Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’

Abstract

High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.

Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Salvia Species for Bioexploration

“…In contrast, the special IGS regions of the two iSNPs, namely trn G-GCC- trn M-CAU and ycf 3- trn S-GGA, were used to discriminate the three studied Salvia species. In previous studies, most of the SNPs were found in intergenic sequences, and the trn G-GCC- trn M-CAU was one of the maximum number of SNPs found four times to distinguish the six Saccharum species [ 52 ]. Meantime, the variable hotspot regions of ycf 3- trn S-GGA also can be useful as the candidate DNA barcodes for Adoxaceae and Caprifoliaceae species, and also for assessing interspecific divergence in Dipsacales species [ 53 ].…”

Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences

“…However, the genetic backgrounds of the cultivars were unclear, and these markers were not informative for inferring the relationships of those species. The chloroplast genome has become an efficient option for increasing plant phylogenomics at multiple taxonomic levels over the past few years [ 33 , 34 , 35 , 36 , 37 ]. For instance, the phylogenies analyzed using the complete chloroplast genomes of three Spondias species revealed a robust phylogenetic topology for Spondias [ 9 ].…”

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

“…robustum, S. officinarum, S. sinense, and S. barberi) of plastid genomes (Li, et al 2022) and one mitochondrial genomes from S. officinarum (Khon Kaen 3) (Shearman, et al 2016), four mitogenomes from S. hybrid (ROC22) ), FN15 , line 15a-53 , and line A1 (Zhou, et al 2022). All reported mitogenome of Saccharum spp.…”