Format: ORAL

De-Zhu Li1, Meng-Yuan Zhou1, Chun-Xia Zeng1, Jun-Bo Yang1, Hong-Tao Li1, Lian-Ming Gao2, Peng-Fei Ma1, Jin-Mei Lu1, Cen Guo3, Ting-Shuang Yi1, Peter M. Hollingsworth4

1 Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming Yunnan 650201, China; 2 CAS Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming Yunnan 650201, China; 3 Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Mengla, Yunnan 666303, China. 4 Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.

Vascular plants dominate terrestrial ecosystems and provide food, drugs, timber, fibers, fuels and ornamentals for human beings. Our understanding of plant diversity remains a substantial challenge and identification becomes particularly difficult where material is juvenile, fragmented, or processed. The combination of plastid rbcL+matK sequences was proposed to be the standard barcode for land plants in 2009, followed by our proposal to incorporate the nuclear ribosomal ITS into barcoding practice. Because of the development of next-generation sequencing, it is possible to enhance the plant barcode, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. Genome skimming has the advantage of using existing protocols, being backward compatible with first-generation barcode, and the depth of sequence coverage can be increased as sequencing costs fall. We made a practical trial of routine recovery of rDNA and plastome sequences from herbarium collections. We sequenced specimens up to 80 years old by using as little as 500 pg of degraded starting DNA, and it can be performed with limited sample destruction. We gathered genome-skimming data of 25,583 individuals representing 20,260 species of 431 genera in 473 families of vascular plants, mainly from biodiversity hotspots in China, to build up a large-scale reference database for the China plant barcode of life initiative. Analyses of recalcitrant genera (or subgenera, or species complex) showed that organelle-scale barcode, together with rDNA sequences increased the discriminatory power by 10-15%. However, using Skmer, a method for estimating genomic distances between the query and reference genome skimming sequences, after removing the rDNA and plastome sequences, the discriminatory power was further increased. Furthermore, using deep genome skimming, particularly where a reference genome is available for the genus, a large number of single-copy orthologs can be acquired, opening up a new avenue for nuclear DNA barcodes.