State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
PLoS One. 2012;7(5):e36869. doi: 10.1371/journal.pone.0036869. Epub 2012 May 11.
Crofton 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 FINDINGS: The 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.
We 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.
三叶鬼针草（Ageratina adenophora）是最危险的入侵植物物种之一，在全球范围内造成了严重的经济损失和环境破坏。然而，三叶鬼针草的序列资源和基因组信息相当有限，使得系统发育鉴定和进化研究非常困难。在这里，我们根据 Illumina 测序报道了三叶鬼针草叶绿体（cp）基因组的完整序列。
方法/主要发现：三叶鬼针草 cp 基因组长 150689bp，包括一个 18358bp 的小单拷贝（SSC）区和一个 84815bp 的大单拷贝（LSC）区，由一对 23755bp 的反向重复（IR）隔开。基因组包含 130 个独特的基因和 18 个在 IR 区重复的基因，基因内容和组织与其他菊科 cp 基因组相似。比较分析确定了五个 DNA 区域（ndhD-ccsA、psbI-trnS、ndhF-ycf1、ndhI-ndhG 和 atpA-trnR），它们包含的简约信息特征高于 2%，可能是条形码和系统发育分析的潜在信息标记。还研究了重复结构、密码子使用和 IR 的收缩，以揭示进化模式。系统发育分析表明，三叶鬼针草与 Guizotia abyssinica 具有姐妹关系，并支持 Asterales 的单系性。
我们在这项研究中组装和分析了三叶鬼针草的叶绿体基因组，这是第一个在 Eupatorieae 族中测序的质体基因组。完整的叶绿体基因组信息对该入侵物种以及菊科内的植物系统发育和进化研究都很有用。
