Background
At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species

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Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.

The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences, pollinator-mediated isolation, diploid hybridization and introgression, and allopolyploidy. These mechanisms have driven spectacular radiations and/or species diversifications in various groups of plants such as Pedicularis L., Saussurea DC., Rhododendron L., Primula L., Meconopsis Vig., Rhodiola L., and many lineages of gymnosperms. Nevertheless, much work is needed toward understanding the evolutionary mechanisms of plant diversifications on the QTP. Well-sampled biogeographic analyses of the QTP plants in the broad framework of the Northern Hemisphere as well as the Southern Hemisphere are still relatively few and should be encouraged in the next decade. This paper reviews recent evidence from phylogenetic and biogeographic studies in plants, in the context of rapid radiations, mechanisms of species diversifications on the QTP, and the biogeographic significance of the QTP in the broader context of both the Northern and Southern Hemisphere biogeography. Integrative multidimensional analyses of phylogeny, morphological innovations, geography, ecology, development, species interactions and diversifications, and geology are needed and should shed insights into the patterns of evolutionary assembly and radiations in this fascinating region.

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Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau.

DNA barcoding of medicinal plant material for identification.

A renaissance in herbal medicine identification: From morphology to DNA

https://air.unimi.it/bitstream/2434/190216/2/omics.pdf

Omic techniques in systems biology approaches to traditional Chinese medicine research: present and future.

Ginsengs (Panax, Araliaceae) are among the plants best known for their medicinal properties. Many ginseng species are endangered due to over-exploitation of natural resources - a situation difficult to remedy while there are no reliable, practical methods for species identification. We screened eleven candidate DNA barcoding loci to establish an accurate and effective Panax species identification system, both for commercial and conservation purposes. We used 95 ginseng samples, representing all the species in the genus. We found considerable differences in the performance of the potential barcoding regions. The sequencing of ATPF-ATPH was unsuccessful due to poly-N structures. The RBCL, RPOB, and RPOC1 regions were found to be mostly invariable, with only four to eight variable sites. Using MATK, PSBK-I, PSBM-TRND, RPS16 and NAD1, we could identify four to six out of eight considerably divergent species but only one to five out of nineteen clusters within the P. bipinnatifidus species group. PSBA-TRNH and ITS were the most variable loci, working very well both in species and cluster identifications. We demonstrated that the combination of PSBA-TRNH and ITS is sufficient for identifying all the species and clusters in the genus.

DNA Barcoding of Panax Species

Linnaeoideae is a small subfamily of erect or creeping shrubs to small trees in Caprifoliaceae that exhibits a wide disjunct distribution in Eurasia, North America and Mexico. Most taxa of the subfamily occur in eastern Asia and Mexico but the monospecific genus Linnaea has a circumboreal to north temperate distribution. In this study, we conducted phylogenetic and biogeographic analyses for Linnaeoideae and its close relatives based on sequences of the nuclear ribosomal ITS and nine plastid (rbcL, trnS-G, matK, trnL-F, ndhA, trnD-psbM, petB-D, trnL-rpl32 and trnH-psbA) markers. Our results support that Linnaeoideae is monophyletic, consisting of four eastern Asian lineages (Abelia, Diabelia, Dipelta and Kolkwitzia), the Mexican Vesalea, and Linnaea. The Mexican Vesalea was formerly placed in Abelia, but it did not form a clade with the eastern Asian Abelia; instead Vesalea and Linnaea are sisters. The divergence time between the eastern Asian lineages and the Mexican Vesalea plus the Linnaea clade was dated to be 50.86 Ma, with a 95% highest posterior density of 42.8 Ma (middle Eocene) to 60.19 Ma (early Paleocene) using the Bayesian relaxed clock estimation. Reconstructed ancestral areas indicated that the common ancestor of Linnaea plus Vesalea may have been widespread in eastern Asia and Mexico or originated in eastern Asia during the Eocene and likely migrated across continents in the Northern Hemisphere via the North Atlantic Land Bridges or the Bering Land Bridge. The Qinling Mountains of eastern Asia are the modern-day center of diversity of Kolkwitzia-Dipelta-Diabelia clade. The Diabeliaclade became highly diversified in Japan and eastern China. Populations of Diabelia serrata in Japan and eastern China were found to be genetically identical in this study, suggesting a recent disjunction across the East China Sea, following the last glacial event.

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Molecular Phylogeny and Biogeographic Diversification of Linnaeoideae (Caprifoliaceae s. l.) Disjunctly Distributed in Eurasia, North America and Mexico

The recently established tribe Gomphostemmateae (Lamiaceae) consists of Gomphostemma, Bostrychanthera and Chelonopsis, but relationships within and between these genera have not been well studied. Only six of the approximately 46 species of Gomphostemmateae have been included in any previous phylogenetic analysis. In the present study, we used DNA sequences of two nuclear regions (ITS, ETS) and five plastid loci (psbA-trnH, rps 16, trnL intron, trnL-trnF spacer, trnStrnG) to reconstruct the phylogeny of the East Asian genus Chelonopsis for the first time. The molecular results indicate that the tribe Gomphostemmateae is monophyletic; Bostrychanthera is embedded in Chelonopsis; and Chelonopsis comprises two clades, one encompassing the taxa of Chelonopsis subg. Chelonopsis and the genus Bostrychanthera and the other consisting of Chelonopsis subg. Aequidens. This split is supported by several morphological characters. These results, which are further strengthened by morphological and cytological data, indicate that Bostrychanthera should be transferred to Chelonopsis. In addition, our results show that within C. subg. Aequidens, sect. Aequidens and sect. Microphyllum are monophyletic. Furthermore, two major clades are concordant with the Sino-Japanese and Sino-Himalayan distribution patterns..

Molecular phylogenetics of Chelonopsis ( Lamiaceae: Gomphostemmateae) as inferred from nuclear and plastid DNA and morphology

Cytological study in the genus Artemisia L. (Asteraceae) from Russia

Pollen grains of 15 taxa of the genus Chelonopsis (14 spp. and 1 variety) from China and Japan and 6 species of the closely related genera Bostrychanthera (1 species) and Gomphostemma (5 species) were examined by light and scanning electron microscopy. Of these, the pollen morphology of 18 taxa was studied for the first time. Pollen grains were found to be tricolpate with polar lengths of 20.8–30.0 μm and equatorial widths of 17.5–27.3 μm. The basic shape of the pollen in most taxa is subprolate or prolate-spheroidal, but spheroidal, subprolate-spheroidal, oblate-spheroidal, and prolate-subprolate grains are also found in some species. The surface is generally reticulate or suprareticulate in Chelonopsis and granulate in Bostrychanthera. In comparison with those of Chelonopsis and Bostrychanthera, the pollen grain surfaces of Gomphostemma are more diverse. In Chelonopsis, pollen is taxonomically useful at the sectional level, and some grains provide enough characters for species delimitation. The potentia...

Pollen morphology of the East Asiatic genus Chelonopsis ( Lamioideae: Lamiaceae) and allied genera, with reference to taxonomic implications and potential pollination ecology

Tsuneo Funamoto

Papers

DNA Barcoding of Panax Species

Molecular Phylogeny and Biogeographic Diversification of Linnaeoideae (Caprifoliaceae s. l.) Disjunctly Distributed in Eurasia, North America and Mexico

Molecular phylogenetics of Chelonopsis ( Lamiaceae: Gomphostemmateae) as inferred from nuclear and plastid DNA and morphology

Cytological study in the genus Artemisia L. (Asteraceae) from Russia

Pollen morphology of the East Asiatic genus Chelonopsis ( Lamioideae: Lamiaceae) and allied genera, with reference to taxonomic implications and potential pollination ecology