Fan Ruifeng, Ma Wei, Liu Shilei, Huang Qingyang
School of Pharmacy Heilongjiang University of Chinese Medicine Harbin China.
Experimental Teaching & Practical Training Center Heilongjiang University of Chinese Medicine Harbin China.
Ecol Evol. 2021 Mar 18;11(9):4550-4563. doi: 10.1002/ece3.7350. eCollection 2021 May.
Some ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution.
The complete chloroplast genomes of (Kunze) Koidz, Nakai, Nakai ex Kitagawa, and (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes.
The whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative () values of > 0.02 were identified. A total of 75-108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C-to-U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single-copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships.
The results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.
一些蕨类植物具有药用特性，并被用于治疗干预。然而，蕨类植物的分类和系统发育关系仍未得到充分报道。鉴于叶绿体基因组为物种鉴定和进化提供了理想信息，本研究对三种未发表和一种已发表的蕨类植物进行了测序，并与其他蕨类植物进行比较，以获取有关它们分类和进化的全面信息。
使用Illumina HiSeq 4000平台对（Kunze）Koidz、Nakai、Nakai ex Kitagawa和（Kunze）Presl的完整叶绿体基因组进行测序。对所有四个物种进行了简单序列重复（SSR）、核苷酸多样性分析和RNA编辑研究。还进行了基因组比较以及反向重复（IR）边界的扩张和收缩分析。基于整个叶绿体基因组的系统发育分析研究了蕨类植物之间的关系。
整个叶绿体基因组大小在148,539至151,341 bp之间，呈现典型的四分体结构。鉴定出10个简约信息（）值> 0.02的高变位点。共鉴定出75 - 108个SSR，所有四个蕨类植物中仅存在6个SSR。SSR中A + T碱基的数量高于G + C碱基。C到U的转换是最常见的RNA编辑事件类型。基因组比较分析表明，单拷贝区域比IR区域更保守。四个蕨类植物的IR边界扩张和收缩情况各不相同。系统发育分析表明，同一属的物种倾向于聚集在一起，关系相对密切。
这些结果提供了有关蕨类植物叶绿体基因组的有价值信息，将有助于蕨类植物的鉴定和分类，以及研究它们的系统发育关系和进化。
