongest CUB (ENC

35)

primarily driven by natural selection that optimizes its expression to ensure the efficient and accurate synthesis of the ribosome

whereas

rps18

gene exhibited clear signals of positive selection across all species against their terrestrial relative by the ratio of non-synonymous and synonymous substitution (Ka/Ks) analysis

suggesti

ng it may be undergoing potential adaptive evolution within Rhizophoraceae mangrove species. Phylogenetic analysis based on common coding sequences (CDSs)

concatenated sequences of

rps14

and

rps18

and relative synonymous codon usage (RSCU) values strongly supported monophyletic groups of four true mangrove genera. This study elucidated the synonymous codon usage patterns within the Rhizophoraceae family

offering valuable insights into their phylogenetic relationships

evolutionary processes

and potential applications in genetic engineering of Rhizophoraceae mangrove species.

关键词

Keywords

references

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