Journal Article

Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China

Nie, Liyun, Liu, Fangling, Tembrock, Luke R., Wu, Zhiqiang, Jiang, Zhuying, Kong, Jiali, Wang, Meixia, Wang, Penghao, Kan, Shenglong, Liu, Xiaoli, Wang, Jie

2025

Overview

Background Ginkgo biloba L., an iconic living fossil, challenges traditional views of evolutionary stasis. While nuclear genomic studies have revealed population structure across China, the evolutionary patterns reflected in maternally inherited plastomes remain unclear, particularly in the Sichuan Basin - a potential glacial refugium that may have played a crucial role in Ginkgo ’s persistence. Results Analysis of 227 complete plastomes, including 81 newly sampled individuals from the Sichuan Basin, revealed three distinct maternal lineages differing from known nuclear genome patterns. We identified 170 sequence variants and extensive RNA editing (235 sites) with a bias toward hydrophobic amino acid conversions, suggesting active molecular evolution. A previously undocumented haplotype (IIA2), predominant in western Sichuan Basin populations, showed close genetic affinity with rare refugial haplotypes. Western populations exhibited higher haplotypic diversity and distinctive genetic structure, supporting the basin’s role as both glacial refugium and corridor for population expansion. Ancient trees (314–784 years) provided evidence for interaction between natural processes and historical human dispersal in shaping current genetic patterns. Conclusions Our findings demonstrate substantial genetic diversity within Sichuan Basin Ginkgo populations and reveal dynamic molecular evolution through plastome variation and RNA editing patterns, challenging the notion of evolutionary stasis in this living fossil. This study provides crucial genomic resources for understanding Ginkgo ’s evolution and informs conservation strategies for this endangered species.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Amino acid sequence / Amino acids / basins / Biological diversity conservation / Biological evolution / Biomedical and Life Sciences / China / Conservation / Editing / Endangered & extinct species / Endangered species / evolution / Evolution & development / Evolution, Molecular / Evolutionary conservation / Extinction / Fossils / Genetic aspects / Genetic diversity / Genetic structure / Genetic Variation / Genetics, Population / Genomes / Genomics / Ginkgo / Ginkgo biloba / Ginkgo biloba - genetics / Glacial periods / Glacial refugia / Haplotypes / Health aspects / humans / Hydrophobicity / Life Sciences / Living fossil evolution / Living fossils / Methods / Molecular evolution / Morphology / Mutation / nuclear genome / Nucleotide sequence / Phylogeny / Plant Sciences / Plastome diversity / Plastomes / Population differentiation / Population genetics / Population growth / Population structure / Population studies / Populations / Protection and preservation / Proteins / Ribonucleic acid / RNA / RNA editing / Structure / Transfer RNA / Tree Biology / Wildlife conservation