title: The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies.
abstract: Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intraspecific polymorphic markers. We therefore sequenced the complete chloroplast genomes of 12 native and 5 invasive individuals of J. vulgaris with next generation sequencing and discovered single-nucleotide polymorphisms (SNPs) and microsatellites. This is the first study in which the chloroplast genome of that many individuals within a single species was sequenced. Thirty-two SNPs and 34 microsatellite regions were found. For none of the individuals, differences were found between the inverted repeats. Furthermore, being the first chloroplast genome sequenced in the Senecioneae clade, we compared it with four other members of the Asteraceae family to identify new regions for phylogentic inference within this clade and also within the Asteraceae family. Five markers (ndhC-trnV, ndhC-atpE, rps18-rpl20, clpP and psbM-trnD) contained parsimony-informative characters higher than 2%. Finally, we compared two procedures of preparing chloroplast DNA for next generation sequencing.
authors: Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, 2300 RA Leiden, The Netherlands. l.j.doorduin@biology.leidenuniv.nl
authors: Leonie
authors: L
authors: Doorduin
authors: Barbara
authors: B
authors: Gravendeel
authors: Youri
authors: Y
authors: Lammers
authors: Yavuz
authors: Y
authors: Ariyurek
authors: Thomas
authors: T
authors: Chin-A-Woeng
authors: Klaas
authors: K
authors: Vrieling
mesh_terms: D019659:Asteraceae / Q000235:genetics*; D020029:Base Pairing / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D018742:DNA, Chloroplast / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D005819:Genetic Markers; D005828:Genetics, Population; D054628:Genome, Chloroplast / Q000235:genetics*; D005843:Geography; D058865:Introduced Species; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D005819:Genetic Markers