The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

中文翻译：

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刺苍耳完整叶绿体基因组序列的特征：比较分析、突变热点鉴定和系统发育意义


入侵物种刺苍耳多年来一直被用作传统中药。不幸的是，尚未对这种植物进行广泛的分子研究。在此，组装并分析了刺 X. spinosum 的完整叶绿体 (cp) 基因组序列。 X. spinosum的cp基因组长度为152,422个碱基对(bp)，具有四部分环状结构。 cp基因组包含115个独特基因，包括80个PCG、31个tRNA基因和4个rRNA基因。比较分析表明，X. spinosum 的 cp 基因组中含有大量重复序列（999 个重复序列）和 701 个 SSR。在基因间间隔区中发现了 14 个分歧（Π > 0.03）。系统发育分析表明，Parthenium 是 Xanthium 和 Ambrosia 的姐妹进化枝，也是 Ambrosiinae 亚族的早期分化谱系，尽管这一发现得到了非常弱的 bootstrap 值的支持。确定的热点区域可用作解决苍耳属系统发育关系和物种鉴定的分子标记。