Ultra-Barcoding Discovers a Cryptic Species in Paris yunnanensis (Melanthiaceae), a Medicinally Important Plant

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.

Keywords: DNA barcodes; Melanthiaceae; Paris liiana; new species; plastomes; ribosomal DNA; species identification.

FIGURE 1

Comparison of morphological features between “typical” Paris yunnanensis (P. yunnanensis s.s.) and “high stem” form (P. liiana sp. nov.). (A) aerial shoot. (B) leaf shape and size. (C) flower. (D) sepals. (E) young fruit. (F) mature fruit.

FIGURE 2

Phylogenetic tree reconstructed via maximum-likelihood (ML) and Bayesian inference (BI) analyses of nuclear ribosomal DNA (nrDNA) sequences. Numbers above branches indicate likelihood bootstrap percentages (BP) and Bayesian posterior probabilities (PP).

FIGURE 3

The plastome map of “typical” Paris yunnanensis (P. yunnanensis s.s.) accessions (A) and “high stem” form (P. liiana sp. nov) accessions (B).

FIGURE 4

Phylogenetic tree reconstructed via maximum-likelihood (ML) and Bayesian inference (BI) analyses of complete plastomes. Numbers above branches indicate likelihood bootstrap percentages (BP) and Bayesian posterior probabilities (PP).

FIGURE 5

Comparison of the development of aerial shoot between “typical” Paris yunnanensis (P. yunnanensis s.s.) and “high stem” form (P. liiana sp. nov.).

FIGURE 6

The distribution of Paris yunnanensis s.s. (“typical” form, blue cycle) and P. liiana sp. nov. (“high stem” form, red cycle).

FIGURE 7

Holotype of Paris liiana sp. nov.