Comparative Chloroplast Genomics of Mangrove Species: Phylogenetic Insights and Evolutionary Analysis

May 06, 2020
plant genomics mangroves chloroplast genome
Comparative Chloroplast Genomics of Mangrove Species: Phylogenetic Insights and Evolutionary Analysis

Mangrove ecosystems serve as critical environmental buffers between land and sea, hosting unique plant species that have adapted to extreme coastal conditions. Despite their ecological importance, the chloroplast genomes of mangrove species remain largely unexplored. In our latest study, published in BioMed Research International, we present complete chloroplast genome assemblies of 14 mangrove species across six taxonomic orders, providing an in-depth comparative analysis of their genomic features and evolutionary adaptations.

Key Findings

  • Chloroplast Genome Assembly and Structure:
    The assembled chloroplast genomes range from 149 kb to 168 kb, exhibiting a conserved structure of two inverted repeats (IRs), one large single-copy (LSC), and one short single-copy (SSC) region. Most genes remain highly conserved, with only four genes showing signs of positive selection.

  • Phylogenetic Insights from Chloroplast DNA:
    Using 44 conserved genes across 71 plant species, we reconstructed the phylogenetic relationships of mangroves within the broader rosid and asterid clades. The tree confirmed the classification of obscure families in Malpighiales and refined the evolutionary positioning of mangrove species in relation to terrestrial plants.

  • Divergence and Molecular Evolution:
    Comparative genomic analyses revealed that chloroplast IR regions exhibit the lowest genetic divergence, indicating evolutionary stability. Additionally, simple sequence repeats (SSRs) were found to be highly variable, suggesting their potential use as genetic markers for population studies.

Reflections

This project is part of our funded research on mangrove symbiotic microbiomes and represents a significant step in XinLab’s environmental genomics initiatives. The research also forms part of the doctoral dissertation of Chengcheng Shi, who has contributed extensively to comparative genomic analyses in this study.

The exploration of mangrove chloroplast genomes aligns with our broader effort to understand how plants adapt to extreme environments and how symbiotic microorganisms contribute to their survival. Working alongside Professor Simon Lee’s team at the University of Macau, we integrated sequencing and bioinformatic approaches to construct high-resolution genomic data, further enriching our knowledge of mangrove phylogeny and molecular evolution.

The full text of this study can be accessed online at BioMed Research International.