Complete Chloroplast Genome Sequence of a Major Invasive Species, Crofton Weed (Ageratina adenophora)

Abstract

BackgroundCrofton weed (Ageratina adenophora) is one of the most hazardous invasive plant species, which causes serious economic losses and environmental damages worldwide. However, the sequence resource and genome information of A. adenophora are rather limited, making phylogenetic identification and evolutionary studies very difficult. Here, we report the complete sequence of the A. adenophora chloroplast (cp) genome based on Illumina sequencing.Methodology/Principal FindingsThe A. adenophora cp genome is 150, 689 bp in length including a small single-copy (SSC) region of 18, 358 bp and a large single-copy (LSC) region of 84, 815 bp separated by a pair of inverted repeats (IRs) of 23, 755 bp. The genome contains 130 unique genes and 18 duplicated in the IR regions, with the gene content and organization similar to other Asteraceae cp genomes. Comparative analysis identified five DNA regions (ndhD-ccsA, psbI-trnS, ndhF-ycf1, ndhI-ndhG and atpA-trnR) containing parsimony-informative characters higher than 2%, which may be potential informative markers for barcoding and phylogenetic analysis. Repeat structure, codon usage and contraction of the IR were also investigated to reveal the pattern of evolution. Phylogenetic analysis demonstrated a sister relationship between A. adenophora and Guizotia abyssinica and supported a monophyly of the Asterales.ConclusionWe have assembled and analyzed the chloroplast genome of A. adenophora in this study, which was the first sequenced plastome in the Eupatorieae tribe. The complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family.

The complete chloroplast genome sequence and phylogenetic analysis of Chuanminshen (Chuanminshenviolaceum Sheh et Shan)

“…3a). The number of tandem repeats in Chuanminshen cp genome was equivalent to that of crofton weed (Nie et al 2012) and slightly more than bamboo (Zhang et al 2011) whereas the longest tandem repeat size was shorter than the crofton weed with 85 bp and bamboo with 65 bp. To investigate the dispersed repeats in Chuanminshen cp genome, we adjusted the setting parameters of the REPuter described above.…”

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

“…With the emergence and development of high-throughput sequencing technology, more and more chloroplast genomes of Asteraceae species have been dissected recently (Nie et al 2012;Liu et al 2013;Bock et al 2014). The available completed genomes provide an opportunity to perform comparative analysis within these members of Asteraceae family at the whole chloroplast genome level.…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…Multiple sequence alignment between six Fritillaria genomes indicated that the IR regions were more conserved than the LSC and SSC regions due to copy correction by gene conversion in IR regions [39]. The most divergent regions were found in IGSs, which have been used in phylogenetic studies [9,28]. For the coding regions, the most divergent regions included matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF.…”

“…Chloroplast genomes provide genomic resources for phylogenetic analysis, and many studies have used protein-coding sequences or whole chloroplast genome sequences [6,28,41]. We used ML and MP analysis to construct a phylogenetic tree focusing on Fritillaria species.…”

“…Chloroplast genomes have been successfully used in numerous phylogenetic studies of angiosperms [27,28]. To identify the phylogenetic position of the six Fritillaria species within the Liliaceae family, 74 protein-coding sequences shared by 11 cp genomes were aligned (Figure 7).…”