Chloroplast Genome of Arisaema takesimense: Comparative Genomics and Phylogenetic Insights into the Arisaema.

Abstract

Arisaema takesimense (Araceae) is a unique species found exclusively in Ulleung Island of Korea. This study presents the complete chloroplast (cp.) genome of A. takesimense, which comprises 174, 361 base pairs and exhibits a typical tetrad structure. The genome encodes 112 unique genes, including 78 protein-coding genes (CDS), 30 tRNA genes, and 4 rRNA genes. In this study, a total of 49 long repeats and 139 simple sequence repeats (SSRs) were identified, predominantly located in intergenic spacer regions (IGS). Additionally, several hotspot regions, including trnS-G, accD-psaI, ndhF and rps15-ycf1, were identified, which are commonly shared among Araceae species. The analysis of these repeats revealed species-specific SSR types and hotspot regions that can be utilized for population genetic studies and species identification. A comparative genomic analysis of eleven Arisaema taxa revealed that the large single copy region (LSC) exhibits the most variability, with non-coding genes displaying more variation than coding genes. The borders between the LSC-IR-SSC regions in Arisaema taxa were generally well-preserved, and there were notable exceptions in the positions of LSC/IRa, LSC/IRb and SSC/IRb junctions for A. takesimense, A. ringens, and A. nepenthoides. A phylogenetic analysis based on the cp. genome revealed a close relationship between A. takesimense and A. bockii. The outcomes of this study substantially increase the genomic resources available for Araceae, serving as a valuable resource for species identification and evaluating intraspecific diversity within the Arisaema genus.