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Background  Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied.    Methods  We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers.    Results  In this study, we characterize the chloroplast genomes (cpDNA) of  Cenchrus longispinus  and  C. echinatus , of which the lengths are 137,144 and 137,131 bp, respectively. These two newly sequenced genomes include 78 protein-coding genes, 30 tRNA, and four rRNA. There are 56 simple single repeats and 17 forward repeats in the chloroplast genome of  C. longispinus . Most of the repeats locate in non-coding regions. However, repeats can be found in  infA, ndhD, ndhH, ndhK, psbC, rpl22, rpoC2, rps14, trnA-UGC, trnC-GCA, trnF-GAA, trnQ-UUG, trnS-UGA, trnS-GCU , and  ycf15 . The phylogenomic analysis revealed the monophyly of  Cenchrus  but not  Panicum  species in tribe Paniceae. The single nucleotide polymorphism sites in  atpB, matK , and  ndhD  were successfully used for developing molecular markers to distinguish  C. longispinus  and related taxa. The simple PCR protocol for using the newly developed molecular markers was also provided.

peerj

Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed, <i>Cenchrus longispinus</i> L., based on next generation sequencing data

Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed, Cenchrus longispinus L., based on next generation sequencing data