Multiple chromosomal configurations and phylogenetic implications in Saccharum mitochondrial genomes
Published 05 December, 2025
Mitochondria play a crucial role in plant growth, fertility, and adaptation. Sugarcane (Saccharum hybrids) represents the world’s primary sugar and energy crop, while S. spontaneum and S. arundinaceum serve as valuable parental germplasm. Despite their importance, limited research exists regarding the mitochondrial genomes of sugarcane and related species.
To that end, a team of researchers from China unveils genetic mysteries of Saccharum mitochondrial genomes. They reported their results in the Journal of Integrative Agriculture.
“This study presents the assembly of mitogenomes from one S. arundinaceum, one S. spontaneum, and five sugarcane cultivars,” shares corresponding author Youxiong Que, a professor at Chinese Academy of Tropical Agricultural Sciences. “Analysis revealed that these mitogenomes, encoding 33 protein-coding genes (PCGs), ranged from 445,578 to 533,662 bp, with GC content between 43.43–43.82%.”
The primary structures of S. arundinaceum consisted of three small rings, while S. spontaneum exhibited one ring and one linear structure, and sugarcane displayed two rings; multiple potential conformations emerged due to repeat-mediated recombination.
“Additionally, this research developed an intron marker SAnad4i3 capable of species differentiation,” say Que. “Our analysis identified between 540 and 581 C to U RNA editing sites in the PCGs, with six RNA editing sites linked to start or stop codon creation in S. arundinaceum, and five sites each in S. spontaneum and sugarcane hybrids.”
Notably, 30–37 fragments homologous to chloroplast DNA were identified, with S. spontaneum containing the highest number. These mitogenomes appear to have undergone substantial genomic reorganization and gene transfer events throughout evolution, including the loss of eight PCGs.
“This study sheds light on the genetic diversity and complexity of the Saccharum complex, establishing a foundation for future germplasm identification and evolutionary research, ” adds Que.
Contact Authors:
Guilong Lu, E-mail: luguilong666@126.com;
Correspondence Youxiong Que, E-mail: queyouxiong@126.com
Funder:
This work was supported by the Chinese Academy of Tropical Agricultural Sciences for Science and Technology Innovation Team of National Tropical Agricultural Science Center (CATASCXTD202402), the Science and Technology Major Project of Guangxi, China (Guike AA23073001), the National Key Research and Development Program of China (2022YFD2301100), the Project of State Key Laboratory of Tropical Crop Breeding, China (NKLTCBCXTD24, NKLTCBHZ04, NKLTCB-RC202401 and SKLTCBYWF202504), the China Agriculture Research System of MOF and MARA (CARS-17), and the Scientific Research Start-up Fund for High-level Introduced Talents of Henan Institute of Science and Technology, China (103020224001/073).
Conflict of Interest:
The authors declare that they have no conflict of interest.
See the Article:
Lu G L, et al. 2025. Multiple chromosomal configurations and phylogenetic implications in Saccharum mitochondrial genomes. Journal of Integrative Agriculture, 24(10): 3909-3925.