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.

Figure 1.

Representative map of the chloroplast genome of J. vulgaris (GenBank accession HQ234669).

Figure 2.

Number of Illumina sequencing reads plotted against percentage of the chloroplast genome mapped for 17 individuals of J. vulgaris.

Figure 3.

Coverage of the chloroplast genome amplified with a long-range PCR for 16 individuals of J. vulgaris.

Figure 4.

(A) Whole chloroplast genome coverage plotted for individual 17 of J. vulgaris, of which DNA was obtained by using the chloroplast extraction method. (B) Whole chloroplast genome coverage plotted for 16 individuals of J. vulgaris run in two lanes total, of which DNA was obtained by using the long-range PCR method.

Figure 5.

Phylograms derived from maximum parsimony (MP) analysis of alignments of DNA sequences of five different Asteraceae species of a total of 27 individual chloroplast regions indicated below the trees. The phylogram called ‘combined regions’ in the middle is derived from MP analysis of all 27 regions together.