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Graph-based mitochondrial genomes of three foundation species in the Saccharum genus

文献类型： 外文期刊

作者： Li, Sicheng 1 ; Wang, Zhen 1 ; Jing, Yanfen 3 ; Duan, Weixing 4 ; Yang, Xiping 1 ;

作者机构： 1.Guangxi Univ, Coll Agr, State Key Lab Conservat & Utilizat Subtrop, Agrobioresources, Nanning 530004, Peoples R China

2.Guangxi Univ, Guangxi Key Lab Sugarcane Biol, Nanning 530004, Peoples R China

3.Natl Key Lab Biol Breeding Trop Crops, Kunming 650221, Peoples R China

4.Guangxi Acad Agr Sci, Guangxi Key Lab Sugarcane Genet Improvement, Sugarcane Res Inst, Nanning, Peoples R China

关键词： Saccharum; Mitochondrial genome; Repeat-mediated recombination; Phylogenetic

期刊名称：PLANT CELL REPORTS （ 影响因子：5.3； 五年影响因子：5.3 ）

ISSN： 0721-7714

年卷期： 2024 年 43 卷 8 期

页码：

收录情况： SCI

摘要： Key message We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.

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