We have developed a rapid genus identification method for poisonous plants. The real-time PCR using the TaqMan® probe method was employed for detection, with the amplified targets being the \"trnL (UAA)-intron\" or \"trnL-trnF intergenic spacer\" regions of chloroplast DNA. The targeted plants were selected six genera (Aconitum, Colchicum, Veratrum, Brugmansia, Scopolia and Narcissus), which have been implicated in many instances of food poisoning in Japan. A tissue lysis solution was used for DNA extraction, which can be completed within approximate 30 min. A master mix corresponding to the tissue lysis solution was used for real-time PCR reagents. As a result, we were able to complete the entire process from DNA extraction to genus identification in 4 to 5 hr. The detection sensitivity was estimated at approximately 1 pg of DNA for all six plant genera. Remarkably, an amplification plot was discerned even with the crude cell lysates of all samples. It was also possible to obtain amplification curves for three plant samples that had been subjected to simulated cooking (boiling). This study suggests that the developed method can rapidly identify six genera of poisonous plants.

This work reports the development and application of a disposable amperometric sensor built on magnetic microcarriers coupled to an Express PCR strategy to amplify a specific DNA fragment of the chloroplast trnH-psbA. The procedure involves the selective capture of a 68-mer synthetic target DNA (or unmodified PCR products) through sandwich hybridization with RNA capture probe-modified streptavidin MBs and RNA signaling probes, labeled using antibodies specific to the heteroduplexes and secondary antibodies tagged with horseradish peroxidase. Amperometric measurements were performed on screen-printed electrodes using the H2O2/hydroquinone system. Achieving a LOD of 3 pM for the synthetic target, it was possible to detect 2.5 pg of peanut DNA and around 10 mg kg-1 of peanut in binary mixtures (defatted peanut flours prepared in spelt wheat). However, the detectability decreased between 10 and 1000 times in processed samples depending on the treatment. The Express PCR-bioplatform was applied to the detection of peanut traces in foodstuff.

Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

BACKGROUND: The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants.
RESULTS: The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica\'s sister species is Caragana jubata, whereas C. turkestanica\'s closest relative is Caragana arborescens.
CONCLUSIONS: The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.

UNASSIGNED: Elymus nutans holds ecological and pastoral significance due to its adaptability and nutritional value, the Qinghai-Tibet Plateau (QTP) is a key hub for its genetic diversity. To conserve and harness its genetic resources in highland ecosystems, a thorough assessment is vital. However, a comprehensive phylogeographic exploration of E. nutans is lacking. The objective of this study was to unravel the genetic diversity, adaptation, and phylogenetics of E. nutans populations.
UNASSIGNED: Encompassing 361 individuals across 35 populations, the species\' genetic landscape and dynamic responses to diverse environments were decoded by using four chloroplast DNA (cpDNA) sequences and nine microsatellite markers derived from the transcriptome.
UNASSIGNED: This study unveiled a notable degree of genetic diversity in E. nutans populations at nuclear (I = 0.46, He = 0.32) and plastid DNA levels (Hd = 0.805, π = 0.67). Analysis via AMOVA highlighted genetic variation predominantly within populations. Despite limited isolation by distance (IBD), the Mekong-Salween Divide (MSD) emerged as a significant factor influencing genetic differentiation and conserving diversity. Furthermore, correlations were established between external environmental factors and effective alleles of three EST-SSRs (EN5, EN57 and EN80), potentially linked to glutathione S-transferases T1 or hypothetical proteins, affecting adaptation. This study deepens the understanding of the intricate relationship between genetic diversity, adaptation, and environmental factors within E. nutans populations on the QTP. The findings shed light on the species\' evolutionary responses to diverse ecological conditions and contribute to a broader comprehension of plant adaptation mechanisms.

Lemna aequinoctialis Welw. is a widely spread species that has diverse physiological and molecular properties. Flower characteristics are important factors in deducing taxonomical status; however, owing to the rarity of flowering observations in Lemna, studying them has been a prolonged challenge. In this study, physiological and morphological analyses were conducted by inducing flowering, and molecular analysis was done based on the two chloroplast DNA loci (matK, atpF-atpH intergeneric spacer) of L. aequinoctialis sensu Landolt (1986) from 70 strains found in 70 localities in Japan, Korea, Thailand, and the US. In total, 752 flowering fronds from 13 strains were observed based on axenic conditions. Two different trends in flower organ development-protogyny and adichogamy-were detected in these strains. Their physiological traits were divided into two groups, showing different morphological features based on frond thickness, root cap, and anther sizes. Molecular analysis showed two lineages corresponding to two physiological groups. These were identified as L. aequinoctialis sensu Beppu et al. (1985) and L. aoukikusa Beppu et Murata based on the description of the nomenclature of L. aoukikusa. These were concluded as independent taxa and can be treated as different species. Furthermore, the distribution of L. aoukikusa is not only limited to Japan.

With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s13205-023-03848-w.

Pleurozium schreberi is a common and widespread species that has been the object of many studies, and its biology and ecology are well known. However, genetic studies on this species are limited or even absent. Because of the lack of any data about the genetic diversity of the moss species P. schreberi in Poland, the present paper describes the results of the studies carrying out for the first time this kind of research based on the atpB-rbcL spacer sequences of chloroplast DNA. A total of 35 specimens of P. schreberi from 19 locations in Poland were sampled. Total genomic DNA was extracted, amplified, and sequenced, and all obtained sequences were analyzed. Our findings suggest the low genetic diversity of P. schreberi in Poland. We detected four different haplotypes, shared between different populations.

Past climatic and topographic variations have created strong biogeographic barriers for alpine species and are key drivers of the distribution of genetic variation and population dynamics of species on the Qinghai-Tibet Plateau (QTP). Therefore, to better conserve and use germplasm resources, it is crucial to understand the distribution and differentiation of genetic variation within species. Elymus breviaristatus, an ecologically important rare grass species with strong resistance, is restricted to a limited area of the QTP. In this study, we investigated the phylogeography of E. breviaristatus using five chloroplast genes and spacer regions in natural populations distributed along the eastern QTP. We identified a total of 25 haplotypes among 216 individuals from 18 E. breviaristatus populations, which were further classified into four haplogroups based on geographical distribution and haplotype network analysis. Notably, we did not observe any signs of population expansion. High genetic diversity was exhibited at both species and population levels, with precipitation being the main limiting factor for population genetic diversity levels. Higher genetic diversity was exhibited by populations located near the Mekong-Salween Divide genetic barrier, suggesting that they may have served as a glacial refuge. The significant pattern of genetic differentiation by environmental isolation highlights the influence of heterogeneous environments on the genetic structure of E. breviaristatus populations. Additionally, the results of ecological niche models indicated that the geographic distribution of E. breviaristatus populations has decreased rapidly since the Last Glacial Maximum but is not threatened by future global warming.

Identifying conservation units is crucial for the effective conservation of threatened species. Previous cases are almost exclusively based on large-scale but coarse sampling for genetic structure analyses. Significant genetic structure can occur within a small range, and thus multiple conservation units may exist in narrowly distributed plants. However, small-scale genetic structure is often overlooked in conservation planning especially for wind-pollinated and wind-dispersed trees, largely due to the absence of dense and elaborate sampling. In this study, we focused on a representative endangered relict plant, Metasequoia glyptostroboides. Using both nuclear microsatellites (nSSRs) and chloroplast DNA (cpDNA) fragments, we sampled across the narrow distribution range of this species and determined its conservation units by exploring its genetic structure and historical demography. cpDNA haplotypes were classified into two groups, but mixed in space, suggesting that the existent wild trees of M. glyptostroboides cannot be divided into different evolutionarily significant units. However, using nSSRs, we detected strong spatial genetic structure, with significant genetic differentiation and weak gene flow between the samples in the east of the species\' distribution range and other samples. The divergence between the two nSSR groups was dated to the Last Glacial Maximum (c. 19.6 kya), suggesting that such spatial genetic structure has been maintained for a long term. Therefore, these two nSSR groups should be considered as different conservation units, that is, management units, to protect intergroup genetic variations, which is likely to be the outputs of local adaptation. Our findings highlight the necessity to reveal small-scale genetic structure and population demography to improve the conservation strategies of evolutionary potential of endangered plants.