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.

Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

“…Cp SSRs have been used widely in plant population genetics (Doorduin et al, 2011; He et al, 2012), polymorphism investigations (Xue et al, 2012), and ecological and evolutionary studies (Roullier et al, 2011; Wang et al, 2013). The SSRs in the five Juglans Cp genomes we investigated were AT rich.…”

Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

“…Seven regions (cssA-trnL, psbI-trnS, rpl33-rps18, trnF-ndhJ, trnG-trnT, trnH-psbA, and trnT-trnL) possessed the completely congruent trees with the life history of species. Among them, trnH-psbA has been frequently applied as a phylogenetic maker for Asteraceae family (Doorduin et al 2011), and psbI-trnS has also been Fig. 4 Sequence alignment of eight sequenced cp genomes in the Asteraceae family.…”

“…Although extensive studies have reported the comparative chloroplast genome analysis in many families (Wu et al 2011;Ghimiray and Sharma 2014), a systematic analysis of the structure and organization of chloroplast genomes in Asteraceae family has not been performed up to now. Here, eight chloroplast genomes belonging to different tribes of Asteraceae family are selected as the representative to perform comparative analysis, including Ageratina adenophora (NC_015621) belonging to the tribe Eupatorieae (Nie et al 2012), Artemisia frigida (NC_020607) (Liu et al 2013), Chrysanthemum indicum (NC_020320), and Chrysanthemum × morifolium (NC_020092) all belonging to the tribe Anthemideae, Guizotia abyssinica (NC_010601) (Dempewolf et al 2010) belonging to the tribe Millerieae, Helianthus annuus (NC_007977) (Timme et al 2007) belonging to the tribe Heliantheae and Jacobaea vulgaris (NC_015543) (Doorduin et al 2011) belonging to the Senecioneae clade as well as Lactuca sativa (DQ383816) (Timme et al 2007) belonging to the tribe Lactucinae, with the purpose to compare and analyze the gene content, genome structure, and RNA editing of Asteraceae cp genomes, which will provide helpful information for better understanding of cp genome evolution within this family.…”

Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)

“…With the rapid development of next-generation sequencing, cp genome-scale data have been increasingly employed to infer phylogenetic relationships at almost any taxonomic levels in the past decade (Jansen et al, 2007; Moore et al, 2007, 2010; Parks et al, 2009; Barrett et al, 2013; Ma P. F. et al, 2014; Carbonell-Caballero et al, 2015; Zhang et al, 2016). In addition, based on comparative genomic analyses, cp genomic hotspots can be identified as DNA barcodes in discriminating species, in terms of informative regions for a specific plant genus, tribe or family (Doorduin et al, 2011; Li et al, 2013, 2014). Our objectives are to: (1) characterize and compare the cp genomes of all six Amana in order to gain insights into their evolutionary patterns; (2) resolve the phylogenetic relationships among all Amana species and among closely related genera; (3) screen and identify the most rapidly evolving DNA regions of the Amana genome for species identification and future phylogeographic studies of the genus.…”