Abstract
Background: Seagrasses are ideal for studying plant adaptation to marine environments. A previous study reported the transfer of lost chloroplast (cp) genes to the nuclear genome. However, it remains unclear whether the lost cp genes were transferred to the mitochondrial (mt) genome.
Result: A divergent evolutionary trajectory was determined between cp and mt genomes across four seagress species. The cp genome exhibited a more stable genome structure, while the mt genome displayed structural diversity. Compared to other monocotyledons, these seagrasses have smaller mt genomes. This study revealed significant gene loss during evolution, including the complete loss of all cp-rpl19 genes in Zosteraceae; most of cp-ndh genes in Hydrocharitaceae; and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in P. iwatensis. Notably, most ribosomal protein genes were lost in both mt and cp genomes. Horizontal gene transfer showed that the deleted cp genes were not transferred to the mt genome. Extensive sequence transfer between the organelles of the four seagrasses was discovered, with the mt genome of Zostera containing a large portion of DNA transferred from the cp genome. Rearrangement analyses revealed an inversion in the cp genome of R. sinensis, which had not been reported previously. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified in seagrasses, potentially associated with their adaptation to the marine environment.
Conclusion: In this study, we assembled and annotated the complete organelle genome of R. sinensis. This study enriches the genomic resources and provides new evidence of dynamic gene evolution in seagrasses.