Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different Genera
<i>Lindera aggregata</i> is a species of the Lauraceae family, which has important medicinal, economic and ornamental values. In this study, we sequenced, assembled and annotated the chloroplast genome of <i>L. aggregata</i> and reannotated and corrected eight unverified anno...
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MDPI AG
2024-02-01
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| Series: | Genes |
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| author | Yujie Shi Zhen Chen Jingyong Jiang Xiaobai Li Wei Zeng |
| author_facet | Yujie Shi Zhen Chen Jingyong Jiang Xiaobai Li Wei Zeng |
| author_sort | Yujie Shi |
| collection | DOAJ |
| description | <i>Lindera aggregata</i> is a species of the Lauraceae family, which has important medicinal, economic and ornamental values. In this study, we sequenced, assembled and annotated the chloroplast genome of <i>L. aggregata</i> and reannotated and corrected eight unverified annotations in the same genus. The chloroplast genomes taxa from Lindera and from different genera of Lauraceae were compared and analyzed, and their phylogenetic relationship and divergence time were speculated. All the 36 chloroplast genomes had typical quadripartite structures that ranged from 150,749 to 154,736 bp in total length. These genomes encoded 111–112 unique genes, including 78–79 protein-coding genes, 29–30 tRNA and 4 rRNA. Furthermore, there were 78–97 SSRs loci in these genomes, in which mononucleotide repeats were the most abundant; there were 24–49 interspersed repeats, and forward repeat types were the most frequent. The codon bias patterns of all species tended to use codons ending with A or U. Five and six highly variable regions were identified within genus and between genera, respectively, and three common regions (<i>ycf1</i>, <i>ndhF-rpl32</i> and <i>rpl32-trnL</i>) were identified, which can be used as important DNA markers for phylogeny and species identification. According to the evaluation of the Ka/Ks ratio, most of the genes were under purifying selection, and only 10 genes were under positive selection. Finally, through the construction of the evolutionary tree of 39 chloroplast genomes, the phylogenetic relationship of Lauraceae was clarified and the evolutionary relationship of <i>Lindera</i> was revealed. The species of genus <i>Lindera</i> experienced rapid adaptive radiation from Miocene to Pleistocene. The results provided valuable insights for the study of chloroplast genomes in the Lauraceae family, especially in the genus <i>Lindera</i>. |
| first_indexed | 2024-04-24T18:14:12Z |
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| language | English |
| last_indexed | 2024-04-24T18:14:12Z |
| publishDate | 2024-02-01 |
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| series | Genes |
| spelling | doaj.art-122d91da73364615ae0e981bae71b2522024-03-27T13:42:52ZengMDPI AGGenes2073-44252024-02-0115326310.3390/genes15030263Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different GeneraYujie Shi0Zhen Chen1Jingyong Jiang2Xiaobai Li3Wei Zeng4Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou 318000, ChinaZhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou 318000, ChinaInstitute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai 317000, ChinaInstitute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, ChinaZhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou 318000, China<i>Lindera aggregata</i> is a species of the Lauraceae family, which has important medicinal, economic and ornamental values. In this study, we sequenced, assembled and annotated the chloroplast genome of <i>L. aggregata</i> and reannotated and corrected eight unverified annotations in the same genus. The chloroplast genomes taxa from Lindera and from different genera of Lauraceae were compared and analyzed, and their phylogenetic relationship and divergence time were speculated. All the 36 chloroplast genomes had typical quadripartite structures that ranged from 150,749 to 154,736 bp in total length. These genomes encoded 111–112 unique genes, including 78–79 protein-coding genes, 29–30 tRNA and 4 rRNA. Furthermore, there were 78–97 SSRs loci in these genomes, in which mononucleotide repeats were the most abundant; there were 24–49 interspersed repeats, and forward repeat types were the most frequent. The codon bias patterns of all species tended to use codons ending with A or U. Five and six highly variable regions were identified within genus and between genera, respectively, and three common regions (<i>ycf1</i>, <i>ndhF-rpl32</i> and <i>rpl32-trnL</i>) were identified, which can be used as important DNA markers for phylogeny and species identification. According to the evaluation of the Ka/Ks ratio, most of the genes were under purifying selection, and only 10 genes were under positive selection. Finally, through the construction of the evolutionary tree of 39 chloroplast genomes, the phylogenetic relationship of Lauraceae was clarified and the evolutionary relationship of <i>Lindera</i> was revealed. The species of genus <i>Lindera</i> experienced rapid adaptive radiation from Miocene to Pleistocene. The results provided valuable insights for the study of chloroplast genomes in the Lauraceae family, especially in the genus <i>Lindera</i>.https://www.mdpi.com/2073-4425/15/3/263Lauraceae<i>Lindera</i>chloroplast genomecomparative analysisphylogeny |
| spellingShingle | Yujie Shi Zhen Chen Jingyong Jiang Xiaobai Li Wei Zeng Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different Genera Genes Lauraceae <i>Lindera</i> chloroplast genome comparative analysis phylogeny |
| title | Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different Genera |
| title_full | Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different Genera |
| title_fullStr | Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different Genera |
| title_full_unstemmed | Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different Genera |
| title_short | Comparative Analysis of Chloroplast Genomes of “Tiantai Wu-Yao” (<i>Lindera aggregata</i>) and Taxa of the Same Genus and Different Genera |
| title_sort | comparative analysis of chloroplast genomes of tiantai wu yao i lindera aggregata i and taxa of the same genus and different genera |
| topic | Lauraceae <i>Lindera</i> chloroplast genome comparative analysis phylogeny |
| url | https://www.mdpi.com/2073-4425/15/3/263 |
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