biostudies-literatureUnknown15(4)He ZSStandard barcodes and ultra-barcode encounter significant challenges when delimiting and discriminating closely related species characterized by deep coalescence, hybrid speciation, gene flow, or low sequence variation. Single-copy orthologs (SCOs) have been widely recognized as standardized nuclear markers in metazoan DNA taxonomy, yet their application in plant taxonomy remains unexplored. This study evaluates the efficacy of SCOs for identifying recently diverged species within the <i>Cymbidium</i> subgenus <i>Jensoa</i>, where ultra-barcodes have previously shown limited resolution. Remarkably, over 90% of the 9094 targeted reference SCOs, inferred from three <i>Cymbidium</i> genomes, were successfully retrieved for all 11 representative species in subg. <i>Jensoa</i> using ALiBaSeq atEcology and evolutione71323https://www.ebi.ac.uk/biostudies/studies/S-EPMC12019701biostudies-literatureSpecimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study in <i>Cymbidium</i> Subgenus <i>Jensoa</i>.PMC12019701Yang JXHuang JLLi DZHe ZSYang JBfalseSpecimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study in <i>Cymbidium</i> Subgenus <i>Jensoa</i>.Standard barcodes and ultra-barcode encounter significant challenges when delimiting and discriminating closely related species characterized by deep coalescence, hybrid speciation, gene flow, or low sequence variation. Single-copy orthologs (SCOs) have been widely recognized as standardized nuclear markers in metazoan DNA taxonomy, yet their application in plant taxonomy remains unexplored. This study evaluates the efficacy of SCOs for identifying recently diverged species within the <i>Cymbidium</i> subgenus <i>Jensoa</i>, where ultra-barcodes have previously shown limited resolution. Remarkably, over 90% of the 9094 targeted reference SCOs, inferred from three <i>Cymbidium</i> genomes, were successfully retrieved for all 11 representative species in subg. <i>Jensoa</i> using ALiBaSeq at2025-01-01T00:00:00Z2025 Apr2026-06-01T11:00:44.895Z2025-07-10T03:08:58.455ZS-EPMC120197014027624410.1002/ece3.71323