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.
Highlights
Cenchrus is a member of 780 genera of Poaceae and has widespread distributions in Asia, Africa, Australia, and America (Govaerts, 2011; Christenhusz & Byng, 2016)
Called long-spined sandbur or spiny burr grass, is native to North America. This species invaded into other continents and became a noxious weed (Strat, Stoyanov & Holobiuc, 2017; Fagaras, 2018)
DNA extraction, chloroplast genome assembly, and comparison The fresh leaves of C. longispinus and C. echinatus were collected in Daecheong Island (Incheon, South Korea) and Texas (USA), respectively
Summary
Cenchrus is a member of 780 genera of Poaceae and has widespread distributions in Asia, Africa, Australia, and America (Govaerts, 2011; Christenhusz & Byng, 2016). Called long-spined sandbur or spiny burr grass, is native to North America This species invaded into other continents and became a noxious weed (Strat, Stoyanov & Holobiuc, 2017; Fagaras, 2018). Development of molecular markers for invasive alien plants in Korea: a case study of a noxious weed, Cenchrus longispinus (Hack.) Fernald, based on generation sequencing data. 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. The simple PCR protocol for using the newly developed molecular markers was provided
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