Characteristics of the Complete Plastid Genome Sequences of the Monotypic Genus Dodecadenia (Family: Lauraceae) and Its Phylogenomic Implications

Abstract

As one of a dozen monotypic genera in the family Lauraceae, the systematic position of Dodecadenia Nees remains controversial. Here, two complete plastomes of Dodecadenia grandiflora 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 D. grandiflora plastid genomes (plastomes), which included 84 protein-coding genes (PCGs), 36 tRNA genes and eight rRNA genes. Codon usage analysis of the D. grandiflora 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 D. grandiflora. Based on 71 plastomes, both Bayesian and maximum likelihood phylogenetic analyses showed that D. grandiflora are nested among the species of Litsea Lam. together with Litsea auriculata Chien et Cheng and suggested that the monotypic genus Dodecadenia Nees should be revised. In addition, the highly variable loci trnG intron and ycf3-trnS could be used as excellent candidate markers for population genetic and phylogenetic analyses of D. grandiflora.