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Characteristics of the Complete Plastid Genome Sequences of the Monotypic Genus <i>Dodecadenia</i> (Family: Lauraceae) and Its Phylogenomic Implications
oleh: Chao Liu, Huanhuan Chen, Jian Cai, Xiangyu Tian, Lihong Han, Yu Song
Format: | Article |
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Diterbitkan: | MDPI AG 2022-08-01 |
Deskripsi
As one of a dozen monotypic genera in the family Lauraceae, the systematic position of <i>Dodecadenia</i> Nees remains controversial. Here, two complete plastomes of <i>Dodecadenia grandiflora</i> Nees were sequenced. The two plastid genomes, with the length of 152,659 bp and 152,773 bp, had similar quadripartite structure. Both consisted of one large single-copy (LSC) region with 93,740 bp and 93,791 bp, one small single-copy region (SSC) with 18,805 bp and 18,846 bp, and a pair of inverted repeats (IR) regions with 20,057 bp and 20,068 bp. A total of 128 genes were annotated for the <i>D. grandiflora</i> plastid genomes (plastomes), which included 84 protein-coding genes (PCGs), 36 tRNA genes and eight rRNA genes. Codon usage analysis of the <i>D. grandiflora</i> plastomes showed a bias toward A/U at the third codon. A total of 122 RNA editing events were predicted, and all codon conversions were cytosine to thymine. There were 30/36 oligonucleotide repeats and 89/94 simple sequence repeats in these two plastomes of <i>D. grandiflora</i>. Based on 71 plastomes, both Bayesian and maximum likelihood phylogenetic analyses showed that <i>D. grandiflora</i> are nested among the species of <i>Litsea</i> Lam. together with <i>Litsea auriculata</i> Chien et Cheng and suggested that the monotypic genus <i>Dodecadenia</i> Nees should be revised. In addition, the highly variable loci <i>trnG</i> intron and <i>ycf3</i>-<i>trnS</i> could be used as excellent candidate markers for population genetic and phylogenetic analyses of <i>D. grandiflora</i>.