Polyploidy, or whole genome duplication (WGD) is widely regarded as key innovation promoting species diversification in plants. However, the hypothesis still remains controversial. Here, we tested the hypothesis by analyzing the association between polyploidy and the diversification of Araceae. Using 1081 single/low copy orthologous clusters from 90 transcriptome datasets, we generated a new time-calibrated phylogeny of Araceae. Based on Ks and gene tree methods, the special WGD event (abbreviation: ψ) was shared by the True Araceae clade, and not shared by Proto-Araceae and the lemnoids clade. By Analyses of time-dependent and trait-dependent diversification models, our results verified that the ψ WGD event was strongly associated with increases of net diversification rates of the True Araceae clade, but did not promote the diversification rates of Proto-Araceae and the lemnoids clade. Finally, functional enrichments analyses revealed that some genes in related to various binding, receptor and channel activity, DNA repair and cellular response to stress, such as heat shock protein, ABC transporter, Glycosyl hydrolase, RING finger, Pectin acetylesterase, Cytochrome P450 and Oxidative-stress-responsive kinase have experienced the expansions in the True Araceae clade. The expansions of these genes may contribute to the adaptation to the harsh tropical environment in the True Araceae clade. In summary, our results reconstructed the phylotranscriptomic framework of Araceae, revealed the diversification history of Araceae, and suggested that WGD may not act as the determining factor but the “Storage Cisterns” for species diversification.

Boehmeria nivea var. strigosa Zeng Y. Wu & Y. Zhao, a new variety of B. nivea (Urticaceae) from southwest China, is here described and illustrated based on evidence from morphology and molecular phylogeny. This new variety is mainly characterized by its green abaxial leaf blade, partly connate stipules, and densely patent strigose hairs. The phylogenetic relationship of rbcL showed that B. nivea var. strigosa formed a monophyletic group with a high support value. The conservation status of B. nivea var. strigosa is assessed as “Near Threatened” (NT) based on IUCN Criteria.

Species delimitation is a difficult task in traditional morphology-based taxonomy. The ultra-barcoding approach, which uses whole plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions as extended DNA barcodes for species identification and delimitation, has been recommended as one of the candidate techniques for plant barcoding 2.0. Yet, the efficacy of this approach in delineating species boundaries remains poorly understood. Here, we attempt to decipher species delimitation in the taxonomically challenging clade, Paris L. section Axiparis H. Li, using phylogenetic inference and multiple sequence-based species delimitation methods (ABGD, SDP, and mPTP) utilizing complete plastomes and nrDNA clusters from multiple accessions per described species. The results suggest that only two species-level taxonomic units that possess not only morphological uniqueness but also genetic distinctiveness and evolutionary independence can be recognized in P. sect. Axiparis. Therefore, previous taxonomic work overemphasized minor intraspecific morphological differences to establish species, and thus resulted in proliferation of as many as seven synonyms in this clade. Inferred from ultra-barcoding analyses, we propose a taxonomic revision of P. sect. Axiparis which will help inform future decisions regarding species conservation in the commercially valuable and severely threatened genus Paris. This case study indicates that the ultra-barcoding approach has great promise for developing a rigorous species delimitation framework that will facilitate credible taxonomic revision especially in taxonomically difficult plant taxa.