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

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.

背景 紫茎泽兰（Ageratina adenophora）是全球范围内危害最为严重的入侵植物物种之一，可造成严重的经济损失与生态环境破坏。然而，目前紫茎泽兰的序列资源与基因组信息仍较为匮乏，导致其系统发育鉴定与进化研究开展难度较大。本研究基于Illumina测序技术，完成了紫茎泽兰叶绿体（chloroplast, cp）基因组的全序列解析。

方法与结果 紫茎泽兰叶绿体基因组全长为150689 bp，包含1个长单拷贝（large single-copy, LSC）区域（84815 bp）、1个短单拷贝（small single-copy, SSC）区域（18358 bp），以及一对分隔上述两个单拷贝区域的反向重复（inverted repeats, IR）区域（各长23755 bp）。该基因组共包含130个单拷贝基因，以及反向重复区域内的18个重复基因，其基因组成与组织结构与其他菊科（Asteraceae）叶绿体基因组高度相似。通过比较基因组分析，本研究鉴定出5个包含超过2%简约信息位点的DNA区域（ndhD-ccsA、psbI-trnS、ndhF-ycf1、ndhI-ndhG与atpA-trnR），这些区域可作为潜在的条形码标记与系统发育分析候选位点。此外，本研究还对重复序列结构、密码子使用偏好以及反向重复区域的收缩扩张模式进行了分析，以揭示其进化规律。系统发育分析结果显示，紫茎泽兰与小葵子（Guizotia abyssinica）为姊妹群，同时支持菊目（Asterales）为单系类群。

结论 本研究完成了紫茎泽兰叶绿体基因组的组装与分析，这是泽兰族（Eupatorieae）中首个被测序的质体基因组（plastome）。完整的叶绿体基因组信息，可为该入侵物种以及菊科植物的系统发育与进化研究提供重要的数据支撑。