Abstract
Homalomena perplexa K.Z.Hein, Vuong, Bao & V.S.Dang has been recently recognized and identified as a Vietnamese endemic species. Its chemical contents and bioactivities have been investigated, but its genomic information is still scarce. In the current study, we sequenced and characterized the complete chloroplast genome of H. perplexa using the next-generation sequencing method. The circular genome was 169,893 bp in length and contained 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Nucleotide diversity analysis revealed only two hypervariable regions between the two Homalomena chloroplast genomes. However, repeat analysis indicated that there were shared and unique repeats between H. perplexa and H. occulta chloroplast genomes. In Araceae chloroplast genomes, there was a high variation of the junctions among the large-single copy, small-single copy, and inverted repeat regions, especially 13 variations identified in Aroideae species. In addition, phylogenetic analysis revealed the monophyly of Araceae subfamilies and a close relationship between Homalomena and Furtadoa genera. The results of this study enlarge the genomic data of the Homalomena genus and provide useful information for further comparative genomic studies of H. perplexa and related species in Aroideae. In addition, updates on comparative chloroplast genomics and phylogenetic relationships add valuable information for further evolutionary studies of Araceae.