Single-Copy Orthologs (SCOs) improve species discrimination: A case study in subgusJensoa(Cymbidium)

Abstract

Standard barcodes and ultra-barcodes face challenges in delimitation and discrimination of closely related species with deep coalescence, hybrid speciation, gene flow or low sequence-variation. Single copy orthologs (SCOs) have been recommended as standardized nuclear markers in metazoan DNA taxonomy. Here, we assessed the performance of SCOs in identifying recently diverged species in subgenus Jensoa (Cymbidium) which has been poorly settled by ultra-barcode. More than 90% of target 9094 reference SCOs inferred from three genomes of Cymbidium were successfully retrieved for all 11 representative species in subg. Jensoa by ALiBaSeq from as low as 5 x depth whole genome shotgun sequences. Species tree reconstructed from multiple refined SCO matrices under multispecies coalescent model successfully discriminated all species and discerned wrongly identified or labeled species. Plentiful and refined SCOs matrices obtained by implementing our pipeline facilitate not only phylogenetic study, but also high-resolution species diagnosing. Biparentally inherited SCOs as multi-locus marker not only advances the force of DNA barcoding, but also facilitates an eventual transition to species-tree-based barcoding strategies.