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

被引:25
作者
Song, Weicai [1 ]
Chen, Zimeng [1 ]
Shi, Wenbo [1 ]
Han, Weiqi [1 ]
Feng, Qi [1 ]
Shi, Chao [1 ,2 ]
Engel, Michael S. [3 ]
Wang, Shuo [1 ]
机构
[1] Qingdao Univ Sci & Technol, Coll Marine Sci & Biol Engn, Qingdao 266042, Peoples R China
[2] Chinese Acad Sci, Plant Germplasm & Genom Ctr, Kunming Inst Bot, Germplasm Bank Wild Species Southwest China, Kunming 650204, Yunnan, Peoples R China
[3] Univ Kansas, Dept Ecol & Evolutionary Biol, Lawrence, KS 66045 USA
基金
中国国家自然科学基金;
关键词
Litsea; chloroplast genome; structural variations; genetic relationship; GENUS LITSEA; SEQUENCE; ANNOTATION; PUZZLE; TOOLS; DNA;
D O I
10.3390/genes13091550
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
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.
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页数:18
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