Format: ORAL

Zheng-Shan He1, De-Zhu Li1,Jun-Bo Yang1

1 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Correspondence De-Zhu Li, and Jun-Bo Yang, No.132 Lanhei Rd, Heilongtan, Kunming, Yunnan 650201, China. Email: dzl@mail.kib.ac.cn; jbyang@mail.kib.ac.cn

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 Cymbidium subgenus Jensoa 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 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. We also test the performance of SCOs in other taxa among embryophytesto screen sevel universal andcapable SCOs as the new barcodes to advance the plant species identification under the multispecies coalescent.