# The Complete Chloroplast Genome of a Vietnam Endemic Aroid, Homalomena perplexa K.Z.Hein, Vuong, Bao & V.S.Dang, and Updated Comparative Genomics in Araceae

## TL;DR

This study sequenced the complete chloroplast genome of a rare Vietnamese plant and compared it to related species to better understand their evolutionary relationships.

## Contribution

The study provides the first complete chloroplast genome of Homalomena perplexa and updates comparative genomics in Araceae.

## Key findings

- The chloroplast genome of H. perplexa is 169,893 bp long with 79 protein-coding genes.
- Phylogenetic analysis confirmed the close relationship between Homalomena and Furtadoa genera.
- Comparative analysis revealed 13 junction variations in Aroideae chloroplast genomes.

## 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.

The complete chloroplast genome of Homalomena perplexa, an endemic aroid to Vietnam, was completely sequenced and characterized. In addition, comparative genomic analysis revealed junction variations and phylogenetic analysis confirmed the infrafamilial relationships of Araceae.