Assessing the genetic and chemical diversity of Taraxacum species in the Korean Peninsula

Genome-wide identification of oxidosqualene cyclase genes regulating natural rubber in Taraxacum kok-saghyz

MAIN CONCLUSION

Nine TkOSC genes have been identified by genome-wide screening. Among them, TkOSC4-6 might be more crucial for natural rubber biosynthesis in Taraxacum kok-saghyz roots. Taraxacum kok-saghyz Rodin (TKS) roots contain large amounts of natural rubber, inulin, and valuable metabolites. Oxidosqualene cyclase (OSC) is a key member for regulating natural rubber biosynthesis (NRB) via the triterpenoid biosynthesis pathway. To explore the functions of OSC on natural rubber producing in TKS, its gene family members were identified in TKS genome via genome-wide screening. Nine TkOSCs were identified, which were mainly distributed in the cytoplasm. Their family genes experienced a neutral selection during the evolution process. Overall sequence homology analysis OSC proteins revealed 80.23% similarity, indicating a highly degree of conservation. Pairwise comparisons showed a multiple sequence similarity ranging from 57% to 100%. Protein interaction prediction revealed that TkOSCs may interact with baruol synthase, sterol 1,4-demethylase, lupeol synthase and squalene epoxidase. Phylogenetic analysis showed that OSC family proteins belong to two branches. TkOSC promoter regions contain cis-acting elements related to plant growth, stress response, hormones response and light response. Protein accumulation analysis demonstrated that TkOSC4, TkOSC5 and TkOSC6 proteins had strong expression levels in the root, latex and plumular axis. Comparison of gene expression patterns showed TkOSC1, TkOSC4, TkOSC5, TkOSC6, TkOSC7, TkOSC8 and TkOSC9 might be important in regulating NRB. Combination of gene and protein results revealed TkOSC4-6 might be more crucial, and the data might contribute to a more profound understanding of the roles of OSCs for NRB in TKS roots.

The complete chloroplast genome sequence and phylogenetic analysis of Tragopogon pratensis L. (Asteraceae)

Currently, the phylogenetic relationships of Tragopogon pratensis Linnaeus (1753) remain unclear. This study presents the first report on the complete chloroplast genome of T. pratensis, which is a quadripartite structure with a length of 153,002 bp and containing a large single copy (LSC, 84,225 bp) region, a small single copy (SSC, 18,407 bp) region, a pair of inverted repeats (IR, 25,185 bp) regions. A total of 134 genes are identified, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes, and 2 pseudogenes. Phylogenetic analysis revealed that T. pratensis is most closely related to T. dubius and that Tragopogon is a monophyletic genus.

The complete chloroplast genome of Taraxacum albidum (Asteraceae), a Japanese endemic dandelion

Taraxacum albidum, a perennial herb of the Asteraceae family, exhibits both tetraploid and pentaploid in Japan. This study sequenced and characterized the complete chloroplast genome of T. albidum, revealing a 151,451 bp sequence with a typical quadripartite structure, comprising one large single-copy (LSC) region of 84,052 bp, one small single-copy (SSC) region of 18,541 bp, and two inverted repeat (IR) regions, IRa and IRb, each 24,429 bp in length. The chloroplast genome, excluding duplicates, contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The GC content of this genome was 37.7%. Phylogenetic analysis revealed that T. albidum is most closely related to T. mongolicum, with the chloroplast genome sequences being nearly identical, differing by only one nucleotide. These findings suggest that the maternal lineage of T. albidum likely originates from T. mongolicum or its closely related species.

Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland

The dandelions from Taraxacumsect.Erythrosperma are taxonomically well distinguished and ecologically restricted to warm and sunlit habitats of steppes, dry and sandy grasslands, and distributed in temperate regions of Europe and Central Asia, with some being introduced to North America. Despite the long tradition of botanical research, the taxonomy and distribution of dandelions of T.sect.Erythrosperma is still underexplored in central Europe. In this paper, by combining traditional taxonomic studies supported by micromorphological, molecular and flow cytometry analyses as well as potential distribution modelling we shed light on taxonomical and phylogenetical relationships between members of T.sect.Erythrosperma in Poland. We also provide an identification key, species-checklist, detailed descriptions of morphology and occupated habitats as well as distribution maps for 14 Polish erythrosperms (T.bellicum, T.brachyglossum, T.cristatum, T.danubium, T.disseminatum, T.dissimile, T.lacistophyllum, T.parnassicum, T.plumbeum, T.proximum, T.sandomiriense, T.scanicum, T.tenuilobum, T.tortilobum). Finally, conservation assessments performed using the IUCN method and threat categories for all the examined species are proposed.

Authentication of Zingiber Species Based on Analysis of Metabolite Profiles

Zingiber corallinum and Zingiber montanum, which belong to the Zingiberaceae family, are traditional Chinese folk medicinal herbs in Guizhou and Yunnan Province of China. They share great similarities in morphology, chemical constituent, and DNA barcoding sequence. The taxonomy of the two Zingiber species is controversial and discrimination of traditional Chinese medicines directly affects the pharmacological and clinical effects. In the present study, we performed a systemic analysis of "super-barcode" and untargeted metabolomics between Z. corallinum and Z. montanum using chloroplast (cp) genome sequencing and gas chromatography-mass spectrometry (GC-MS) analysis. Comparison and phylogenetic analysis of cp genomes of the two Zingiber species showed that the cp genome could not guarantee the accuracy of identification. An untargeted metabolomics strategy combining GC-MS with chemometric methods was proposed to distinguish the Zingiber samples of known variety. A total of 51 volatile compounds extracted from Z. corallinum and Z. montanum were identified, and nine compounds were selected as candidate metabolic markers to reveal the significant difference between Z. corallinum and Z. montanum. The performance of the untargeted metabolomic approach was verified with unknown Zingiber samples. Although the cp genomes could not be used to identify Zingiber species in this study, it will still provide a valuable genomics resource for population studies in the Zingiberaceae family, and the GC-MS based metabolic fingerprint is more promising for species identification and safe application of Z. corallinum and Z. montanum.

The complete chloroplast genome of Gaultheria fragrantissima Wall. (Ericaceae) from Yunnan, China, an aromatic medicinal plant in the wintergreens

Gaultheria fragrantissima (Ericaceae) is an aromatic medicinal plant with high concentrations of the secondarymetabolite methyl salicylate (oil of wintergreen). In this study, the complete chloroplast genomeof G. fragrantissima was sequenced. The complete plastome is 176,196 bp in length, and the GCcontent is 36.6%. The plastome comprises 110 unique genes (76 protein-coding, 30 tRNA and 4 rRNA).Phylogenetic analysis fully supported a sister relationship between G. fragrantissima and G. hookeriwithin the Leucothoides clade of Gaultheria. This chloroplast genome will serve as a valuable referencefor future taxonomic and phylogenetic research.

Diversity and authentication of Rubus accessions revealed by complete plastid genome and rDNA sequences

Complete plastid genome (plastome) and ribosomal DNA (rDNA) sequences of three Rubus accessions (two Rubus longisepalus and one R. hirsutus) were newly assembled using Illumina whole-genome sequences. Rubus longisepalus Nakai and R. longisepalus var. tozawai, described as different varieties, have identical plastomes and rDNA sequences. The plastomes are 155,957 bp and 156,005 bp and the 45S rDNA transcription unit sizes are 5809 bp and 5811 bp in R. longisepalus and R. hirsutus, respectively. The 5S rDNA transcription unit is an identical 121 bp in three Rubus accessions. We developed three DNA markers to authenticate R. longisepalus and R. hirsutus based on plastome diversity. Phylogenomic analysis revealed that the Rubus species classified as two clades and R. longisepalus, R. hirsutus, and R. chingii are the most closely related species in clade 1.