Species delimitation and interspecific relationships of the endangered herb genus Notopterygium inferred from multilocus variations

Morphology and ITS sequences provide insights into the phylogeny of Tongoloa (Apiaceae) from China

BACKGROUND

Tongoloa is a genus comprising approximately 20 species, primarily distributed in the mountainous regions of southwest China. The insufficiency of specimen materials and morphological similarities among species render it a taxonomically challenging genus within the Apiaceae family. To elucidate the phylogenetic relationships and taxonomy of Chinese Tongoloa, this study utilized a total of 115 nrITS sequences, including 47 recently obtained sequences, for phylogenetic reconstruction.

RESULTS

Phylogenetic relationships reconstructed from ITS sequences indicate that the East Asia Clade and the Komarovia Clade are sister groups, and Tongoloa belongs to the East Asia Clade. Species of Tongoloa are subdivided into 3 distinct groups, all sharing similar fruit morphologies and are clearly differentiated from related taxa. Several Tongoloa-like members classified under other genera are interpreted to be closely related to Tongoloa. Morphological and molecular data indicate that Tongoloa, Sinolimprichtia subclade and Chinese Trachydium subclade are separate yet genetically contiguous taxa. It is confirmed that Tongoloa zhongdianensis belongs to the Hymenidium Clade, while Sinocarum is classified within the Acronema Clade. Two new taxa are found in the Hengduan Mountains.

CONCLUSION

Tongoloa is a genus within the East Asia Clade of Apiaceae, and the phylogeny reconstructed based on ITS sequences divides it into 3 main groups. By integrating fruit morphology and molecular phylogenetic analyses, we preliminary clarified the intricate taxonomic relationships among Tongoloa and related taxa. These results provide valuable opportunities for a deeper understanding of the phylogeny of Tongoloa.

Phytochemistry and Biological Profile of the Chinese Endemic Herb Genus Notopterygium

Notopterygium, a plant genus belonging to the Apiaceae family, is utilized in traditional Chinese medicine for its medicinal properties. Specifically, the roots and rhizomes of these plants are employed in phytotherapy to alleviate inflammatory conditions and headaches. This review provides a concise overview of the existing information regarding the botanical description, phytochemistry, pharmacology, and molecular mechanisms of the two Notopterygium species: Notopterygium incisum and N. franchetii. More than 500 distinct compounds have been derived from these plants, with the root being the primary source. These components include volatile oils, coumarins, enynes, sesquiterpenes, organic acids and esters, flavonoids, and various other compounds. Research suggests that Notopterygium incisum and N. franchetii exhibit a diverse array of pharmacological effects, encompassing antipyretic, analgesic, anti-inflammatory, antiarrhythmic, anticoagulant, antibacterial, antioxidant, and anticancer properties on various organs such as the brain, heart, digestive system, and respiratory system. Building activity screening models based on the pharmacological effects of Notopterygium species, as well as discovering and studying the pharmacological mechanisms of novel active ingredients, will constitute the primary development focus of Notopterygium medicinal research in the future.

Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.

The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis

Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.

DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes

The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.

The complete chloroplast genome of Keteleeria evelyniana

Here, we report the complete chloroplast genome of Keteleeria evelyniana. The genome is 116,940 bp in size, which is comprised of a large single-copy (LSC) region of 74,075 bp, a small single-copy (SSC) region of 40,425 bp, and two short inverted repeat (IR) regions of 1,220 bp. The overall GC content of the plastome was 38.5%. The new sequence comprised 103 unique genes, including 74 protein-coding genes, 4 rRNA genes, and 25 tRNA genes. Phylogenetic analysis showed that K.evelyniana was close to Keteleeria hainanensis and Keteleeria davidiana.

Comparison of Chloroplast Genomes among Species of Unisexual and Bisexual Clades of the Monocot Family Araceae

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17-18 genes are duplicated in the inverted repeat (IR) regions, comprising 6-7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.

The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae

Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales.