Exploring Heliconia chloroplast genomic features through assembly and analysis of four complete chloroplast genomes

Abstract

Abstract Background In the field of Heliconia phylogeny, the analysis has traditionally relied on the use of partially conserved chloroplast and nuclear genes, which serve as important markers for studying coevolution. However, the lack of complete chloroplast genomes for Heliconia species has posed a challenge in achieving a more comprehensive understanding of Heliconia chloroplast genomes and developing specific molecular markers for conducting in-depth phylogenetic studies within the genus. Results In this study, we performed sequencing and assembly of the complete chloroplast genomes of four representative Heliconia species of the Zingiberales order: Heliconia bihai, Heliconia caribaea, Heliconia orthotricha, and Heliconia tortuosa. The chloroplast genomes of these Heliconia species exhibited the typical quadripartite structure and ranged in length from 161,680 bp to 161,913 bp, all containing 86 protein-coding genes. Comparative analysis between the Heliconia chloroplast genomes and those of Zingiberales species revealed a high overall similarity in chloroplast genome structure. However, we observed significant variability in the single-copy (SC) regions and noticed a high degree of A/T base preference. Additionally, there were variable amplifications in the inverted repeat (IR) regions. While no genes with high nucleotide diversity were identified, three positively selected genes in Heliconiaceae, including ndhD, rpl2 and ycf2, were discovered when compared to other Zingiberales plants. Moreover, phylogenetic analysis provided strong support for the formation of a monophyletic clade consisting of Heliconiaceae species. This clade was nested within the tribe Heliconiaceae of the Zingiberales order, with high bootstrap support, reinforcing their evolutionary relatedness. Conclusions The results of this study have offered insights into the chloroplast genomes of Heliconia, and the dataset produced by our research serves as a valuable resource for subsequent studies on the Heliconia evolutionary trajectory.