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

Abstract

BackgroundGenomic 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.MethodsWe employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers.ResultsIn 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.

Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae)

“…SNPs are useful in population studies due to its extremely abundant presence in the angiosperms genomes ( Cui et al, 2017 ; Fischer et al, 2017 ; Pantoja et al, 2017 ), and are effective in phylogenetic analysis ( Leaché & Oaks, 2017 ). In addition, various molecular markers have been developed for different angiosperm species based on SNP data from chloroplast genomes ( Khlestkina & Salina, 2006 ; Wang et al, 2015a ; Wang et al, 2015b ; Hyun et al, 2019 ; Xia et al, 2019 ). We successfully developed a molecular marker, inferred from SNP data, to distinguish C. crispus from C. acanthoides and C. tenuiflorus ( Fig.…”