Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships

doi:10.3390/genes13091550

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	Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships
	Song, Weicai; Chen, Zimeng; Shi, Wenbo; Han, Weiqi; Feng, Qi; Shi, Chao; Engel, Michael S.; Wang, Shuo
	2022
发表期刊	GENES
卷号	13 期号:9 页码:1550
摘要	Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species of the genus are widely used for a wide range of medicinal and industrial aspects. At present, most studies related to the gene resources of Litsea are restricted to morphological analyses or features of individual genomes, and currently available studies of select molecular markers are insufficient. In this study, we assembled and annotated the complete chloroplast genomes of nine species in Litsea, carried out a series of comparative analyses, and reconstructed phylogenetic relationships within the genus. The genome length ranged from 152,051 to 152,747 bp and a total of 128 genes were identified. High consistency patterns of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) were discovered across the genus. Variations in gene length and the presence of the pseudogene ycf1(psi), resulting from IR contraction and expansion, are reported. The hyper-variable gene rpl16 was identified for its exceptionally high Ka/Ks and Pi values, implying that those frequent mutations occurred as a result of positive selection. Phylogenetic relationships were recovered for the genus based on analyses of full chloroplast genomes and protein-coding genes. Overall, both genome sequences and potential molecular markers provided in this study enrich the available genomic resources for species of Litsea. Valuable genomic resources and divergent analysis are also provided for further research of the evolutionary patterns, molecular markers, and deeper phylogenetic relationships of Litsea.
关键词	Litsea chloroplast genome structural variations genetic relationship GENUS LITSEA SEQUENCE ANNOTATION PUZZLE TOOLS DNA
DOI	10.3390/genes13091550
收录类别	SCI
WOS记录号	WOS:000858240700001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74755
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Song, Weicai,Chen, Zimeng,Shi, Wenbo,et al. Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships[J]. GENES,2022,13(9):1550.
APA	Song, Weicai.,Chen, Zimeng.,Shi, Wenbo.,Han, Weiqi.,Feng, Qi.,...&Wang, Shuo.(2022).Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships.GENES,13(9),1550.
MLA	Song, Weicai,et al."Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships".GENES 13.9(2022):1550.

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