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

Abstract

Saccharum belongs to the Andropogoneae and cultivars species in Saccharum contributes nearly 80% sugar production of 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 the 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 mitogenome of three Saccharum species, and systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitochondrial genomes revealed the differential features of the Saccharum mitochondrial genomes.

Assembly and comparative genome analysis of four mitochondrial genomes from Saccharum complex species

“…In M. sinensis , the transfer length, quantity, and proportion of MTPT fragments were the highest among all organelle genomes. The total length of MTPT fragments in Saccharum was approximately 3 kb, which was approximately 8% and 25% of the length of the mitochondrial and chloroplast genomes, respectively ( Li et al., 2024 ).…”

“…Few comparative analyses of plant mitochondrial genes have so far revealed the relationship between species evolution and mitochondrial conformation. The simplest structures of the mitochondrial genomes of Saccharum robustum and S. officinarum in the genus Saccharum can be described as two-ring structures (300 kb and 144 kb), and the structure of the S. spontaneum as a 380-kb linear structure and a 100-kb-ring structure ( Li et al., 2024 ). The diploid N. porphyrocoma , closely related to Saccharum , exhibited a single cyclic structure.…”

“…Six species related and within Saccharum complex were selected for analysis, including S. bicolor (NC013816.1), T. arundinaceum (in this study), M. sinensis (in this study), E. rockii (in this study), N. porphyrocoma (in this study), and S. spontaneum ( Li et al., 2024 ), to conduct comparative mitogenome analysis and collinearity analysis. To investigate the similarity of mitogenome sequences within the Saccharum complex and closely related species, homologous sequences between the four relatives were detected using Blastn (2.5.0+) (parameters: e-value 1e −10 ).…”

“…Currently, only the mitogenomes of Saccharum spp. have been published ( Li et al., 2024 ), leaving numerous properties of Saccharinae mitogenomes yet to be discovered. In this research, we de novo assembled the complete mitogenome of four Saccharinae species ( T. arundinaceum , M. sinensis , E. rockii , and N. porphyrocoma ) using a combination of second-generation Illumina sequencing and third-generation PacBio sequencing technologies.…”