Abstract
Ultra-barcoding is a technique using whole plastomes and nuclear ribosomal DNA (nrDNA) sequences for plant species identification. Paris yunnanensis is a medicinal plant of great economic importance for the pharmaceutical industry. However, the alpha taxonomy of P. yunnanensis is still uncertain, hindering effective conservation and management of the germplasm. To resolve long-standing taxonomic disputes regarding this species, we newly generated the complete plastomes and nrDNA sequences from 22 P. yunnanensis accessions. Ultra-barcoding analyses suggest that P. yunnanensis as currently circumscribed is made up of two distinct genetic lineages, corresponding to the two phenotypes (“typical” and “high stem” form) identified early in our study. With distinct morphologies and distribution, the “high stem” form should be recognized as a previously unrecognized species; here it is described as a new species, P. liiana sp. nov. Moreover, the ultra-barcoding data do not support treatment of P. yunnanensis as a conspecific variety under Paris polyphylla. Our study represents a guiding practical application of ultra-barcoding for discovery of cryptic species in taxonomically challenging plant taxa. The findings highlight the great potential of ultra-barcoding as an effective tool for resolving perplexing problems in plant taxonomy.
Highlights
DNA barcoding involves the standardized use of one or a few DNA regions for identification and discrimination of species (Hebert et al, 2003; Hollingsworth, 2011; Hollingsworth et al, 2016), as well as the discovery of cryptic or novel species (Hebert et al, 2003; Bell et al, 2012)
158,172–1,067,241 and 8,299–22,466 reads were mapped to the reference plastome and ribosomal DNA sequences, respectively (Supplementary Table S1)
De novo assembly based on these data covered the entire plastome and nuclear ribosomal DNA (nrDNA) for all samples, with average coverage ranging from 44,917 to 1,011 and 211,637 to 572,407 times, respectively
Summary
DNA barcoding involves the standardized use of one or a few DNA regions for identification and discrimination of species (Hebert et al, 2003; Hollingsworth, 2011; Hollingsworth et al, 2016), as well as the discovery of cryptic or novel species (Hebert et al, 2003; Bell et al, 2012). Complete plastid genomes (plastomes) and entire nuclear ribosomal DNA (nrDNA) sequences harbor many more sequence variations, making them far more sensitive and effective than standard DNA barcodes, especially among very closely related taxa (Nock et al, 2011; Kane et al, 2012; Ruhsam et al, 2015; Ji et al, 2019a; Zhu et al, 2019; Li et al, 2020). Practical application of this technique for discovery of cryptic or novel species in taxonomically difficult plant taxa is still absent from literature
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