Wheat chloroplast pangenome reveals frequent intramolecular recombination in the inverted repeat regions

作者：Hua Zhang, Xuebing Qiu, Zhiliang Zhang, Jijin Zhang, You Qing, Yafei Guo, Xinyue Song, Chengzhi Liang, Yanling Sun, Yang Zhao, Changbin Yin, Jing Wang, Fei Lü, Mingsheng Chen · 发表于：BMC Plant Biology · 年份：2025 · DOI：10.1186/s12870-025-07577-5 · 被引用次数：5 · 研究领域：Genomics and Phylogenetic Studies、Genome Rearrangement Algorithms、Chromosomal and Genetic Variations

BACKGROUND: In eukaryotes, the mutation rate of the chloroplasts is lower than that of the nuclear genomes. Advances in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologies, together with improvements in genome assembly algorithms, have substantially propelled research in chloroplast genomics. Although nearly 9,000 chloroplast genomes have been released, chloroplast population genetics for specific species remains unexplored. The chloroplast genome possesses a quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeats (IRs). A longstanding question is why the maternally inherited chloroplast genome does not appear to suffer from the Muller’s ratchet effect. It has been hypothesized that intramolecular recombination within the chloroplast genome may counteract this effect; however, direct evidence for such recombination remains lacking. RESULTS: We conducted chloroplast population data analysis in hexaploid wheat and its ancestral relatives. One the basis of the pan-genome constructed and phylogeny analysis of chloroplast genomes of all samples, we calculated the chloroplast diversity of hexaploid wheat (π = 0.0001) is the lowest among the three ploidy types tested. Additionally, we found that during the formation of hexaploid wheat, only the chloroplasts from tetraploid wheat were inherited. Moreover, Aegilops tauschii contributed solely as the paternal provider of nuclear g...