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Astylus atromaculatus Blanchard, 1843 (Coleoptera: Melyridae) is a pollinivorous beetle native to southern South America, which has invaded South Africa more than a century ago. Adults and/or larvae may occasionally damage flowers, seeds, and seedlings of various crops. Severe cattle intoxication has also been reported in Argentina, Uruguay, and South Africa following consumption of alfalfa and forage grasses infested with A. atromaculatus. Despite its economic impact, essential genetic information is lacking for this species. The present paper provides the first DNA barcode reference sequences for A. atromaculatus based on the standard 5’ fragment (658 bp) of the cytochrome c oxidase subunit I gene. The sequences obtained exhibited pairwise distances of ≤ 1.82% among them, and ~ 90% nucleotide identity with the homologous gene fragment in the morphologically similar Astylus variegatus Germar, 1824. The use of this molecular marker to explore the intraspecific variability of A. atromaculatus in central Argentina showed 21 different haplotypes, out of 32 individuals analyzed. A very high haplotype diversity (Hd = 0.962 ± 0.019) and a moderate nucleotide diversity (π = 0.00778 ± 0.00079) were recorded. The haplotype network displayed a diffuse structure due to the abundance of singletons and possible missing haplotypes, with the most common haplotype comprising only 15.6% of the specimens collected. Future research with increased sampling size and geographic coverage will allow for a better understanding of the population genetics of this pest, and consequently, for developing efficient management practices. [ABSTRACT FROM AUTHOR]

The effectiveness of plant-based therapies depends on precise botanical identification. However, tribal communities and practitioners sometimes misclassify medicinal plants due to a lack of scientific understanding. Plants cannot always be identified simply by morphology; the DNA-based approach uses a small segment of genomic DNA to authenticate medicinal plant species. Many tribal communities in Bangladesh have utilized plants for healing purposes for centuries. Therefore, this research used DNA sequences to identify Bangladeshi ethnomedicinal plants. DNA was extracted from the fresh leaves of eight important medicinal plants using the AddPrep Genomic DNA Extraction Kit and stored at − 20 °C. Three important loci (matK, rbcL and psbA-trnH) were amplified using PCR, and the sequences of these regions were analyzed for identification. rbcL and matK showed amplification success rates of 100% and 75% respectively, while for psbA-trnH the level was 50%, which subsequently led to the production of a total of 18 novel sequences. To validate the taxonomic identity of the samples, a MEGABLAST sequence comparison was performed, with nine species-level (50%) and nine genus-level (50%) identifications confirmed. The neighbor-joining method was used to construct four phylogenetic trees. The sequences obtained from the plant (leaf) samples and downloaded sequences from NCBI were employed, with the topologies of the trees being identical. Our findings demonstrate that partial genome sequencing is a viable way of identifying medicinal plants and closely related species utilizing the three plastid loci rbcL, matK and psbA-trnH, which are efficient and feasible DNA markers for plant authenticity. [ABSTRACT FROM AUTHOR]

The predaceous water beetle Menthles indicus is reported after a lapse of about five decades from India. The molecular phylogeny of the species has been described using CO1 gene sequence, which shows the species closely related to Methles cribratellus, by a genetic distance of 8–9%. [ABSTRACT FROM AUTHOR]

The evergreen tree species Aquilaria sinensis holds significant economic importance due to its specific medicinal values and increasing market demand. However, the unrestricted illegal exploitation of its wild population poses a threat to its survival. This study aims to contribute to the conservation efforts of A. sinensis by constructing a library database of DNA barcodes, including two chloroplast genes (psbA-trnH and matK) and two nuclear genes (ITS and ITS2). Additionally, the genetic diversity and structure were estimated using inter-simple sequence repeats (ISSR) markers. Four barcodes of 57 collections gained 194 sequences, and 1371 polymorphic bands (98.63%) were observed using DNA ISSR fingerprinting. The Nei's gene diversity (H) of A. sinensis at the species level is 0.2132, while the Shannon information index (I) is 0.3128. The analysis of molecular variance revealed a large significant proportion of total genetic variations and differentiation among populations (Gst = 0.4219), despite a relatively gene flow (Nm = 0.6853) among populations, which were divided into two groups by cluster analysis. There was a close genetic relationship among populations with distances of 0.0845 to 0.5555. This study provides evidence of the efficacy and dependability of establishing a DNA barcode database and using ISSR markers to assess the extent of genetic diversity A. sinensis. Preserving the genetic resources through the conservation of existing populations offers a valuable proposition. The effective utilization of these resources will be further deliberated in subsequent breeding endeavors, with the potential to breed agarwood commercial lines. [ABSTRACT FROM AUTHOR]

Herein we describe and illustrate Indopria angulata Theertha and Rajmohana gen. et sp. n. (Hymenoptera: Diapriidae) from India, along with its mt COI DNA barcode data. The genus is treated as a member of the tribe Diapriini (subfamily: Diapriinae). The new genus is proposed based on an Integrative Taxonomic Approach (ITA) with the unique combination of the morphological data and high genetic divergence for the mt COI barcode within the tribe Diapriini. Morphologically, a semi-abrupt 3-segmented clava, the presence of a median incision on the anterior syntergite, paddle-shaped forewings with angular frenal gutters, elongated marginal fringes, submarginal vein closely approximated to forewing fore margin and marginal venation distinctly surpassing basal third of wing length, together distinguish Indopria gen. n. from related genera. The specialized wing morphology can be interpreted as an adaptation to inhabit aquatic environments. Initial studies suggest the distribution of the species in the aquatic environs of east India and Andaman Islands. [ABSTRACT FROM AUTHOR]

The growing concern about migratory birds potentially spreading ticks due to global warming has become a significant issue. The city of Nantong in this study is situated along the East Asia-Australasian Flyway (EAAF), with numerous wetlands serving as roosting sites for migratory birds. We conducted an investigation of hard ticks and determined the phylogenetic characteristics of tick species in this city. We utilized three different genes for our study: the mitochondrial cytochrome oxidase subunit 1 (COX1) gene, the second internal transcribed spacer (ITS2), and the mitochondrial small subunit rRNA (12 S rRNA) gene. The predominant tick species were Haemaphysalis flava (H. flava) and Haemaphysalis longicornis (H. longicornis). Additionally, specimens of Haemaphysalis campanulata (H. campanulata) and Rhipicephalus sanguineus (R. sanguineus) were collected. The H. flava specimens in this study showed a close genetic relationship with those from inland provinces of China, as well as South Korea and Japan. Furthermore, samples of H. longicornis exhibited a close genetic relationship with those from South Korea, Japan, Australia, and the USA, as well as specific provinces in China. Furthermore, R. sanguineus specimens captured in Nantong showed genetic similarities with specimens from Egypt, Nigeria, and Argentina. [ABSTRACT FROM AUTHOR]

Vaccinium uliginosum Linn. is an important wild fruit resource in China. It is primarily distributed throughout the forest regions of Da Xing'an, Xiao Xing'an, and Changbai Mountains. However, to the best of our knowledge, its genetic diversity and structure have not been reported yet. In this study, 378 wild V. uliginosum samples from 12 different populations were analyzed for genetic diversity and structure using chloroplast matK and expressed sequence tag-derived simple sequence repeat high-throughput sequencing (EST-SSRseq) molecular markers. The results indicated that the level of genetic diversity in the natural populations of Chinese V. uliginosum was low, genetic variation was noted among the populations, and genetic differentiation among the populations was not apparent. Based on STRUCTURE analysis, the 12 analyzed populations were divided into two subgroups, Da Xing'an and Changbai Mountains, and only a small amount of gene exchange was observed between these subgroups. Geographical isolation and asexual reproduction were the primary reasons for the low genetic diversity. Thus, a combination of in situ protection and artificial domestic cultivation may help protect wild V. uliginosum. [ABSTRACT FROM AUTHOR]

To investigate the food composition and overlap in trophic niches of sympatric sika deer (Cervus nippon hortulorum) and roe deer (Capreolus pygargus), we used plant DNA barcoding to qualitatively assess winter food composition in their feces. We collected feces from sika deer and roe deer in the southern Laoyeling and extracted fecal DNA, amplified it using primers for the rbcL gene region of the plant, and sequenced it using high-throughput sequencing techniques. We analyzed 40 valid fecal samples in winter (20 from sika deer and 20 from roe deer). The results showed 56 families, 84 genera, and 84 species of plants for sika deer and 51 families, 83 genera, and 84 species for roe deer. Unlike traditional methods, using DNA barcoding revealed a large number of herbage plants in the winter food composition (43.90% for sika deer and 51.50% for roe deer). NMDS plot reveals significant ecological niche differentiation (R = 0.3062, P < 0.05) between sika deer and roe deer. Our study successfully applied DNA barcoding to the study of ungulates' feeding habits. [ABSTRACT FROM AUTHOR]

Background: The COI mitochondrial gene has been chosen as the "DNA barcode in animals" and the large quantity of genetic information in public databanks gives solid support for the use of DNA barcoding as a promising tool for the development of a specific molecular detection system. Methods and results: The present study aimed to develop a Specific Molecular Detection System (SMDS: FishDNAIDs) (primers and probe sets) for the following four target species: Prochilodus nigricans, Potamorhina altamazonica, Psectrogaster rutiloides and Triportheus angulatus, in qPCR assays. In silico and in vitro tests (using gDNA) were performed to test these sets. The database generated contained the cytochrome c oxidase subunit I (COI) nucleotide sequence for 183 specimens of Characiformes, distributed in 34 species representing eight families. In silico, primers designed for the target species amplified different species from the same genus, except for P. rutiloides, which amplified only the target species. In the in vitro test, using the SYBRGreentm and TaqMan® fluorescence systems, both sets detected the respective target species (P. nigricans, P. altamazonica, P. rutiloides and T. angulatus). In the qPCR assays using SYBRGreentm, species considered to be related were also detected, in addition to the target species, with the exception of P. amazonica and P. essequibensis (correlated to P. rutiloides). All target species were detected in the qPCR assays using the TaqMan® system; however, with the SMDS PALT, the target species P. altamazonica was detected with low CT values (22.21 ± 0.17) as well as the correlates of P. latior and P. pristigaster, though with high CT values (23.51 ± 0.19 and 30.21 ± 0.95). This assay uniquely identifies known adult tissue samples from all four species. Conclusions: The primers and probe sets developed can act as powerful tools for detecting the target Characiformes species. [ABSTRACT FROM AUTHOR]

Spodoptera spp. (Lepidoptera: Noctuidae) are economically important insect pests of cereal and vegetable crops in Tropical and Subtropical regions, but little is known of their distribution and diversity in countries of the Caribbean, in particular, Jamaica. In this study, larvae collected from hosts in three major vegetable producing regions of Jamaica were characterized based on morphological characters and mitochondrial cytochrome c oxidase I (COI) sequence data. Three species were identified, i.e., S. exigua, S. latifascia and S. frugiperda. All three species were prevalent on bunching onions (Allium fistulosum). S. exigua was also found on bell pepper (Capsicum annum) and S. frugiperda on corn (Zea mays). Species clades at 99% confidence were obtained in phylogenetic analyses with Jamaican COI sequences and those from different geographical locations. Separate clustering occurred with native S. latifascia and non-native S. exigua populations of the Americas. S. frugiperda corn and rice strains were closely related to native populations of the Americas and populations which invaded Africa and Asia, including those with recorded insecticide resistance. Low intraspecific genetic distances of ≤ 0.6% were obtained with the three species and apart from two exceptions, interspecific distances ranged from zero to 1.4%. Based on this sampling, the Jamaican populations are consistent with those previously reported in the Americas and elsewhere. The results provide new information about the genetic diversity of Spodoptera species affecting vegetable crops in Jamaica and establish a baseline for further studies. [ABSTRACT FROM AUTHOR]

The xanthid genus Medaeops Guinot, 1967 currently contains seven species reported from the Indo-West Pacific region. However, only one species, Medaeops granulosus (Haswell, 1882), has been recorded from China seas and was once thought to be widespread in the Indo-West Pacific region. In this study, two species of the Medaeops granulosus species-group were identified during the analysis on Medaeops crabs from China seas. Medaeops japonicus (Rathbun, 1898), which had previously been considered a junior synonym of M. granulosus, is shown to be a distinct species that can be distinguished from M. granulosus by the lower first anterolateral tooth, the larger and concentrated granules on carapace dorsally, and the different shape of the male's first gonopod. In addition, a new recorded species, Medaeops edwardsi Guinot, 1967, was reported from China seas for the first time. A molecular analysis was conducted to determine the status of each species, and an updated key for species of the genus Medaeops was provided. [ABSTRACT FROM AUTHOR]

Biological scientists have established 'Biodiversity Informatics' to map the global diversity of biological organisms by using cutting-edge bioinformatics tools. This review depicts an overview of microbial diversity's status worldwide and discusses microbial biodiversity in the marine and terrestrial ecosystems. The study shows how the 'Biodiversity Informatics' could help scientists to map the variety of microbial species recorded in terrestrial and marine habitats. The status of microbial biodiversity globally is also discussed. Besides, it also illustrates how biologists could utilize databases to explore not only microbial biodiversity but also various species of fauna and flora. We have represented microbial biodiversity informatics and its growth, tools and technologies, data management, digital taxonomy for biodiversity informatics to categorize microbial species. Moreover, molecular biodiversity informatics and current progress of biodiversity informatics have also been discussed. Finally, we have also depicted the policy and managerial implications and research gaps in this direction. Our article will lead to the novel path, which will show the interdisciplinary approaches of biodiversity informatics with the support of metagenomics and genomics. [ABSTRACT FROM AUTHOR]

Key message: The combination of nuclear and chloroplast barcode regions was very effective for distinguishing pomegranate genotypes. The simultaneous use of molecular, biochemical and morphological markers had a complementary function. Exclusion of similar genotypes regardless of their geographic region based on different markers helps to reduce the size of the collection, especially when building a core collection is the ultimate goal. Accurate identification of genotypes and their relationships is one of the major challenges in the study of plant taxonomy, especially at the subspecies level. For this purpose, molecular, biochemical, and morphological markers are commonly used in different plant species. In the present study, the sequences of three DNA barcode regions, including the ITS, trnl-F, and matK regions, and all their possible combinations were examined in 21 pomegranate (Punica granatum L.) accessions. In addition, 18 morphological and biochemical characteristics of the genotypes were measured simultaneously to confirm the distinctions. The results show that the combination of three barcode regions (ITS + trnl-F + matK) has the highest efficiency due to the highest number of variable sites as well as parsimony informative sites. Considering the phylogenetic trees obtained from the barcode regions and the morpho-biochemical traits, it can be seen that genotype 808 is clearly different from the other genotypes. Of the genotypes studied in this experiment, ten genotypes were classified into close groups based on their geographic origin in both the barcode and morpho-biochemical clusters. However, genotypes 709, 712, and 708, which were grown in different geographical areas, had similar characteristics, so they were grouped in close branches in both dendrograms. This suggests that the simultaneous use of molecular and morphological markers is essential for distinguishing pomegranate genotypes. [ABSTRACT FROM AUTHOR]

Carbapenem-resistant Enterobacterales pose significant global health challenges due to their rapid spread and ability to hydrolyse various beta-lactam antibiotics. Rapid tests for these carbapenemase genes are crucial to ensure appropriate prescription administration and infection control. In this study, we developed a rapid visual nanodiagnostic platform for multiplexed detection of carbapenemase genes using a lateral flow strip. The nanodiagnostic strip was designed with separate barcoded DNA tetrahedrons for the blaKPC and blaNDM genes. These tetrahedrons were distributed on a nitrocellulose membrane at two different test lines as capture probes. When tested against a panel of carbapenemase genes, the tetrahedral probes captured single-stranded amplicons of asymmetric PCR via strand hybridisation. The amplicons acted as bridging elements, binding the DNA-modified gold nanoparticles to the test line of the strip, resulting in clear visual readouts specific to the blaKPC and blaNDM genes. By employing barcoded tetrahedrons and asymmetric PCR in conjunction with the lateral flow strip, a single diagnostic test enabled the detection of multiple carbapenemase genes. The test yielded results as low as 0.12 fM for blaKPC and 0.05 fM for blaNDM within 75 min. Furthermore, the strip effectively identified specific carbapenemase genes in clinical isolates using real-time PCR, antibody-based lateral flow systems for carbapenemase detection, and carbapenemase phenotype experiments. Thus, the strip develop has a high potential for testing blaKPC and blaNDM genes in practice. [ABSTRACT FROM AUTHOR]

Background: Cinnamomum verum (true cinnamon) and Cinnamomum cassia (cassia cinnamon) are two important species belonging to family Lauraceae. These species are recognized by morphological, chemical composition and essential oil contents. The appropriate identification of species would be considerably improved by a genetic method. The main objective of the present study was to develop molecular markers distinguishing between C. verum and C. cassia. Methods and results: A total 71 ISSR (Inter simple sequence repeat) and four universal barcoding (ITS, rbcL, matK, and psbA-trnH) genes were used to distinguish both the species. No sequence variation was observed between the two species for any DNA barcode gene. However, one ISSR i.e. ISSR-37 showed a clear distinction between the species and produced 570 bp and 746 bp amplicons in C. verum and C. cassia, respectively. The polymorphic bands were converted into species-specific SCAR markers. The SCAR-CV was specific to C. verum and amplified 190 bp band, however there was no amplification seen in the C. cassia samples. Conclusion: The SCAR marker generated in this study can be employed as efficient, economical, and reliable molecular tool for the identification of C. verum. [ABSTRACT FROM AUTHOR]

In Europe, Magnolia species are planted as ornamental trees in public and private green spaces. Over the last four years, from 2018 to 2021, powdery mildew symptoms have been observed on magnolia trees in several localities in north-east, west, and south Romania. The fungus was detected mainly on leaves, causing, in early stages, whitish patches on both leaf sides and later, leaf discoloration, necrosis, and distortion. Combining morphological features with analysis of ITS-rDNA sequences from Romanian samples and sequences available on GenBank, the pathogen causing the powdery mildew of magnolias was identified as Erysiphe magnifica (U. Braun) U. Braun & S. Takam., a species recently introduced to Europe and present only in a few countries. Our finding is the first report of E. magnifica in Romania, bringing new evidence for its geographic expansion. No other species of Erysiphales has been reported from Romania on magnolias. [ABSTRACT FROM AUTHOR]

Two filamentous endophytic ascomycete fungi with different phenotypes were isolated and characterized from the vegetative tissue of Rheum spiciforme, a threatened and endemic trans-Himalayan medicinal herb. The visible morphological characteristics and microscopic features allowed the recognition of the endophytes as Fusarium proliferatum and Aureobasidium pullulans. Molecular identification involved partial DNA sequence analyses of internal transcribed spacer (ITS), elongation factor 1α (EF-1α), and calmodulin (CAL) regions of F. proliferatum DNA, and ITS and large subunit (LSU) of the nuclear ribosomal DNA (rDNA) of A. pullulans. The respective phylogenetic analyses by the Maximum Likelihood Method based on the combined ITS-EF-1α-CAL and ITS-LSU sequences showed that the former isolate is closest to F. proliferatum and the latter to A. pullulans. Moreover, using the LC-QTOF-MS technique, selected populations of R. spiciforme (one population with endophytes and another showing no apparent colonization), as well as the isolated endophytes, were evaluated for various specialized chemical constituents belonging to anthraquinone (rhein, physcion, emodin, and aloe-emodin), stilbenoid (piceatannol and resveratrol), and flavonoid (rutin, quercetin, and naringenin) class of compounds. Except for rutin, the results demonstrated that the identified endophytes possibly play an important role in sharing the metabolite synthesis machinery of the host. The current study may contribute to a better comprehension of the host-endophyte relation and open the door to the cost-effective synthesis of highly-valuable bioactive chemicals from microbial sources. [ABSTRACT FROM AUTHOR]

Two intergenic spacers cpDNA barcoding regions were used to assess the genetic diversity and phylogenetic structure of a collection of 25 Prunus accessions. The trnH-psbA and trnL-trnF intergenic spacers were able to distinguish and identify only four Prunus species. The average aligned length was 316–352 bp and 701–756 bp for trnH-psbA and trnL-trnF, respectively. The overall evolutionary divergence was higher in trnH-psbA than trnL-trnF. The transition/transversion bias (R) recorded as 0.59 in trnL-trnF and 0.89 in trnH-psbA. The number of invariable sites, nucleotide diversity (Pi), and the average number of nucleotide differences (k) was higher in the trnH-psbA region. The trnL-trnF records was above the other region in the number of variable sites, number of singleton variable sites, and the parsimony informative sites. Phylogenetic relationships among the 25 accessions of Prunus species were investigated. Most of the different Prunus species clustered in a homogenized distribution in both regions, except for the plum (P. domestica) accession (African Rose) was assigned with the peach (P. persica) accessions. The two intergenic cpDNA trnH-psbA and trnL-trnF were able to distinguish and identify the four Prunus species accessions. [ABSTRACT FROM AUTHOR]

Gynnidomorpha gentianae Suzuki and Jinbo sp. nov. (Lepidoptera: Tortricidae: Tortricinae), whose larva causes damage to Gentiana scabra Bunge var. buergeri (Miq.) Maxim. ex Franch. et Sav., is described from Japan (Hokkaido and Honshu). In this paper, we provide diagnoses and descriptions for this species based on the Japanese specimens. [ABSTRACT FROM AUTHOR]

Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms. [ABSTRACT FROM AUTHOR]

Tumors comprise diverse cancer cell populations with specific capabilities for adaptation to the tumor microenvironment, resistance to anticancer treatments, and metastatic dissemination. However, whether these populations are pre-existing in cancer cells or stochastically appear during tumor growth remains unclear. Here, we show the heterogeneous behaviors of cancer cells regarding response to anticancer drug treatments, formation of lung metastases, and expression of transcription factors related to cancer stem-like cells using a DNA barcoding and gene expression recording system. B16F10 cells maintained clonal diversity after treatment with HVJ-E, a UV-irradiated Sendai virus, and the anticancer drug dacarbazine. PBS treatment of the primary tumor and intravenous injection of B16F10 cells resulted in metastases formed from clones of multiple cell lineages. Conversely, BL6 and 4T1 cells developed spontaneous lung metastases by a small number of clones. Notably, an identical clone of 4T1 cells developed lung metastases in different mice, suggesting the existence of cells with high metastatic potential. Cas9-based transcription recording analysis in a human prostate cancer cell line revealed that specific cells express POU5F1 in response to an anticancer drug and sphere formation. Our findings provide insights into the diversity of cancer cells during tumor progression. [ABSTRACT FROM AUTHOR]

The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet's life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society. [ABSTRACT FROM AUTHOR]

We describe a new tanaidid species, Zeuxo molybi sp. n., from Kominato, Chiba, Japan. Zeuxo molybi closely resembles the Japanese congener Zeuxo ezoensis, but differs in having (1) the pereopod-1 carpus without dorsodistal spiniform setae; (2) two or three ventrodistal simple setae on the pereopod-1 propodus in females, and three or four in males; and (3) the pereopod-6 propodus with four or five flattened denticulate setae. The two species also differ in the pattern of dorsal pigmentation on the carapace. Kimura 2-parameter distances between the two species were 15.6–16.9% for the cytochrome c oxidase subunit I (COI) gene and 2.8% for the 18S rRNA gene; the former value is much greater than intraspecific distances previously reported for Z. ezoensis (0–1.5%), confirming our conclusion from morphology that Z. molybi and Z. ezoensis are not conspecific. In a COI-based maximum-likelihood phylogenetic tree, the Japanese taxa Z. molybi, Z. ezoensis, and Z. cf. normani did not form a clade. [ABSTRACT FROM AUTHOR]

The Southern Ocean is experiencing complex climate change, and the Amundsen Sea is one of the regions that has responded most rapidly to climate change. Due to their role in ecosystems, environmental sensitivity and high endemism, Antarctic demersal fish are a favorable group that can act as an indicator of the response of Antarctic organisms to climate change. However, our knowledge of Antarctic fish fauna is insufficient, with knowledge gaps even in their taxonomy. This situation is greatly influenced by the limitations of traditional taxonomy and thus calls for alternative solutions such as DNA barcoding. In this study, DNA barcoding analyses of 69 fish samples obtained from the Amundsen Sea were conducted using the mitochondrial COI gene. Based on the molecular species delimitation results, 13 fish species were found to belong to two orders, six families, and 12 genera. Both the maximum likelihood and Bayesian inference methods showed that the phylogenetic relationships of Bathydraconidae were paraphyletic, which was consistent with previous phylogenetic research. Our research showed that the COI gene, as a DNA barcode, is not only suitable for the identification of Antarctic fish species but also reflects some phylogenetic characteristics that might provide important evidence and support for studies of Antarctic fish phylogenetic relationships. In summary, our study provides an important reference for fish diversity and taxonomy in the Amundsen Sea, which may further enhance our understanding of the biodiversity, taxonomy and biogeography of fish in this area. [ABSTRACT FROM AUTHOR]

Background: Kala zeera [Bunium persicum (Boiss.) Fedtsch] is one of the important spice crops of North Western Himalayas with lot of medicinal and culinary values. In spite of having great importance, this crop is under the threat of extinction due to loss of habitat and lack of awareness. The limited availability of the seeds has ultimately increased the economic value of this spice. The upmarket of Kala zeera leads to its adulteration with other black seeds and cumin seeds. The present investigation was undertaken to evaluate polyphenolics and antioxidant properties of Kala zeera genotypes collected from North Western Himalayas and to develop DNA barcodes that can ensure their purity and can also guide in conservation of selected Kala zeera germplasm lines. Methods and results: Various locations of North Western Himalayas were explored for collecting 31 diverse germplasm lines of Kala zeera. The collected germplasm was maintained at our experimental stations during 2019–2020 and 2020–2021. These genotypes were evaluated for different seed traits and the methanolic extract from Kala zeera seeds was examined for total phenolic content, total flavonoid content, antioxidant activities by DPPH and FRAP. The results revealed significant variation in seed traits, polyphenolic content and antioxidant properties. 100 seed weight ranged from 0.05 to 0.35 g, TPC ranged from 7.5 to 22.56 mg/g, TFC ranged from 0.58 to 4.15 mg/g, antioxidant properties DPPH ranged from 168 to 624.4 μg/ml and FRAP ranged from 0.72 to 6.91 mg/g. Further, three different barcodes (ITS, rbcL and psbA-trnH) were used to reveal the authenticity of selected Kala zeera. MEGA 5 software was used for clustering and the barcodes did clustering based on geographical distribution of Kala zeera germplasm. Conclusion: Based on molecular barcoding, best barcode combination was identified that may discriminate the Kala zeera germplasm vis-a-vis can authenticate their purity. Moreover, the identified DNA barcodes will have significant role in studying the evolutionary biology of Bunium species and will be important for designing a strategy to conserve the selected Kala zeera germplasm lines. The identified genotypes with high phenolic content and antioxidant activity can further be utilized in Kala zeera breeding programmes. [ABSTRACT FROM AUTHOR]

The morphological and microscopy were combined with DNA-barcoding, together with rapid TLC for the characterization of Piper betle (PB), P. nigrum (PN), P. retrofractum (PR), P. sarmentosum (PS), and P. wallichii (PW), five medicinal Piper plants announced in the Thai Herbal Pharmacopoeia (THP). The authentic plants collected from various locations and voucher Piper products bought from commercial sites in Thailand were studied. The reproductive parts of authentic plants were subjected to ensure their morphological characters. Using sequencing analysis and genetic divergence for analyzing discriminatory performance, ITS2 was selected from eight candidate DNA markers to authenticate the origin of Piper crude drugs together with microscopic and TLC profiles for examining their characters, admixtures, adulterants, and substituents. PB and PR exhibited unique characters of the species, with no admixture, adulteration, and substitution. PN showed no variable characters of morphology and genetics. However, the microscopy could illustrate some commercial products of PN sold in Thailand have been adulterated with rice starch and roasted rice. In the herbal trade, PS has been sold in the form of mixed leaf, root, and stem more than the isolated part, but there is no variable character of the species. PW has shown more than one character of species explained by microscopic, chemical components, and genetic data. In conclusion, the conventional and molecular pharmacognostic data combined with chemical profile of authentic five Piper plants could be applied to indicate the plant origin and clarify the situations of admixture, adulteration, and substitution of the commercial Piper products launched in Thailand. [ABSTRACT FROM AUTHOR]

Members of the cephalopod family Sepiadariidae Fischer, 1882, commonly called 'bottletail squids', are known primarily from the Indo-Pacific and southwest Pacific. To date, only one species is known to occur in New Zealand waters: Sepioloidea pacifica (Kirk, 1882). However, researchers have long suspected the presence of additional species in the genus Sepioloidea d'Orbigny, 1845 in Férussac & d'Orbigny 1835-1848. The majority of known Sepioloidea material from New Zealand national collections was examined; both morphological and, where available, molecular characters are compared. As a result, two new species, Sepioloidea virgilioi sp. nov. and Sepioloidea jaelae sp. nov., are recognised and described. Diagnostic morphological characters include the tentacular club sucker arrangement and hectocotylus structure. Molecular data support the recognition of these two new taxa, with sampled populations of each of the three available Sepioloidea falling within three monophyletic clades following analysis of COI (cytochrome c oxidase subunit I) sequence data. The minimum interspecific distance is 11.09%—far greater than the maximum intraspecific distance (1.57%). A revised diagnosis for S. pacifica sensu stricto is also provided. [ABSTRACT FROM AUTHOR]

The island of Penang lying off the northwestern coast of Peninsular Malaysia, is one of the historical places for ichthyological exploration in Southeast Asia and the type locality of three freshwater species and one euryhaline species. Freshwater ecosystems on the island are currently threatened by multiple causes. To facilitate further environmental-oriented monitoring actions, we reexamined the fish diversity by surveying several freshwater localities across the island. All collected specimens were vouchered, morphologically identified and then genetically characterized using the "Barcode" fragment of the cytochrome oxidase I gene. We collected a total of 52 fish species, including 37 (21 native + 16 introduced) strictly-adapted freshwater species. Five native and 10 introduced species represent new records for the island. Genetic analyses revealed low cryptic diversity within morphologically identified species. Combining our results with those of previous surveys, a total of 63 fish species are now known from Penang freshwaters, however, five native species were not collected in the last 60 years and their conservation status is certainly at risk on the island. Overall, the presence of many introduced species along with the general degradation of freshwater habitats of Penang Island threaten its native fish diversity. [ABSTRACT FROM AUTHOR]

The root-knot nematode Meloidogyne enterolobii is amongst the most aggressive plant-parasitic nematodes, causing significant yield loss to a wide range of host plants. Damage caused by this group are comparable to the other most common and destructive root-knot nematodes, including M. incognita, M. arenaria, M. javanica, and M. hapla. Therefore, this pest is subject to quarantine in many countries over the world and more attention needs to be paid to improve management. It is notable that many Meloidogyne species were identified based on a single approach (either morphological or molecular characterisation), leading to a number of incorrectly reported species and mislabelled sequences on GenBank. To avoid this, the use of molecular barcodes for identifying Meloidogyne species is recommended, but their utilisation should be validated by multiple approaches in any study. Our study provided detailed morphological characterisation of M. enterolobii that can be used to supplement the diagnosis of M. enterolobii. Importantly, reliable molecular barcodes, that are unequivocally linked to detailed morphological and morphometric data, were provided in our study, contributing to quarantine service tools that can be used to limit the dispersal of this damaging pest. In addition, molecular phylogenetic trees based on COI, COII/16S rRNA, Nad5 mtDNA, ITS, and D2-D3 of 28S rRNA regions were constructed for better understanding the relationship between root-knot nematodes. [ABSTRACT FROM AUTHOR]

Dendrobium officinale is widely used as a traditional medicine across East Asia. It has several medicinal and ornamental values. Therefore, D. officinale is frequently adulterated with other Dendrobium species in the market. Morphological similarities in Dendrobium species limit the easy identification of individual specimens. In this study, DNA barcoding was used as the sequence model system, and SNP-specific sites were explored for the identification of D. officinale. In this study, a total of 45 Dendrobium species including 25 D. officinale and 20 different Dendrobium species were explored. The identification abilities of 9 DNA barcodes were determined using 45 Dendrobium materials, and the findings showed that they had different identification capabilities. High-resolution melting curve analysis (HRM) technology was used to differentiate D. officinale species from non-D. officinale species, using DNA barcode ITS2 which had the strongest identification capability. Intraspecific sequence variability among 25 D. officinale samples was significantly diverse. DNA barcode sequences analysis identified single nucleotide polymorphism (SNP) sites in 4 DNA barcode sequences (ITS2, ycf1b, psbK-psbI, and psbA-trnH). SNP site-specific primers were designed using the amplification refractory mutation system (ARMS), and intraspecific identification of D. officinale was verified using real-time PCR. In addition, D. officinale samples No. 05 and 24 were identified. The findings of this study provide information on the accurate identification of D. officinale samples. Furthermore, it provides a novel insight into the identification of species with similar evolutionary histories and into determining the quality of medicinal materials. [ABSTRACT FROM AUTHOR]

Chiroptera stands out for the richness of species and a variety of unique characteristics. However, the morphological similarities in some taxa of this group can result in neglected diversity, as pointed out in several molecular studies. In this sense, the DNA barcode has been useful in the identification and delimitation of species. In the state of Paraná, in the southern region of Brazil, molecular studies in this group are rare and many species are not registered in the public genetic database. Thus, we identified at the molecular level Chiroptera species that occur in the northwestern region of Paraná and compared the data obtained with species deposited in the Barcode of Life Database (BOLD), in addition to carrying out OTUs delimitation tests. We conclude that Chiroptera has an underestimated diversity in Paraná, with some species awaiting description. Our results suggest the existence of poorly resolved taxa, and in general the group needs new studies with different approaches to solve its taxonomy. [ABSTRACT FROM AUTHOR]

Taxonomic studies based on molecular markers led to the description of a new species, Hypnea pseudomusciformis, to accommodate three morphologically divergent species that occur on the coast of Brazil and have identical DNA barcode sequences (H. musciformis, H. nigrescens, and Hypnea valentiae). These three previous species were then identified as morphological variants of H. pseudomusciformis. Later, phylogeographic studies revealed that H. pseudomusciformis is subdivided in three distinct haplotype groups with significant intraspecific divergence for the COI-5P marker. Moreover, each haplogroup presents physiological and morphological differences related to each of the three floristic provinces along the Brazilian coast: tropical, transition, and warm temperate. Therefore, these haplogroups were denominated as ecotypes. In this work, we tested the biological species concept (BSC) in two crossing experiments: (i) between specimens belonging to different haplogroups (obtained from tropical and warm temperate provinces) and (ii) between different morphological variants ("musciformis" and "nigrescens") belonging to the same haplogroup. As a result, we observed that all crosses performed were positive and the reach of fertility in all tetrasporophytic plants of the F1 and F2 generations. Therefore, we concluded that (i) specimens from tropical and warm temperate provinces and (ii) specimens identified as "musciformis" and "nigrescens" belong to the same biological entity, despite their intraspecific molecular divergences and physiological differences and their differences in morphology, respectively. When testing and confirming the biological concept of species, we also validate previous works or confirm that the species has great phenotypic and physiological plasticity, which allows its occurrence in different niches and in provinces with different abiotic characteristics. The BSC proved to be a valuable tool for responding to conflicts raised by the DNA barcode technique. [ABSTRACT FROM AUTHOR]

Fall armyworm (Spodoptera frugiperda) is a noctuid moth from the Americas with a broad host range that threatens a range of important crops. It consists of two morphologically indistinguishable strains ('corn' and 'rice') that have different host plant preferences. It was detected for the first time in Australia in 2020 following its rapid dispersal through Africa and Asia. Species identification of S. frugiperda in 48 specimens from seven locations in the Northern Territory was confirmed by DNA barcoding and morphological assessment. The majority of specimens possessed the mitochondrial haplotype associated with the 'rice-strain', whereas two specimens had a haplotype identified as the 'corn-strain'. The two mitochondrial haplotypes observed in our study are identical to the most common haplotypes previously observed in Africa. Analysis of a nuclear gene identified all specimens as 'corn-strain'. The agreement of both mitochondrial and nuclear markers as 'corn-strain' haplotypes occurred in two samples only, suggesting discrepancies between the mitochondrial and nuclear markers analysed. As fall armyworm spreads to other locations in Australia, further monitoring and genetic characterization of populations is recommended to investigate strain, genetic diversity and population structure. Monitoring of populations in association with host plant preferences will provide valuable information on host plant preferences and strain characterisation. [ABSTRACT FROM AUTHOR]

Garcinia L. is a pantropically distributed genus with high species richness in South East Asia. It is a tropical evergreen plant with distinct morphological characteristics and has a high degree of endemism. Outstanding features of the Garcinia L. genus are monopodial growth, leafy texture, oil cavities containing yellow or light-colored resins present on all parts of the plant and polygamodioecious reproductive behavior. The current study was conducted to develop barcodes for different species of the genus Garcinia L., distributed widely in the Western Ghats of India. We assess the discrimination power of the plant DNA barcode (rbcL, matK, trnH-psbA, rpoB-trnCGAR and ITS), across major Garcinia L. species. Our results clearly demonstrate the value of plastid barcode data, previously unavailable for Garcinia L. species. Ten Garcinia L. species and three outgroup taxa selected from the Western Ghats of India for evaluation using four regions in the plastid genome (rbcL matK, trnH-psbA, rpoB-trnCGAR) and nuclear-transcribed spacer (nrITS) in order to discriminate them at the species level. A characteristic feature of all barcodes, maximum likelihood analysis, and Wilcoxon signed-rank test were used for species discrimination. The number of conserved sites were more using matK primer whereas more variables and informative sites found in rpoB-trnCGAR loci. For internal branches of species-specific clusters, maximum likelihood analysis showed a more resolved topology. Wilcoxon signed-rank test indicated a higher divergence for coding and non-coding regions. DNA barcoding was found to be a practical and rapid method for identifying more endemic species. These findings will potentially be helpful in delineating the various species of Garcinia L. [ABSTRACT FROM AUTHOR]

Holy Basil—Ocimumtenuiflorum—is one of the popular new "superfoods" thought to act as an antioxidant and to reduce stress and anxiety. However, it is often surrogated with other Ocimum species differing in their chemical profiles that may even pose health risks to the consumers. Moreover, even specific chemotypes of Holy Basil itself can be toxicologically relevant, because they sometimes contain the carcinogen compound methyleugenol. Using DNA barcoding based on plastidic markers, O.tenuiflorum can be differentiated from other species of Ocimum. However, this approach is still suboptimal in handling larger sample numbers and in tracing chemotypes that accumulate methyleugenol. We have, therefore, designed a trait-related DNA barcode based on the enzyme eugenol O-methyltransferase (EOMT), responsible for the synthesis of methyleugenol. We show that a multiplex PCR combining trait-related and trait-independent markers can differentiate O.tenuiflorum from other Ocimum species and identify methyleugenol chemotypes of O.tenuiflorum, even in dried material sold as mixtures. [ABSTRACT FROM AUTHOR]

The process of molecular identification of species known as DNA barcoding consists on discriminating taxa based on cumulative differences of their DNA sequences and is widely used within animals, including birds. Finding the best genomic tools, such as primers, to reach most of the species within the studied groups and evaluating the coverage breadth and physicochemical properties of primers before testing in the laboratory, can save time and financial resources. Therefore, this work aimed to retrieve the available primers for the COI gene currently used on the molecular identification of birds and evaluate them for its coverage range, physicochemical properties, and performance on in silico PCR. Afterwards, we provide the best primer subsets to cover the highest number of avian sequences and the best individual primers for each bird order in terms of coverage breadth. Thirty-one bird orders had at least one COI sequence to serve as template, 152 primers available for assessing the COI gene were evaluated, and 118 could bind to at least one template sequence. No primer subset alone could cover all template sequences; however, when combining two subsets, the complete coverage of avian COI sequences analyzed was achieved. We were able to find optimal primer subsets for more specific taxonomic groups or for analysis involving the complete avian group, in order to guide researchers in the process of choosing the best primer set for each individual barcoding goal. [ABSTRACT FROM AUTHOR]

Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe. It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology overcomes the challenges associated with traditional methods along with prospects for future research. [ABSTRACT FROM AUTHOR]

Distinguishing among commercial varieties or accessions in a germplasm repository presents considerable challenges when dealing with common crops or large collections. In the genus Pisum L. the third intron of the gene STAYGREEN (SGR), responsible for the green/yellow cotyledon variation, contains a complex of repeat sequences that display considerable indel and single nucleotide (SNP) polymorphism. In a sample of 137 Pisum L. accessions obtained from various germplasm collections 76 alleles were identified, ranging from about 600 to 1500 nucleotides in length. In most cases alleles differed by insertion/deletion (indel) polymorphisms in addition to single base changes. The amplicon was particularly useful for distinguishing wild accessions (those with dehiscent pods and dormant seeds). Among the 51 P. sativum L. accessions examined with a definite wild phenotype there were 44 SGR alleles. When this allelic variation was combined with location data for the wild accessions, each allele could be assigned a unique geographical location. Similarly, of the 10 P. fulvum Sibth. & Sm. accessions analyzed, only a group of three had the same allele, two of which are known to be replicates. We were able to confirm the identities of several P. sativum accessions from different germplasm collections, as well as identifying two cases where supposedly synonymous accessions gave different intron sequences. In addition, a group of wild pea accessions from Greece, Sicily, and Portugal exhibited a unique repeat sequence not found in any other wild accession, suggesting that these accessions constitute a distinct lineage. The rate of nucleotide site variation in this fragment of the SGR locus was found to be about 2.22 × 10–8 substitutions per site per year. This value is similar to those found for many other sequences in herbaceous papilionoid tribes, although it is at the faster end of the distribution of herbaceous legume substitution rates. We propose that both a fast substitution rate as well as the formation and rearrangement of indels have contributed to the high level of variation we detected at SGR. This PCR product should prove valuable in the identification of Pisum accessions, for quality control operations in germplasm repositories, and for exploring the evolutionary relationships within the genus. [ABSTRACT FROM AUTHOR]

Batoid fishes are among the most endangered marine vertebrates, yet conservation efforts have been confounded by incomplete taxonomy. Evidence suggest that the critically endangered 'common skate' actually represents two species: the flapper skate (Dipturus intermedius) and the blue skate (Dipturus batis). However, knowledge of the geographic range of these two nominal species is limited. Here, DNA sequencing is used to distinguish these species, allowing their spatial distributions to be clarified. These records were also used as the basis for species distribution modelling, providing the first broad scale models for each species across the Northeast Atlantic. Samples were obtained from Iceland, the UK (specifically Shetland), the North Sea and the Azores. Results suggest that D. batis was commonly distributed in the Western Approaches and Celtic Sea, extending out to Rockall and Iceland. D. intermedius generally appears to be less abundant, but was most frequent around northern Scotland and Ireland, including the northern North Sea, and was also present in Portugal. Two individuals were also identified from seamounts in remote areas of the Atlantic around the Azores, the furthest south and west the species has been found. This supports reports that the flapper skate historically had a much wider distribution (which was also highlighted in the distribution model), emphasising the large scale over which fisheries may have led to extirpations. Furthermore, these Azorean samples shared a unique control region haplotype, highlighting the importance of seamounts in preserving genetic diversity. [ABSTRACT FROM AUTHOR]

Background: Jewel orchid is the common name of several orchid species which can be alike in morphological characteristics, but variable in medicinal properties. At present, two DNA barcode loci, namely, maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL), are intensively utilized for plant identification. However, the discrimination effectiveness of these loci is variable among plant species. This study was carried out to compare the identifying efficacy of these two loci on jewel orchid population collected throughout Vietnam. Results: The results revealed that 21 jewel orchid accessions studied were segregated into four different species with significant variations. The discrimination power of matK and rbcL markers in this jewel orchid study displayed different efficiency level. The rbcL gene has higher distinguishing potential than either matK gene alone or the combination of both genes. Conclusion: The findings of this project could provide valuable information that is necessary for classification, plant origin identification, breeding, and conservation program of jewel orchid in Vietnam. [ABSTRACT FROM AUTHOR]

The method of DNA barcoding has become a reliable tool that allows fast and accurate identification and verifies biodiversity in the hands of an experienced taxonomist. This method is very popular in various fields of human activity because of its ease of use and economic benefit. Examples of use are presented and the potential of the DNA barcoding method of living organisms in areas such as environmental monitoring (identification of invasive species, parasites and their carriers, pests), food and pharmaceutical industries (detection of counterfeit products, determination of product quality), and forensics are shown. [ABSTRACT FROM AUTHOR]

Key message: We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon.D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. [ABSTRACT FROM AUTHOR]

Rays (Batoidea) are among the most threatened groups of vertebrates. Slow growth and low fecundity make many species vulnerable to overfishing, but increased demand for gill rakers in traditional Chinese medicine and elasmobranch meat means exploitation continues. In response, protection has increased, with manta and devilrays (Mobulidae) and sawfishes (Pristidae) now listed on Convention on International Trade in Endangered Species (CITES). This protection requires an accurate assay for species identification, even when parts of the body have been removed or products have been processed. Therefore, we developed and tested a new COI minibarcode to identify ray species among processed samples. This assay was tested on 25 samples from across four batoid orders and showed consistent amplification. In 68% of cases, a correct top match was identified on GenBank and BOLD, but its accuracy should be much higher (particularly due to extensive taxonomic revisions in this group). Bioinformatic analysis of existing sequences also showed 81% of minibarcodes were matched back to a single species and 100% correctly back to all other taxonomic ranks. This increased to 91% when only including records published in the previous 2 years (that should help to account for recent taxonomic revisions). Analysis of skate 'wings' and cooked samples was highly successful, allowing the unambiguous identification of species. These results suggest this minibarcode will be highly useful in identifying ray species and could have a range of applications from the analysis of processed products to investigations of environmental DNA, making them an effective tool in the conservation of endangered batoids. [ABSTRACT FROM AUTHOR]

A mini-barcoding system was developed to help identify endangered unionid mussels in the Lake Biwa system in Japan. A single primer set was designed to amplify a ca. 140-bp barcode fragment based on the published mitochondrial 16S rRNA gene sequences (ca. 350 bp) of Japanese unionids. The new primers successfully amplified genomic DNA from the foot tissues of 81 specimens of 12 target taxa from the Lake Biwa region. Sequencing, BLAST-searches and phylogenetic analyses of the amplified fragments confirmed that the mini-barcode had the same identification ability as the original sequences for Lake Biwa taxa. The mini-barcoding system also obtained the short barcodes from excreted materials, indicating its usefulness in nondestructive identification of these mussels. [ABSTRACT FROM AUTHOR]

In August 2018, a tree-of-heaven (Ailanthus altissima) showing symptoms of powdery mildew was found in Pisa, Italy. Morphological characteristics of the anamorph and molecular sequence analysis of the internal transcribed spacer region of rDNA verified the fungus as Erysiphe platani. In a pathogenicity test, powdery mildew patches were present on leaf surfaces 2 weeks after inoculation with the isolate. This is the first report of E. platani causing powdery mildew on ailanthus in the Mediterranean basin. The fungus, whose historical host range was confined to the genus Platanus, has expanded its host range to Ailanthus in Italy. [ABSTRACT FROM AUTHOR]

Leafhoppers (Cicadellidae) occur in all biogeographical regions and feed on a wide range of host plants. Classic identification of leafhoppers is based only on the morphology of male genitalia, while DNA barcoding is an effective tool to identify different leafhopper species in any stage of their life cycle. Phylogenetic relationships among leafhoppers remain unexplored, but recent phylogenies have begun to interpret the evolutionary relationships of previously recognized tribes and subfamilies. Here we used mitochondrial Cytochrome Oxidase I sequences to barcode and determine the phylogenetic relationship among eight leafhopper genera collected from Egypt. Eight leafhopper samples from eight different genera were collected from various plants using a sweeping net and aspirator. Males of seven species were available while females only were available from the one genus (Austroagallia sp.). Novel leafhopper-specific mtDNA COI degenerate primers were designed. Our results showed that the mean of intraspecific COI sequence divergence in leafhoppers was 0.45%, with a range from 0.15% to 1.23%, and the divergences of most species were over 2%. For the first time, we were exploring the evolutionary relationships among surveyed genera (Austroagallia, Empoasca, Eupteryx, Exitianus, Macrosteles, Nephotettix, and Orosius) using a robust phylogenetic supertree. Our results demonstrate that DNA barcoding is likely to be a powerful tool for identifying and understanding leafhoppers' evolution. [ABSTRACT FROM AUTHOR]

Background: Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels. Results: Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap’ s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry. Conclusion: To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification. [ABSTRACT FROM AUTHOR]

Integrative approaches are particularly useful to resolve taxonomic uncertainties in species-rich groups that have undergone explosive radiation, such as Hypostomini (suckermouth armored catfishes). This tribe encompasses the genera Hypostomus and Pterygoplichthys, but the actual number of species in each genus and the intergeneric interrelationships are confusing or unknown for some ecoregions in the Neotropics. Here, we analyzed three endemic species Hypostomus chrysostiktos, H. jaguar and H. unae from Northeastern Mata Atlântica in northeastern Brazil based on meristic characters, geometric morphometrics, chromosomal data, DNA barcode and species delimitation algorithms. The current taxonomic status of these catfishes is challenged. While H. unae and H. jaguar revealed a close evolutionary relationship similar to those observed within Hypostomus from other basins, H. chrysostiktos was herein more closely related to Pterygoplichthys, being invariably recovered as a highly distinctive taxonomic unit than to Hypostomus. Therefore, we recommend the reallocation of H. chrysostiktos as Pterygoplichthys chrysostiktos and a thorough systematic review of Pterygoplichthys, particularly focusing on putative convergence traits in relation to Hypostomus. [ABSTRACT FROM AUTHOR]

The dried fruits of Terminalia plant (Combretaceae) called "Samo" have been used as herbal medicine in Thai traditional medicine. Four "Samo" crude drugs, namely, Samo thai, Samo thed, Samo dee-ngu, and Samo phiphek, are used as the main ingredients in Triphala and Trisamo recipes. Their commercial products are available in processed and powdered form, but are difficult to authenticate by conventional methods. In this study, we aimed to discriminate species of genus Terminalia for the identification of their crude drugs by a DNA barcoding technique. A total of 208 closely related nucleotide sequences were obtained from nine Terminalia species collected from Thailand and the DDBJ/EMBL/GenBank database. An effective DNA barcode marker was selected from six DNA loci (matK, rbcL, psbA-trnH, ITS, ITS1, and ITS2) and their two-locus combination. All sequences were analyzed by three major methods: (1) BLAST search; (2) the genetic divergence method using Kimura 2-parameter (K2P) distance matrices; and (3) tree topology analysis based on the neighbor-joining method. Comparison of the six candidate DNA loci indicated that ITS identified Terminalia with 100% accuracy at the species and genus levels in the BLAST1 method. ITS2 showed the highest K2P variability. The data from the single markers and the two-locus combinations revealed that only the two-locus combinations, namely, the combinations of rbcL, ITS, ITS1, and ITS2 with psbA-trnH, clearly discriminated all the species. From the results of DNA sequence analysis and the three methods, ITS2 is recommended for the identification of Terminalia species to supplement psbA-trnH. [ABSTRACT FROM AUTHOR]

Metacercariae of Clinostomum Leidy, 1856 are frequently encountered in freshwater fish. In 2015, a provisional species of Clinostomum in People's Republic of China (PRC) was distinguished from C. complanatum (Rudolphi, 1819) in Europe based on divergent cytochrome c oxidase I (CO1). However, in subsequent studies in East Asia, the same divergent CO1 genotype was identified as C. complanatum. These matching sequences suggest that either the provisional East Asian species was incorrectly distinguished from C. complanatum in 2015 or that C. complanatum in East Asia was misidentified in later studies. We tested these alternatives by sequencing the mitochondrial genome of C. complanatum in Italy, which was 5.7% divergent from a previously published sequence from Clinostomum in PRC, including differences in 80 of 3390 (2.4%) translated amino acids. Partial CO1 sequences of specimens from PRC and those from Italy, Romania, and Turkey also each formed reciprocally monophyletic clades. Partial CO1 from the East Asian clade varied by mean 3.6% (range 2.4–4.8%) from C. complanatum from Italy, Romania, and Turkey; mean intra-clade CO1 variation was 0.3% (range 0–1.9%). Metacercariae from Europe and East Asia display significant morphometric variation, and data from the literature suggest morphological differences in the genital complex of adults. Although sequences of nuclear rDNA did not differ between isolates from the west and East Asia, taken together, these results lead us to describe a new species of Clinostomum. [ABSTRACT FROM AUTHOR]