The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629–25,859 bp) separated by the large single-copy (81,482–82,218 bp) and small single-copy (17,366–17,465 bp) regions. Each cp genome equivalently contains 112 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 78 protein coding genes. Gene content, gene order, AT content, and IR/SC boundary structure are nearly identical among all Amana cp genomes. However, the relative contraction and expansion of the IR/SC borders among the six Amana cp genomes results in length variation among them. Simple sequence repeat (SSR) analyses of these Amana cp genomes indicate that the richest SSRs are A/T mononucleotides. The number of repeats among the six Amana species varies from 54 (A. anhuiensis) to 69 (Amana kuocangshanica) with palindromic (28–35) and forward repeats (23–30) as the most common types. Phylogenomic analyses based on these complete cp genomes and 74 common protein-coding genes strongly support the monophyly of the genus, and a sister relationship between Amana and Erythronium, rather than a shared common ancestor with Tulipa. Nine DNA markers (rps15–ycf1, accD–psaI, petA–psbJ, rpl32–trnL, atpH–atpI, petD–rpoA, trnS–trnG, psbM–trnD, and ycf4–cemA) with number of variable sites greater than 0.9% were identified, and these may be useful for future population genetic and phylogeographic studies of Amana species.

Liliaceae, distributed mainly across the temperate Northern Hemisphere, are of great horticultural, culinary and medical importance, but are also a family with a long history of taxonomic uncertainty. Challenges in accurate species identification persist and phylogenetic relationships among genera in the family continue to be unresolved and/or weakly supported due to the use of limited molecular markers with insufficient variability. Here, nine newly sequenced plastomes for nine Liliaceae genera have been combined with previously published plastome data for this family, providing a total of 86 complete plastid genome sequences covering all 15 currently recognized genera for analyses. All these plastid genomes (146.9–158.3 kb) possess the typical quadripartite structure with conserved genome arrangement and content. Phylogenomic analyses strongly confirm the recognition of four subfamilies: Tricyrtidoideae with four genera; Medeoloideae with two genera; Lilioideae with eight genera and Calochortoideae, for Calochortus alone, as sister to Medeoloideae and Lilioideae. At least ten intergenic spacer regions that may serve as universal markers were identified in the family and, on a finer scale, nine and seven intergenic spacer regions are especially variable in Lilium and Fritillaria, respectively. The intergenic spacer regions rpoB-trnC, trnS-trnG, trnT-psbD and trnT-trnL, which showed high phylogenetic effectiveness, may be the best choices for future phylogenetic, phylogeographic and population genetic studies.

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The genera Oreosolen and Scrophularia (Scrophulariaceae) were assumed to be closely related due to the considerable similarity in morphology. Their sister relationship was even suggested in a few molecular phylogenetic studies. However, this proposed relationship is not so convincing due to insufficient sampling of Scrophularia. In this study, the systematic position of Oreosolen was reassessed based on more sampling of both taxa and molecular traits. A total of 104 accessions representing 89 taxa were sampled, including 87 (85 taxa) of Scrophularia, 14 (one taxon) of Oreosolen, and three outgroups. The phylogenetic relationships between Oreosolen and Scrophularia were inferred based on one nuclear (internal transcribed spacer) and three plastid (trnL‐F, psbA‐trnH, and trnQ‐rps16) DNA regions using maximum parsimony, maximum likelihood, and Bayesian inference methods. The results revealed that Oreosolen was nested within Scrophularia and thus its generic status was not supported. Its type species, Oreosolen wattii Hook. f., was then transferred to Scrophularia and a new combination (Scrophularia wattii (Hook. f.) P. Li) was proposed. Oreosolen and its sympatric ally, Phlomoides rotata (Benth. ex Hook. f.) Mathiesen (= Lamiophlomis rotata (Benth. ex Hook. f.) Kudô, Lamiaceae), might undergo convergent evolution of acaulescence and rosulate leaves driven by the harsh alpine environment.

Amana Honda (Liliaceae), known as ‘east Asian tulips’, is a spring ephemeral genus endemic to Sino-Japanese Floristic Subregion, mainly distributed in eastern and central China, Japan and the Korean peninsula. Chromosome numbers are reported here for the first time from 89 populations of Amana (representing all seven accepted species, two new species about to be published, and two suspected new species). Three ploidy levels are found in this genus. These are diploid (2n = 2x = 24) and tetraploid (2n = 4x = 48) in the widespread A. edulis, while all the narrow endemics are diploid, except for one population of A. tianmuensis, which is triploid (2n = 3x = 36). The northernmost and southernmost populations of A. edulis are diploid and tetraploid, respectively, while diploids and tetraploids coexist in between, with gradual transition to diploids as the latitude increases. This may indicate polyploids have an advantage in tolerance of environmental stress and are more adaptable to high-temperature environment in subtropical regions than diploids. The species and cytotype distributions in Amana are complex, and these results provide hypotheses about the origins of the genus and the polyploid cytotypes.