Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses

doi:10.3389/fpls.2023.1144406

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	Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses
	Li,Chun-Jiao; Xie,Xin-Tong; Liu,Hong-Xin; Wang,Ruo-Nan; Li,De-Zhu
	2023
发表期刊	FRONTIERS IN PLANT SCIENCE
卷号	14 页码:1144406
摘要	Lobelia species, as rich source of the alkaloid lobeline which has been shown to have important biological activity, have been used in folk medicine throughout East Asia to treat various diseases. However, Lobelia is a complex and varied genus in East Asia and is thus difficult to identify. Genomic resources would aid identification, however the availability of such information is poor, preventing a clear understanding of their evolutionary history from being established. To close this gap in the available genomic data, in this study, 17 plastomes of East Asian lobelias were newly sequenced and assembled. Although the plastomes of Lobelia sect. Hypsela, L. sect. Speirema, and L. sect. Rhynchopetalum shared the gene structure, the inverted repeat (IR)/large single copy (LSC) boundaries, genome size, and the number of repeats were variable, indicating the non-conservative nature of plastome evolution within these sections. However, the genomes of the Lobelia sect. Delostemon and L. sect. Stenotium showed rearrangements, revealing that these two sections might have undergone different evolutionary histories. We assessed nine hotspot genes and 27-51 simple sequence repeat motifs, which will also serve as valuable DNA barcode regions in future population genetics studies and for the delineation of plant species. Our phylogenetic analysis resolved the evolutionary positions of the five sections in agreement with previous evolutionary trees based on morphological features. Although phylogenetic reconstruction of Lobelioideae based on the rpoC2 gene has rarely been performed, our results indicated that it contains a considerable amount of phylogenetic information and offers great promise for further phylogenetic analysis of Lobelioideae. Our site-specific model identified 173 sites under highly positive selections. The branch-site model exhibited 11 positive selection sites involving four genes in the East Asian branches. These four genes may play critical roles in the adaptation of East Asian taxa to diverse environments. Our study is the first to detect plastome organization, phylogenetic utility, and signatures of positive selection in the plastomes of East Asian lobelias, which will help to further advance taxonomic and evolutionary studies and the utilization of medicinal plant resources.
关键词	East Asian lobelias plastomes phylogenomic framework highly divergent regions positive selection adaptive evolution INVERTED REPEAT HIGH-ALTITUDE CAMPANULACEAE GENOMES SELECTION EXPANSION SEQUENCE TOOLS GENE DNA
学科领域	Plant Sciences
DOI	10.3389/fpls.2023.1144406
WOS记录号	WOS:000968066100001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74980
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Li,Chun-Jiao,Xie,Xin-Tong,Liu,Hong-Xin,et al. Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses[J]. FRONTIERS IN PLANT SCIENCE,2023,14:1144406.
APA	Li,Chun-Jiao,Xie,Xin-Tong,Liu,Hong-Xin,Wang,Ruo-Nan,&Li,De-Zhu.(2023).Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses.FRONTIERS IN PLANT SCIENCE,14,1144406.
MLA	Li,Chun-Jiao,et al."Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses".FRONTIERS IN PLANT SCIENCE 14(2023):1144406.

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