The conservative chloroplast genomic features and comparative analysis provide new evidence for the unification of Pennisetum and Cenchrus

Many species in the genera Pennisetum and Cenchrus are utilized as biofuel feedstocks due to their high biomass yield and lignocellulosic content. However, some species possess two Latin names and are used confusingly in practical production and research reports, indicating a dispute regarding the true taxonomic affiliation of these species with the two genera. Therefore, it is necessary to investigate the genetic evolutionary relationships of multiple species within the two genera to assess the degree of differentiation. The chloroplast (cp) genome, as a crucial genetic resource, provides us with the opportunity to uncover the genetic evolutionary relationships of species within the two genera. We conducted a comprehensive examination and comparative analysis of the 33 cp genomes from Pennisetum and Cenchrus species, including 12 newly assembled and annotated cp genomes. The results indicated a high degree of conservation among the 33 cp genomes in terms of genome structure, gene number, gene types, inverted repeat (IR) boundary features, and codon usage frequency. Comparative genomic analysis revealed a higher level of differentiation in the single copy regions compared to the IR regions. Phylogenetic analysis revealed mixed clustering of species in both genera without obvious genus-level differentiation, indicating their close evolutionary relationship. In summary, we comprehensively reveal the cp genomic features of 33 species within two genera, and conduct multi-scale comparative genomic analysis. These findings represent a significant supplementation to the plastid genome of the Pennisetum and Cenchrus species, providing new insights into the phylogeny and genetic evolutionary relationships of these two genera. • The chloroplast genome characteristics of Pennisetum and Cenchrus species are very conserved. • Some hotspots were shared by species from both genera. • Pennisetum and Cenchrus species were mixed and clustered in the phylogenetic tree. • Our study results support the view that the two genera should be unified.