Chloroplast genome, an effective strategy for identifying hybrid species, using Dendrobium 'Black Gold' as an example.

Background: Misusing Dendrobium hybrid varieties in herbal products poses a substantial challenge to authenticity and safety concerns. D. 'Black Gold', a hybrid of D. nobile and D. officinale, closely mimics D. officinale in appearance. However, the accurate identification of genetic traits has been impeded by the scarcity of genetic data. Molecular markers derived from chloroplast genomes (cp genomes) have emerged as practical tools for authenticating cultivars.

Results: In this study, three Dendrobium species (D. 'Black Gold', D. nobile, and D. officinale) cp genomes were de novo sequenced, assembled, And characterized. The Analysis revealed high conservation in gene organization and structure across the three genomes. The genome sizes ranged from 150,114 bp to 150,602 bp, with the large single-copy (LSC) regions spanning 84,781 bp to 85,089 bp, the small single-copy (SSC) regions ranging from 13,799 bp to 14,503 bp, and the inverted repeat (IRa and IRb) regions varying from 26,011 bp to 26,309 bp. A total of 73 to 86 protein-coding genes (PCGs), 38 to 39 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes were identified in the three species. Phylogenetic analysis revealed that D. officinale is the maternal parent of D. 'Black Gold'. The crown group divergence of Dendrobium species was estimated to have occurred approximately 29.22 million years ago (Mya). Additionally, eight highly variable regions were identified, with the accD-psaI and matK-rps16 region confirmed as effective molecular markers for distinguishing D. 'Black Gold' from related species.

Conclusions: These findings provide valuable insights into the genetic characteristics of D. 'Black Gold' and offer a reliable strategy for distinguishing hybridized counterparts. This research not only aids in precisely identifying Dendrobium hybrids but also supports future studies on their conservation and utilization.