Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region

Weiyue Sun; Zuoying Wei; Yuefeng Gu; Ting Wang; Baodong Liu; Yuehong Yan

doi:10.3389/fpls.2024.1328080

Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region

Front Plant Sci. 2024 Apr 11:15:1328080. doi: 10.3389/fpls.2024.1328080. eCollection 2024.

Authors

Weiyue Sun^{1

2}, Zuoying Wei³, Yuefeng Gu², Ting Wang³, Baodong Liu^{1

2}, Yuehong Yan²

Affiliations

¹ Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China.
² Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China.
³ Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China.

Abstract

Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.

Keywords: divergent hotspot; evolutionary; phylogenomics; pteridophytes; sequence characteristic.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment (2019HJ2096001006). National Natural Science Foundation of China (31800450), and Strategic Pilot Science and Technology Project of Chinese Academy of Sciences (XDA19050404).