Comparative analysis of switchgrass chloroplast genomes provides insights into identification, phylogenetic relationships and evolution of different ecotypes

Switchgrass (Panicum virgatum L.) plays a crucial role as a valuable forage and bioenergy resource. There are two ecotypes of switchgrass, upland and lowland, which exhibit significant differences in their adaptability to various environmental stressors. To enhance ecotype identification and gain a comprehensive understanding of the evolutionary relationships between these two ecotypes at the population level, we assembled 20 switchgrass chloroplast genomes (10 uplands and 10 lowlands) collected from different latitudinal regions. All chloroplast genomes displayed the typical quadripartite structure, with sizes ranging from 139,497 bp (J170. A) to 139,746 bp (J440. A and J636. B). The annotation of these 20 switchgrass chloroplast genomes revealed a consistent number of genes, including 40 transfer RNAs, eight ribosomal RNAs, and 86 protein-coding genes. Through multiscale analyses of the chloroplast genomes, we observed conservation in the upland and lowland chloroplasts in terms of IR boundaries, repetitive sequences, and codon usage. Our comparative chloroplast genome analysis revealed that large single copy regions exhibited the highest nucleotide diversity, followed by small single copy regions, while inverted repeat regions showed a relatively conserved pattern. Additionally, we identified a hotspot, trnG-GCC-trnM-CAU, which was exclusive to the lowland ecotype, suggesting its potential to differentiate between the two ecotypes. In the phylogenetic analysis, we found that some accessions from both ecotypes were intermixed and clustered into one clade, highlighting the complexity of the phylogenetic evolution process. In conclusion, we employed population-level comparative genomic analysis to investigate genetic variations and phylogenetic relationships among different ecotypes, thereby offering novel insights into the evolutionary dynamics and classifications of switchgrass.