刺苍耳完整叶绿体基因组序列的特征：比较分析、突变热点鉴定及系统发育意义。

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications.

机构信息

Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do, Republic of Korea, 38541.

Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Republic of Korea.

出版信息

BMC Genomics. 2020 Dec 2;21(1):855. doi: 10.1186/s12864-020-07219-0.

BACKGROUND

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.

RESULTS

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.

CONCLUSION

The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

背景

刺苍耳作为一种传统中药已被使用多年。不幸的是，目前尚未对该植物进行广泛的分子研究。

结果

本研究组装并分析了刺苍耳的完整叶绿体（cp）基因组序列。刺苍耳的 cp 基因组长度为 152422 碱基对（bp），具有四分体的圆形结构。cp 基因组包含 115 个独特的基因，包括 80 个 PCGs、31 个 tRNA 基因和 4 个 rRNA 基因。比较分析显示，刺苍耳的 cp 基因组中含有大量的重复序列（999 个重复）和 701 个 SSRs。在基因间 spacer 区域发现了 14 个分歧（Π>0.03）。系统发育分析表明，泽兰实蝇与苍耳属和 Ambrosia 属是姐妹群，并且是 Ambrosiinae 亚科的一个早期分支，但该结果仅得到一个非常弱的 bootstrap 值支持。