A DNA barcode database for the woody plants of Japan

DNA barcode databases are increasingly available for a range of organisms facilitating the wide application of DNA barcode –based pursuits. Here we announce the development of a comprehensive DNA barcode database of the Japanese woody flora representing 43 orders, 99 families, 303 genera and 834 species and comprising 77.3% of genera and 72.2% of species of woody plants in Japan. A total of 6,216 plant specimens were collected from 223 sites (municipalities, i.e. city, town, village) across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This database utilised three chloroplast DNA regions (rbcL, trnH –psbA and matK) and consists of 14,404 barcode sequences. Individual regions varied in their identification rates with species-level and genus-level rates for rbcL, trnH –psbA and matK being 57.4%/ 96.2%, 78.5%/ 99.1 % and 67.8%/ 98%, respectively. Identification rates were higher using region combinations with total species level rates for two region combinations (rbcL & trnH, rbcL & matK, and trnH –psbA & matK) ranging between 90.6 —95.8%, and for all three regions equal to 98.6%. Genus level identification rates were even higher ranging between 99.7 —100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode database is an effective resource for investigations of woody plants in Japan using DNA barcodes and provides a useful template for development of libraries for other components of the Japanese flora.

Molecular evidence for the status of Bidens connata Muhl. ex Willd. and B. decipiens Warnst. in the old and new World

Earlier, we have established that the European blackjack, which in many literary sources is cited as an invasive North American Bidens connata, was described by Carl Warnstorf back in 1895 as B. decipiens and had a hybrid origin (B. frondosa × B. cernua). In this study, we continue to compare the genomes of B. connata and B. decipiens by molecular genetics and cytological methods. The objects are the F1 offsprings of B. frondosa, B. connata, and B. cernua collected in 2018 from Minnesota and Wisconsin (USA), grown from seeds in the greenhouse conditions of N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, as well as samples of B. decipiens, B. frondosa and B. cernua collected from Eastern Europe (Belarus and European Russia). The nucleotide sequences of nuclear (ITS 1–2) and chloroplast (trnL– trnF and rpl32–trnL) DNA were studied. Analysis of the ITS 1–2 site showed that B. connata individuals of North America are not hybrids. Analysis of the chloroplast DNA regions confirmed that both taxa, B. connata and B. decipiens, are evolutionarily close to B. cernua. Bangladesh J. Plant Taxon. 28(1): 1-10, 2021 (June)

Evaluation of Genetic Diversity by DNA Barcoding of Local Lotus Populations from Thua Thien Hue Province

Background: DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Nelumbo. Methods: Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions of thirty three lotus samples which were collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequenced products were analyzed using Minimum Evolution method in the MEGA 7.0 program.Result: We did not observe high variability in nucleotide sequences within the rbcL region (0.135%). White Nelumbo, while, the most encoding matK (8.013%) and variable trnH-psbA (with different number of repeating regions TAAAA) intergenic regions was the most useful for Nelumbo barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of white and pink lotus varieties of N. nucifera specie according to the adopted classification of the genus Nelumbo. The results confirm that the use of matK, rbcL and trnH-psbA or combine all three regions together is insufficient for DNA barcoding in white and pink lotus varieties of N. nucifera specie and better discrimination within the genus Nelumbo. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in GeneBank under the following accession numbers: rbcL (MN011708 to MN068956); matK (MN011719 to MN068978) and trnH-psbA (MN011730 to MN086252).

Molecular reappraisal of relationships between Photinia, Stranvaesia and Heteromeles (Rosaceae, Maleae)

Photinia, Stranvaesia and Heteromeles are considered to be related genera belonging to the tribe Maleae of Rosaceae. Stranvaesia comprises five species distributed in eastern Asia while Photinia consists of about 30 species found in eastern Asia and Mexico. Heteromeles is a monotypic genus distributed in northwestern Mexico and southwestern US. Distinctions between these three genera rely on morphological features of leaves, flowers, and fruits, but some character states that are supposed to be diagnostic of Stranvaesia also occur in species of Photinia. In order to clarify the taxonomic delimitations of the three genera, sequences from one nuclear gene (PepC) and three intergenic chloroplast DNA regions (trnS-trnG, psbA-trnH and trnL-trnH) were used to estimate the phylogeny of Photinia, Stranvaesia and Heteromeles. All Maximum parsimony, maximum likelihood, and Bayesian analyses supported the conclusion that the evergreen species Stranvaesia davidiana should be merged into Photinia, and another two deciduous species S. amphidoxa and S. tomentosa should be transferred to the genus Pourthiaea. Additionally, one Photinia species P. bodinieri should be transferred into Stranvaesia. Finally, it is suggested that Heteromeles arbutifolia should be merged into Photinia. Taxonomic treatments have been made to those species mentioned above, three new combinations have been proposed and six lectotypes have been designated here.

Defining phylogenetic relationship of Nepeta x tmolea and its parents via DNA barcoding

Nepeta viscida and N. nuda subsp. nuda and N. × tmolea were examined in this study. Mainly fresh leaf pieces, dried with silica grains, were used for DNA extraction procedures via DNA isolation kits. Standard PCR techniques were executed using three different primer sets (one nuclear DNA region (nrITS) and two chloroplast DNA regions (rpl32-trnL and trnA(Leu)-trnA(Phe)-trnL-F). DNA sequences were analysed and evaluated using different molecular approaches and software. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study. According to our result, N. × tmolea have some intermediate characters compared to its parents. nrITS data give more information phylogenetically, and also the most polymorphic loci are seen in nrITS data. Morphological and molecular data contribute to define separation of N. × tmolea. Consequently, the inconstant molecular structure and hybrid nature of N. × tmolea specimens were shown and interpreted in this study.

Saxifraga damingshanensis (S. sect. Irregulares, Saxifragaceae), a new species from Guangxi, China

Saxifraga damingshanensis (Saxifragaceae), a new species from Damingshan Nature Reserve in Guangxi Province, is described and illustrated. A morphological comparison between the new species and its putative relatives, S. mengtzeana and S. luoxiaoensis, is presented. The new species is morphologically similar to S. mengtzeana, but it can be easily distinguished by its non-peltate leaf, both surfaces of mature leaf blade covered with white glandular trichome, petals 3-veined and margin entire. Phylogenetic analysis, based on two chloroplast DNA regions (matK and psbA-trnH), confirmed that the new species belongs to S. sect. Irregulares. The new species is currently only known from Damingshan, Guangxi and we assign it an IUCN Red List preliminary status as Data Deficient.

Saxifraga shennongii, a new species of Saxifragaceae from Hunan Province, China

Saxifraga shennongii L. Wang, W.B. Liao et J. J. Zhang, a new species of Saxifragaceae from Hunan, China, is described and illustrated. The new species belongs to genus Saxifraga sect. Irregulares and can be distinguished from other species by stolons absent, basal leaf blade subrounded and abaxially spotted, absence of foliar embryos in the sinus, petiole sparsely short glandular pilose or glabrous and inflorescence branches up to 10 cm long. Phylogenetic analysis based on four chloroplast DNA regions (rbcL, psbA-trnH, matK and psaJ-rpl33) confirmed that the new species differed from those similar species of Saxifraga sect. Irregulares. The new species is similar to S. daqiaoensis and S. mengtzeana, but differs in indumentum and the shape of leaf.

Rehderodendron truongsonense (Styracaceae), a new species from Vietnam

Rehderodendron truongsonense, a new species from Vietnam, is described and illustrated. In the treatment of the Styracaceae for the Flore du Cambodge, du Laos, et du Viêtnam, specimens of this species were recognized as R. macrocarpum Hu. These specimens clearly differ from R. macrocarpum, however, as well as from all other species of Rehderodendron (where these characters are known) by, e.g., an evergreen versus deciduous habit, fewer secondary veins of the leaf blade, shorter inflorescences and corolla lobes, large and conspicuous lowermost bracteoles, the presence of eight ovules per carpel, and a fruit with ca. 10 to 20 ribs that are indistinct. Phylogenetic analysis based on five chloroplast DNA regions (clpP-psbB, ndhD-psaC-ndhE-ndhG, rpl22-rps19, rps18-rpl20, and psbI-trnS-GCU) placed the new species as nested within Rehderodendron and sister to R. gongshanense. This new species is endemic to the Truong Son Mountain Range, from which the epithet is derived, and we assign it an IUCN Red List preliminary status as Near Threatened.

Molecular phylogeny of the genus Hylodesmum (Fabaceae)

The phylogenetic relationships of 12 Hylodesmum species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses based on two chloroplast DNA regions (rps16-trnQ and trnL-F) and one nuclear marker (internal transcribed spacer, ITS). All analyses yielded reliable relationships among the major lineages within Hylodesmum, suggesting that Hylodesmum is monophyletic. Neither the traditionally defined Desmodium sect. Podocarpium nor D. sect. Repanda within the genus was supported as being monophyletic based on the ITS analyses and the combined ITS and chloroplast dataset analyses. The phylogenetic topologies indicated that the three species included in D. sect. Repanda were separated into different clades, which suggested that D. sect. Repanda is paraphyletic. Generally, the clades retrieved by phylogenetic analyses within D. sect. Podocarpium were consistent with traditionally defined groups except for the American group. The molecular analysis provides information regarding the revision of the traditional taxonomic system of Hylodesmum and for the evaluation of the systematic positions of each species within the genus Hylodesmum.