Comparative Chloroplast Genome Analysis of Two Deciduous Phalaenopsis species, Phylogenetic Relationships, and Development of Indel markers

Background: Phalaenopsis is a taxonomically controversial genus and the most horticulturally valuable group in the family Orchidaceae. Inconsistencies among morphological characteristics and the lack of genomic resources have greatly impeded studies of the taxonomy and evolutionary relationships of this particular genus. The chloroplast genomes of Phalaenopsis wilsonii f. wilsonii and Phalaenopsis braceanum remains pending. Results: : Here, we successfully obtained the entire chloroplast genome sequences of P. wilsonii f. wilsonii and P. braceanum and subsequently compared them with chloroplast genomes of various other species. Our aim was to enhance our understanding of the taxonomy of Phalaenopsis , as well as aid the utilization of wild orchid resources. The chloroplast genomes of Phalaenopsis wilsonii f. wilsonii and Phalaenopsis braceanum exhibited similar lengths, measuring 145,874 bp and 145,935 bp, respectively. These genomes comprised a total of 128 genes, which consisted of 75 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes, and 7 pseudogenes. The GC content was 36.79%. By conducting a comparative analysis of these two chloroplast genomes, we observed a significant resemblance in their structural properties, amino acids frequencies, and codon usage bias. The biased usage of certain amino acid codons in deciduous orchids might be associated with their resistance to various types of adverse conditions (e.g., drought and nutrient deficiency). Among the four types simple sequence repeats (SSRs) that have been identified, A/T repeats constituted the highest occurrence. Seven protein-coding genes, including petN , psaI , psbH , psbM , rpl33 , rpl23 , and rps16 , were under positive selection.Ten InDel markers greater than 10 bp were developed and used to distinguish between these two species. Phylogenetic analysis revealed that P. braceanum was sister to P. stobariana ; the combined P. braceanum + P. stobariana clade was sister to P. wilsonii . Conclusions: : Our study provided novel findings concerning the chloroplast genomes of P. wilsonii f. wilsonii and P. braceanum . Our data provide key molecular resources for Phalaenopsis species that will aid future studies of the genetic evolution and environmental adaptation of orchids. The divergent hotspots identified could be serve as valuable resources for the creation of molecular markers, enabling the identification of Phalaenopsis species and facilitating phylogenetic investigations between closely related species or individuals with morphological traits similar to those of Phalaenopsis .