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The genus  Pennisetum  (Poaceae) is both a forage crop and staple food crop in the tropics. In this study, we obtained chloroplast genome sequences of four species of  Pennisetum  ( P. alopecuroides ,  P. clandestinum ,  P. glaucum , and  P. polystachion ) using Illumina sequencing. These chloroplast genomes have circular structures of 136,346–138,119 bp, including a large single-copy region (LSC, 79,380–81,186 bp), a small single-copy region (SSC, 12,212–12,409 bp), and a pair of inverted repeat regions (IRs, 22,284–22,372 bp). The overall GC content of these chloroplast genomes was 38.6–38.7%. The complete chloroplast genomes contained 110 different genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analysis of nucleotide variability identified nine intergenic spacer regions ( psbA-matK, matK-rps16, trnN-trnT, trnY-trnD-psbM, petN-trnC, rbcL-psaI, petA-psbJ, psbE-petL , and  rpl32-trnL ), which may be used as potential DNA barcodes in future species identification and evolutionary analysis of  Pennisetum . The phylogenetic analysis revealed a close relationship between  P. polystachion  and  P. glaucum , followed by  P. clandestinum  and  P. alopecuroides . The completed genomes of this study will help facilitate future research on the phylogenetic relationships and evolution of  Pennisetum  species.

Comparative Analysis of the Chloroplast Genome for Four Pennisetum Species: Molecular Structure and Phylogenetic Relationships