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High-throughput sequencing has become a prominent tool to assess plant-associated microbial diversity. Still, some technical challenges remain in characterising these communities, notably due to plant and fungal DNA co-amplification. Fungal-specific primers, Peptide Nucleic Acid (PNA) clamps, or adjusting PCR conditions are approaches to limit plant DNA contamination. However, a systematic comparison of these factors and their interactions, which could limit plant DNA contamination in the study of plant mycobiota, is still lacking. Here, three primers targeting the ITS2 region were evaluated alone or in combination with PNA clamps both on nettle (Urtica dioica) root DNA and a mock community. PNA clamps did not improve the richness or diversity of the fungal communities but increased the number of fungal reads. Among the tested factors, the most significant was the primer pair. Specifically, the 5.8S-Fun/ITS4-Fun pair exhibited a higher OTU richness but fewer fungal reads. Our study demonstrates that the choice of primers is critical for limiting plant and fungal DNA co-amplification. PNA clamps increase the number of fungal reads when ITS2 is targeted but do not result in higher fungal diversity recovery at high sequencing depth. At lower read depths, PNA clamps might enhance microbial diversity quantification for primer pairs lacking fungal specificity. [ABSTRACT FROM AUTHOR]

Thirty years ago, DNA sequences were obtained from an extinct Aotearoa New Zealand animal for the first time. Since then, ancient DNA research has provided many – often unexpected – insights into the origins of New Zealand's terrestrial and marine vertebrate fauna. Because recent human activities in New Zealand have caused the decline or extinction of many endemic plant, bird, reptile, and marine mammal species, ancient DNA has been instrumental in reconstructing their identities and origins. However, most ancient DNA studies focusing on New Zealand species have been restricted to vertebrates, with small sample sizes, and/or relatively few genetic markers. This has limited their power to infer fine-scale biogeographic patterns, including (pre)historic distributions and range-shifts driven by past climate and environmental change. Recently, 'next-generation' methodological and technological advances have broadened the range of hypotheses that can feasibly be tested with ancient DNA. These advances represent an exciting opportunity for further exploring New Zealand biogeography using ancient DNA, but their promise has not yet been fully realised. In this review, we summarise the last 30 years of ancient DNA research into New Zealand faunal biogeography and highlight key objectives, challenges, and possibilities for the next 30 years and beyond. [ABSTRACT FROM AUTHOR]

Native to South Africa and Madagascar, the invasive fireweed, Senecio madagascariensis Poiret (Asteraceae), is a target for biological control in Australia and Hawaii, where substantial infestations persist. Earlier studies in the weed's region of origin, namely KwaZulu-Natal Province in South Africa, assessed the seasonal abundance of stem-boring insect herbivores in S. madagascariensis populations. The weevil Gasteroclisus tricostalis (Thunberg) (Curculionidae) and moth Metamesia elegans (Walsingham) (Tortricidae) were prioritised as candidate agents for Australia due to their persistence across seasons. In this study, the host ranges of these two candidate agents were assessed by comparing the stem-boring curculionids and lepidopterans that are associated with S. madagascariensis with those associated with non-target Senecio species in the KwaZulu-Natal Midlands region. DNA barcoding of the adults and endophagous larvae recovered during field sampling of S. madagascariensis and 17 non-target Senecio species in 2017/18, as well as those from earlier field surveys, was used to differentiate the insect species and elucidate their host-plant affinities. Although weevil larvae were recovered from the stems of seven non-target Senecio species, G. tricostalis was associated only with Senecio inaequidens DC. and Senecio skirrhodon DC., both in the S. madagascariensis species complex. Lepidopteran larvae were associated with three non-target Senecio species, all in the S. madagascariensis species complex, with M. elegans associated only with Senecio harveianus MacOwan and S. inaequidens. These results suggest that G. tricostalis and M. elegans have restricted host ranges and that further host-specificity studies in quarantine are warranted to demonstrate their suitability for release. [ABSTRACT FROM AUTHOR]

Ottelia acuminata (O. acuminata) is an edible and medicinal submerged plant endemic to southwestern China, yet there is little information available concerning its nutritional or bio-active composition. This study aimed to evaluate in detail the nutritional profile and phenolic composition of O. acuminata (inflorescence, peduncle, and leaf) and investigate a protective activity in phenolic extracts on DNA damage induced by •OH and ROO• radicals. O. acuminata was excellent sources of protein (17.7–24 g/100 g DW), TPC (11.43–19.00 mg GAE/g DW), ascorbic acid, and minerals (especially potassium, calcium, and iron). Interestingly, the protein contained a high amount of EAA with a ratio (EAA11/TAA) in the range of 47.79–50.93%, BCAA and MSG-like AA. The inflorescences and leaves of O. acuminata contained abundant UFA with a ratio of UFA/TFA more than 50%. Five phenolic compounds, with a predominance of luteolin, luteolin-7-O-glucoside and chlorogenic acid, were identified by HPLC. Phenolic extracts of O. acuminata displayed a significant protective effect on DNA damage, which effect was comparable to that of the positive control (trolox). It was concluded that O. acuminata is an excellent vegetable with a high nutritional value and a great potential as a natural antioxidant. [ABSTRACT FROM AUTHOR]

Pyrrolizidine alkaloids (PAs) and their corresponding N-oxides (PANOs) are natural protoxins biosynthesised by many plant species and are responsible for occasional fatal intoxication outbreaks due to the consumption of contaminated food. However, only in rare cases has the origin of the contamination been determined. Although their presence has been studied in many matrices, occurrence data on popular widely used cooking herbs, seeds, spices and leafy vegetables is very scarce. Therefore, a systematic study on the occurrence of PA/PANOs contaminations in these popular herbal items, available on the Belgian market, was performed, by means of a validatedtargeted LC-MS/MS analysis, followed by multilocus DNA metabarcoding to track back the origin of the contamination for seven highly to moderately contaminated samples. Our results clearly indicate that 21% of the seed spices and 25% seed-based aromatic mixes contain an amount higher than 400 μg of the 30 summed targeted PAs and PANOs per kg, the value which is currently under discussion by the European member states to be set as a maximum threshold. For both the herbs and the herb-based mixes only 7% of analysed samples exceeded these levels. As a proof of concept, multilocus DNA metabarcoding was performed on six highly contaminated samples, belonging to each subtype matrix, containing high levels of heliotrine type of PA/PANOs. Each time the analysis demonstrated the presence of DNA from a plant species belonging to the plant genus Heliotropium. Moreover, a contaminated leafy vegetable sample, containing solely senecionine type PA/PANOs, contained DNA from Senecio vulgaris. Taken together, it can be stated that the proposed combinatory chemical and molecular techniques could be used to verify if a PA/PANO(s) contamination occurred in these popular cooking items and to pinpoint the origin the contamination, which is pivotal in the case of a detrimental intoxication or intoxication outbreak. [ABSTRACT FROM AUTHOR]

G-quadruplexes (G4s) are non-canonical structures that can be formed in DNA and RNA sequences which carry four short runs of guanines. They are distributed in the whole genome but are enriched in gene promoter regions, gene UTRs and chromosome telomeres. The whole array of their functional roles is not fully explored yet but there is solid evidence supporting their implication in a number of processes like regulation of transcription, replication and telomere organization, among others. During the last decade, there is an increased research interest for G4s that has resulted in a better understanding of their role in several physiological and pathological conditions. On the other hand, these structures are poorly studied in plant species and animals of agricultural interest. Here, we summarize the current methods that are used for studying G4s, we review the studies concerning plants and farm animals and we discuss the advantages of a more thorough inclusion of G4s research in the agricultural sciences. [ABSTRACT FROM AUTHOR]

Complexes are currently synthesized from plant origin because of their therapeutic effect against certain diseases with toxicity. Hence, in this work, four new transition metal(II) mixed ligand complexes have been synthesized using a curcumin Schiff base (primary ligand) and lawsone (as co-ligand). The geometry of these complexes was explored by elemental analyses, molar conductance, thermal analysis, magnetic moment values, IR, NMR, Mass, electronic and EPR spectral studies. Electronic absorption titrations, viscosity measurements and molecular docking studies reveal that all the metal complexes interact with the CT DNA by groove binding. Among all the complexes, the copper(II) complex (complex 1) exhibits a higher Kb value (3.5 × 10−4 M) which reveals that it has a strong binding efficiency toward the CT DNA. The complexes also possess strong DNA cleavage efficiency. Cytotoxicity investigations on Artemia salina show that all the complexes possess higher cytotoxic effect than the ligand. Moreover, all the metal complexes have better antimicrobial efficacy than the ligand. Swiss ADME, PASS and pkCSM online softwares are helpful to predict the pharmacokinetic and biological actions of the curcumin Schiff base. Theoretical results obtained from the in silico study are experimentally corroborated by in vivo anti-inflammatory screening study. All the above studies demonstrate that the copper complex possesses biological activity similar to that of the drug like molecules. Synthesis and characterization of four novel transition mixed ligand complexes using plant moieties Promising in vivo anti-inflammatory agents and in vitro DNA metallonucleases Cytotoxicity investigation on Artemia salina Higher cytotoxic effect for the complexes than the ligand Identification of copper(II) complex as lead like molecule among all [ABSTRACT FROM AUTHOR]

Antigenotoxic properties of plant- and plant-like derived foods may embody nutritional strategies against DNA damage. Marine macroalgae have shown DNA-protective effects, but their nutraceutical potential and the influence of growing conditions on these properties is underexplored. Hence, we aimed to assess the genoprotection potential of wild-harvested vs. aquacultured Ulva rigida on Drosophila melanogaster, following a dietary exposure, in the presence and absence of a genotoxic agent (streptonigrin) using phytochemical profiling. DNA damage was evaluated with a single cell gel electrophoresis (comet) assay improved with endonucleases. An origin-based phytochemical profile was found, with aquacultured algae showing higher relative amounts of fatty alcohols, sterols, sesquiterpenoids and glycerol esters. Although U. rigida from both sources showed a DNA-protective action, especially against streptonigrin-induced genotoxicity, aquacultured algae demonstrated higher potential, which may be linked to the distinctive phytochemical profile. Overall, this study provided scientific evidence for the genoprotective activity of U. rigida and its confirmation as a functional food. [ABSTRACT FROM AUTHOR]

Leukemia is a malignant hematological disease and chemotherapy remains the most important tool for its treatment. As chemotherapy has many side effects and could lead to resistance in cancer cells, plant-based medication is being considered as a new strategy in cancer treatment. Datura innoxia from the Solanaceae family is used in traditional medicine. The present study investigated the effect of an aqueous extract of D. innoxia aqueous leaf-extract on human chronic myeloid leukemia cells (K562 cell line) and human B lymphoblastoid cells (FS-2 cells) as the noncancerous cell line. The interaction of the D. innoxia extract with double-stranded DNA and histones was studied using multiple spectroscopic techniques. The total phenolic and flavonoid contents were determined through colorimetric analysis and the major polyphenols were quantified by HPLC-DAD analysis. The results demonstrated that the D. innoxia extract inhibited proliferation of the K562 cell line in a dose- and time-dependent manner (IC50 = 0.6 mg/ml), but had a slightly toxic effect on human B lymphoblastoid cells. The spectroscopy results suggest that the D. innoxia extract interacted with both DNA and histones in solution and that D. innoxia could be suggested as an anticancer drug. [ABSTRACT FROM AUTHOR]

Due to their beneficial health effects, strawberry tree (Arbutus unedo L.) leaves have for decades been used as herbal remedy in countries of the Mediterranean region. This pilot study is the first to investigate the liver function and DNA integrity in rat hepatocytes evaluated after 14 and 28 day treatments with strawberry tree water leaf extract and arbutin, administered per os to Lewis rats of both genders at a daily dose 200 mg/kg b.w. We focused on two types of biomarkers: enzyme serum markers of liver function (AST, ALT, and LDH), and primary DNA damage in the liver cells, which was estimated using the alkaline comet assay. At the tested dose, strawberry tree water leaf extract showed acceptable biocompatibility with liver tissue both in male and female rats, especially after shorter exposure. Our results also suggest that oral administration of single arbutin to rats was not associated with significant impairments either in the liver function or DNA integrity in hepatocytes. Considering that prolonged exposure to the tested compounds revealed minor changes in the studied biomarkers, future in vivo studies have to further clarify the biological and physiological relevance of these findings. [ABSTRACT FROM AUTHOR]

High-quality DNA is a prerequisite for a range of molecular biology experiments and thus DNA extraction is one of the most important steps for several downstream experiments. DNA isolation directly from seeds could save time and effort, particularly for large-scale experiments where growing and maintaining multitude of genotypes in parallel is cumbersome. However, seeds often contain polysaccharides, polyphenols, mucilage, oils, etc., which cause DNA extraction from seeds difficult and sometimes a research limiting step. In the present study, we have considered many previous protocols and optimized these methods to devise a general method for extraction of DNA from the seeds of diverse plant genera. The new SGS buffer (sucrose, glycerol and sodium dodecyl sulphate) was used to extract intact DNA from seeds with yield and quality better than in the previous protocols. Moreover, the proposed protocol is devoid of hazardous and expensive reagents and can be scaled up. [ABSTRACT FROM AUTHOR]

There are relatively few studies of DNA content in the Vernonieae (Asteraceae) tribe. The first studies were realized in theLessingianthusgenus and determined the DNA content of 25 species. After DNA content, ploidy level and the total karyotype were compared in 6Chrysolaenaspecies. The aim of this study was to present, for the first time, the DNA content values ofVernonanthuraandVernoniaand to thereby expand knowledge of the Vernonieae tribe. A total of 19 natural populations belonging to the generaVernonanthuraandVernoniawere studied for the first time. The results were compared with other Vernonieae genera and with other Asteraceae tribes. Our results found that Vernonieae have the smallest range of 1C value variation in Asteraceae. Furthermore, there were differences in the DNA content ofVernoniaandVernonanthura. These results show that low DNA content and herbaceous habit inVernoniaare characters derived from the higher DNA content and woody habit present inVernonanthura. These results could indicate a hybrid origin of one species and allow the determination of both the ploidy and chromosome number of other taxa. The results observed inVernonanthuraspecies showed a highly significant correlation between 1C-value and latitude. [ABSTRACT FROM AUTHOR]

The nucleolus forms as a consequence of ribosome biogenesis, but it is also implicated in other cell functions. The identification of nucleolus-associated chromatin domains (NADs) in animal and plant cells revealed the presence of DNA sequences other than rRNA genes in and around the nucleolus. NADs display repressive chromatin signatures and harbour repetitive DNA, but also tRNA genes and RNA polymerase II-transcribed genes. Furthermore, the identification of NADs revealed a specific function of the nucleolus and the protein Nucleolin 1 (NUC1) in telomere biology. Here, we discuss the significance of these data with regard to nucleolar structure and to the role of the nucleolus and NUC1 in global genome organization and stability. [ABSTRACT FROM AUTHOR]

To further investigate the phylogenetic relationship between Rubus coreanus and its relatives in the section Idaeobatus, we used genomic in situ hybridization (GISH) to ascertain the degree of their genomic homology. Genomic DNA from R. parvifolius and R. inopertus hybridized throughout the centromeric and sub-terminal regions on 14 and 12 chromosomes of R. coreanus, respectively. The probes from R. niveus and R. ellipticus var. obcordatus gave robust signals at the same region of eight chromosomes. R. ellipticus and R. pinfaensis generated strong signals at the centromeric and sub-terminal parts of six chromosomes. The hybridization signals from the R. tsangii and R. corchorifolius probes existed only at the telomeric parts of four chromosomes. The two signals at the sub-terminal region on chromosome 6 of R. coreanus might be 45S rDNA repeats. These results indicated that R. coreanus and R. parvifolius shared many repeat sequences. It could be deduced that the genome of R. parvifolius was most closely related to that of R. coreanus among the species tested, R. inopertus came next, while R. tsangii and R. corchorifolius showed the farthest relationship. The phylogenetic relationships between R. parvifolius and R. coreanus, as well as among the five subsections were mainly discussed. [ABSTRACT FROM AUTHOR]

The development of a duplex real-time polymerase chain reaction (PCR) method allowing the simultaneous detection of sesame and flaxseed DNA in commercial food products is described. This duplex real-time PCR technique is based in the design of sesame- and flaxseed-specific primers based on the ITS1 region and two TaqMan fluorescent probes. The method was positive for sesame and flaxseed, and showed no cross-reactivity for all other heterologous plant and animal species tested. Sesame and flaxseed could be detected in a series of model samples with defined raw and heat-treated sesame in flaxseed, and flaxseed in sesame, respectively, with detection limits of 1.3 mg kg−1 for sesame and 1.4 mg kg−1 for flaxseed. The applicability of the assay for determining sesame and flaxseed in different food matrices was investigated by analysing a total of 238 commercial foodstuffs. This PCR method is useful for highly selective and sensitive detection of traces of sesame and flaxseed in commercial food products. [ABSTRACT FROM AUTHOR]

Jurinea pinnata(Lag.) DC. is one of the three species of the genus that grows in the Iberian Peninsula. This species grows on gypsum and dolomite, substrates rich in endemic taxa. Actually, the genusJurineaCass. is particularly rich in endemic taxa associated with special substrates. The island-like distribution ofJ. pinnatamakes it an interesting case for the study of genetic differentiation processes. The geographical proximity ofJ. pinnataandJ. humilismakes this evolutionary puzzle even more difficult to solve. These facts could affect the genetic attributes of the species as far as diversity and differentiation are concerned. Our field research involved the sampling of individuals from eight populations ofJ. pinnata.Of them, six were located in the Guadix-Baza Basin. We used sequences of ribosomal and plastid DNA to perform the genetic analyses. Results revealed no differences between individuals occurring on the two kinds of substrates and evidences of hybridization betweenJ. pinnataandJ. humilis. Furthermore, the phylogenetic analysis revealed a possible polyphyletic origin for the adaptation to special substrates within theJurineagenus, while monophyly was observed in species from the Iberian Peninsula. This could indicate a more general adaptation to arid or saline environments. [ABSTRACT FROM AUTHOR]

Three monophyletic branches are strongly supported in a phylogenetic analysis of the Teloschistaceae based on combined data sets of internal transcribed spacer and large subunit nrDNA and 12S small subunit mtDNA sequences. These are described as new monotypic genera: Jasonhuria S. Y. Kondr., L. Lőkös et S. -O. Oh, Loekoesia S. Y. Kondr., S. -O. Oh et J. -S. Hur and Olegblumia S. Y. Kondr., L. Lőkös et J. -S. Hur. Three new combinations for the type species of these genera are proposed. [ABSTRACT FROM AUTHOR]

Background:Hybridisation between locally common and rare plant species is of conservation concern as it may lead to the extinction of the rare taxon.Rumex aquaticus(2n= ca. 200, Polygonaceae) is a widespread Euro-Siberian species but rare in the British Isles. It hybridises freely with the locally abundant congenerR. obtusifolius(2n= 40) producing fertile and viable hybrids. Aims:We aimed to establish whether hybridisation poses an extinction threat toR. aquaticusin Britain. Methods:Flow cytometry, AFLPs and morphological characters were used to assess the extent of hybridisation betweenR. obtusifoliusandR. aquaticus. Results:Flow cytometry was the most useful tool to distinguish between hybrids and parental species and indicated that out of 88 samples from two hybrid populations, 85% were likely to be F1s and only 15% were likely to be back-crosses toR. aquaticus. AFLP markers were only able to identify putative F1 hybrids reliably and 11 morphological traits could not distinguish unambiguously between hybrids and pureR. aquaticus. Conclusions:Although our data suggest that genetic assimilation of pureR. aquaticuspopulations is unlikely to be the case in the future, there is a potential threat from demographic swamping by hybrids and targeted protection ofR. aquaticushabitat is proposed as a management strategy. [ABSTRACT FROM PUBLISHER]

Ethidium bromide (EtBr) is used to stain DNA in agarose gel electrophoresis, but this dye is mutagenic and carcinogenic. We investigated N-719, which is a visible, reliable and organic Ruthenium-based dye, and five fluorescent alternatives for staining plant DNA. For prestaining and poststaining, N-719, GelRed, and SYBR Safe stained both DNA and PCR product bands as clearly as EtBr. SYBR Green I, methylene blue, and crystal violet were effective for poststaining only. The organic dye N-719 stained DNA bands as sensitively and as clearly as EtBr. Consequently, organic dyes can be used as alternatives to EtBr in plant biotechnology studies. [ABSTRACT FROM AUTHOR]

Lichen studies, including biodiversity, phylogenetic relationships, and conservation concerns require definitive species identification, however many lichens can be challenging to identify at the species level. Molecular techniques have shown efficacy in discriminating among lichen taxa, however, obtaining genomic DNA from herbarium and fresh lichen thalli by conventional methods has been difficult, because lichens contain high proteins, polysaccharides, and other complex compounds in their cell walls. Here we report a rapid, easy, and inexpensive protocol for extracting PCR-quality DNA from various lichen species. This method involves the following two steps: first, cell breakage using a beadbeater; and second, extraction, isolation, and precipitation of genomic DNA. The procedure requires approximately 10 mg of lichen thalli and can be completed within 20 min. The obtained DNAs were of sufficient quality and quantity to amplify the internal transcribed spacer region from the fungal and algal lichen components, as well as to sequence the amplified products. In addition, 26 different lichen taxa were tested, resulting in successful PCR products. The results of this study validated the experimental protocols, and clearly demonstrated the efficacy and value of our KCl extraction method applied in the fungal and algal samples. [ABSTRACT FROM AUTHOR]

Traded forms of spice and spice powders are often subjected to admixing with inferior substances by design or default, affecting public health and national prestige.Cinnamomum verum(true cinnamon), a high-value spice, is often adulterated with its inferior species such asC. cassiaandC. malabatrum. The presence and detection of the spurious species in traded barks (whole or powder) of true cinnamon is posing problems. DNA markers are now used to detect such adulteration. Here we report the application of a DNA barcoding method to detect these adulterants in traded market samples of true cinnamon using the barcoding locirbcL, matKandpsbA-trnH.The PCR success rate, sequencing efficiency, inter and intra specific divergence, and occurrence of single nucleotide polymorphisms (SNPs) were utilized to assess the potential of each barcode loci to authenticateC. verumfrom its related adulterants. The amplification and sequencing success was 100% forrbcLandpsbA-trnHwhilematKfailed to amplify in the market samples. The locus ofrbcLshowed higher interspecific divergence whilepsbA-trnHexhibited lower interspecific divergence. SNPs specific toC. cassiawere detected inrbcLlocus in seven out of the ten market samples studied thereby confirming the presence ofC. cassiaadulteration in commercial samples of true cinnamon. Out of the three loci,rbcLlocus proved to be efficient in tracing out adulterants in traded cinnamon. The SNP sites in this locus can be exploited in designingC. cassiaspecific primers, enabling kit development for easy detection of adulterants at the band level itself thereby bypassing the cost of sequencing. [ABSTRACT FROM AUTHOR]

PCR-based methods are widely used in the European Union and in other countries for the detection, identification, and quantification of genetically modified organisms (GMOs). The preparation of good-quality DNA from plant samples for GMO detection can be a challenging task, particularly if the DNA will be used for quantitative analysis. Two DNA extraction methods, namely manual (NucleoSpin Food kit from Machery-Nagel) and high-throughput partially automated (NucleoMag Plant kit from Machery-Nagel) methods, which utilize different DNA separation principles, were used for the isolation of DNA from maize flour samples. Despite the higher DNA recovery obtained using the high-throughput isolation method, a lower PCR efficiency was achieved, most likely due to the presence of PCR inhibitors in the extracts. We found both DNA extraction methods suitable for GMO analysis. [ABSTRACT FROM AUTHOR]

Fourteen new species in the Latin American Clade (LAC) of the Ceratocystisfimbriata complex recently were distinguished from C. fimbriata sensu stricto largely based on variation in ITS rDNA sequences. Among the 116 isolates representing the LAC, there were 41 ITS haplotypes. Maximum parsimony (MP) analysis of ITS sequences produced poorly resolved trees. In contrast, analyses of mating-type genes (MAT1-1-2 and MAT1-2-1) resolved a single MP tree with branches of high bootstrap and posterior probability support. Four isolates showed intragenomic variation in ITS sequences. Cloning and sequencing of PCR products from a single haploid strain identified two or more ITS sequences differing at up to 16 base positions and representing two described species. Isolates from introduced populations that appeared to be clonal based on microsatellite markers varied at up to 14 bp in ITS sequence. Strains of seven Brazilian ITS haplotypes and an isolate from Ipomoea batatas (on which the species name C. fimbriata was based) were fully interfertile in sexual crosses. These analyses support three phylogenetic species that differ in pathogenicity: C. platani, C. cacaofunesta and C. colombiana. Five ITS species (C. manginecans, C. mangicola, C. mangivora, C. acaciivora, C. eucalypticola) appear to be ITS haplotypes that have been moved from or within Brazil on nursery stock. The taxonomic status of other species delineated primarily by ITS sequences (C. diversiconidia, C. papillata, C. neglecta, C. ecuadoriana, C. fimbriatomima, C. curvata) needs further study, but they are considered doubtful species. [ABSTRACT FROM AUTHOR]

The Cauliflower Mosaic Virus 35S promoter sequence, CaMV P-35S, is one of several commonly used genetic targets to detect genetically modified maize and is found in most GMOs. In this research we report the finding of an alternative P-35S sequence and its incidence in GM maize marketed in Jordan. The primer pair normally used to amplify a 123 bp DNA fragment of the CaMV P-35S promoter in GMOs also amplified a previously undetected alternative sequence of CaMV P-35S in GM maize samples which we term V3. The amplified V3 sequence comprises 386 base pairs and was not found in the standard wild-type maize, MON810 and MON 863 GM maize. The identified GM maize samples carrying the V3 sequence were found free of CaMV when compared with CaMV infected brown mustard sample. The data of sequence alignment analysis of the V3 genetic element showed 90% similarity with the matching P-35S sequence of the cauliflower mosaic virus isolate CabbB-JI and 99% similarity with matching P-35S sequences found in several binary plant vectors, of which the binary vector locus JQ693018 is one example. The current study showed an increase of 44% in the incidence of the identified 386 bp sequence in GM maize sold in Jordan's markets during the period 2009 and 2012. [ABSTRACT FROM AUTHOR]

Trunk rot poses a substantial threat to Sanbu-sugi, one of the most economically important cultivars of Japanese cedar (Cryptomeria japonica). The etiology of this disease, inchtding its main agents, is incompletely known. This trunk rot was attributed to Fomitiporia (Phellinus) hartigii or F. (Phellinus) punctata. Here we phylogenetically analyzed DNA sequences of four markers from a set of strains isolated from trunk-rot symptoms and recovered a single, monophyletic clade, indicating that a single taxon is involved. This clade was identified as Fomitiporia torreyae, a species described from eastern China. This analysis also proved that trunk rot and/or dieback of other conifers and broadleaf trees, including Sawara cypress (Chamaecyparis pisifera), Japanese umbrella pine (Sciadopitys verticillata) and Japanese pear (Pyrus pyrifolia var. culta), were caused by the same species. The phylogenetic approach to Fomitiporia revealed that the F. torreyae clade was closely related to F. bannaensis but clearly distinct from F. punctata, which originally was thought to be the cause of trunk rot in Sanbu-sugi. Fomitiporia torreyae is redescribed on the basis of more than 40 specimens from multiple hosts from Japan and China. Fomitiporia juniperina comb. nov. is proposed. [ABSTRACT FROM AUTHOR]

A rapid identification assay for Waitea circinala (anamorph: Rhizoctonia spp.) varieties zeae and circinata causing patch diseases on turfgrasses was developed based on the universally primed PCR (UP-PCR) products cross-blot hybridization. Tester isolates belonging to the two varieties of W. circinata were amplified with a single UP primer L21, which generated multiple DNA fragments for each variety. Probes were prepared with UP-PCR products of each tester isolate by labeling with digoxigenin. Field-collected W. circinata isolates and representative isolates of different R. solani anastomosis group (AG) and AG subgroups were amplified with L21, immobilized on nylon membrane and cross hybridized with the two probes. Isolates within a W. circinata variety cross-hybridized strongly, while non-homologous isolates did not cross-hybridize or did so weakly. Closely related W. circinata varieties zeae and circinata were clearly distinguished with this assay. Sequence-characterized amplified region (SCAR) markers also were developed from UP-PCR products to identify isolates of Thanatephorus cucumeris (anamorph: R. solani) AG 1-IB and AG 2-2IIIB. These two AGs are commonly isolated from diseased, cool-season turf-grasses. The specific SCAR markers that were developed could differentiate isolates of AG 1-IB or AG 2- 2IIIB groups. These SCAR markers did not amplify a product from genomic DNA of nontarget isolates of Rhizoclonia. The specificities and sensitivities of the SCAR primers were tested on total DNA extracted from several field-grown, cool-season turf species having severe brown-patch symptoms. First, the leaf samples from diseased turf species were tested for the anastomosis groups of the causal pathogen, and thereafter the total DNA was amplified with the specific primers. The specific primers were sensitive and unique enough to produce a band from total DNA of diseased turfgrasses infected with either AG 1-IB or AG 2-2IIIB. [ABSTRACT FROM AUTHOR]

This study was designed to examine essential oil based changes at the genetic and physiological level on Zea Mays seeds. To this end EO obtained from Origanum vulgare by hydrodistilation were analyzed by gas chromatography/mass spectrometry. The most abundant contents were observed as caryophyllene oxide (34.44%), β-caryophyllene (20.40%) and α-cadinol (7.02%). Total of the volatiles were applied to Zea mays' seeds at four different (0.1, 0.2, 0.4, 0.8 μl/mL) concentrations. Comparing with the control germination, some DNA alterations were observed in random amplified polymorphic DNA profiles of germinated EO treated seeds. The alterations affected the genomic template stability. On the other hand, data observed from protein profiles by using SDS-Page showed some differentiation between band profiles of EO treated samples and control group. The results suggest that EO not only affect the DNA, but also its products (proteins). As a conclusion, the possible biological activities of EO of Origanum vulgare L. ssp vulgare are related to their genotoxic activity. [ABSTRACT FROM AUTHOR]

The Asteraceae family has been broadly studied, but the values of genome size of only 3.5% of their species are known. To expand these data, we carried out a flow cytometric study of nuclear DNA content in a wide range of taxa of this family, filling gaps in some less studied groups. In addition, some chromosome counts have been performed (46 taxa, including the first one in two species and one subspecies). We provide genome size data for 167 taxa (184 accessions). Of these, data are new for 128 species and subspecies (141 accessions), 40 genera, three tribes (Barnadesieae, Gochnatieae and Nassauvieae) and two subfamilies (Barnadesioideae and Gochnatioideae). Most values (about 75%) are small or very small (1C ≤ 3.5 pg). The second reports on 17 species previously studied with other methods (i.e. first flow cytometric assessments) are also given. Finally, we contribute results for 22 species for which a first flow cytometric assessment has been published during the preparation of this article. The current data-set moves the percentage of coverage approximately from 3% to 4.7% at the specific level, from 6% to 11.6% at the generic level, from 34.9% to 41.9% at the tribal level and from 33% to 50% at the subfamily level. [ABSTRACT FROM AUTHOR]

The geographic position of Lebanon in the Mediterranean basin at the transition of two major landmasses, Eurasia and Africa, has contributed to its high plant diversity and makes its flora particularly interesting to study. This paper contributes to the plant DNA C-value database of native Lebanese taxa. These data should reinforce biodiversity evaluation, systematic and evolution studies involving processes of speciation such as polyploidisation. C-values have been estimated by flow cytometry using propidium iodide as intercalary fluorochrome stain. Each sample comprised at least five individuals. Where possible, several populations were measured for each species. This study presents C-values for 225 taxa belonging to 55 families and 141 genera. C-values are novel for 193 taxa including 126 plants endemic to the Eastern Mediterranean region. These are the first values for 50 genera. In this panel, genome size ranged from 1C = 0.28 pg inHypericum thymifoliumto 54.69 pg inFritillaria alfredae.The life growth form and life cycle type are analysed according to the genome size class. Cases of polyploidy are reported for some species usually considered as only diploid. Examination of C-value variation through flow cytometry constitutes a powerful tool to screen taxonomic heterogeneity, opening further investigations. [ABSTRACT FROM AUTHOR]

Cytogenetic characterization by karyotyping and determination of DNA content by flow cytometry of five species ofChrysolaena(Vernonieae, Asteraceae) was performed. This is the first study of nuclear DNA content realized in the genus. The 2C-values were compared with the ploidy level and the total karyotype length (TKL) of each species. Mitotic analysis revealed a base chromosome numberx = 10 for all entities and different ploidy levels, from diploid (2n = 2x = 20) to octoploid (2n = 8x = 80). All species showed bimodal karyotypes composed of metacentric and submetacentric chromosomes. The average chromosome size (ML) varied from 1.86 μm to 2.70 μm, while the TKL ranged from 18.65 μm to 80.55 μm. The intrachromosomal asymmetry index (A1) varied from 0.27 to 0.38, while the interchromosomal asymmetry index (A2) ranged from 0.19 to 0.25. A new cytotype is reported for the first time forC. propinqua. Accessory chromosomes found inC. verbascifolia,C. cognata,C. flexuosa, andC. propinquaare also reported as new. [ABSTRACT FROM AUTHOR]

Laccaria (Hydnangiaceae, Agaricales, Basidiomycota) is one of the more intensively studied ectomycorrhizal genera; however, species boundaries within Laccaria and the closely related Hydnangium and Podohydnangium in Australia have not yet been examined with molecular sequence data. Based on morphological characters, eight native species of Laccaria are currently recognized in Australia, as well as three Hydnangium species and the monotypic Podohydnangium australe. Sequences of the internal transcribed spacer region of nuclear rDNA (ITS), RNA polymerase beta subunit II (rpb2) and translation elongation factor 1 alpha (teƒ1α.) were generated from 77 collections of Laccaria, Hydnangium and Podohydnangium from Australia. Ten phylogenetic species and a further 11 potential species (represented by singletons) of Laccaria in Australia are delimited from sequence analyses. Most of the morphological species contained cryptic phylogenetic species, but these species were always nested entirely within a given morphological species, although not always as sister taxa. The rpb2 locus performed best as a species barcode with pairwise and patristic distance measures. The ITS sequence region returned the least resolved gene tree of the three regions examined and was the least useful as a barcode region. Based on the phylogenetic topology, there appears to have been multiple gains and/or losses of the ectomycorrhizal association of some species with the myrtle beech, Nothofagus cunninghamii as well as of sequestrate basidiocarps and two-spored basidia. [ABSTRACT FROM AUTHOR]

Identification of living beings is a core problem in biology. Identification can be achieved by several methods, but in recent decades, molecular techniques have become more and more common. DNA barcoding is an initiative that was launched less than 10 years ago, but which has already gained a reputation in biological studies. The method was originally applied to metazoans, but it was rapidly used to discriminate plants. However, in plants there were several problems, including the choice of the right markers, their universality and the discrimination power. On the whole, DNA barcoding in plants is slightly behind when compared to animals, but it is likely that the gap will be filled in a short period of time. In a DNA barcoding approach, molecular and bioinformatics are deeply linked to generate the identification system. In this paper, we summarize the recent advances in DNA barcoding bioinformatics, by reviewing the principal approaches and critically analyzing the procedures. [ABSTRACT FROM AUTHOR]

In this study, symptoms closely resembling those caused byPseudomonas syringaepv.actinidiaewere found in kiwifruit plants (Actinidia chinensiscv. Hort16A) growing in Jeju province, Korea. Bacterial strains including strain KKH3Twere isolated from representative lesions on kiwifruit plants. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed these bacteria in a separate cluster within the genusPectobacterium. Strain KKH3Tshowed the highest similarity (98.7%) to the recognised bacteriaPectobacterium carotovorumsubsp.carotovorumandPectobacterium wasabiae. To justify subspecies level differentiation, the partial nucleotide sequences ofatpD,carAandrecAfrom strain KKH3Twere compared with those from other members of the familyEnterobacteriaceae. Distant relationships between strain KKH3Tand six reference strains ofPectobacteriumspp. were evident in the phylogenetic tree. The results of the DNA–DNA hybridisation and polyphasic analysis revealed that strain KKH3Tbelongs to another subspecies ofP.carotovorum, for which the namePectobacterium carotovorumsubsp.actinidiaesubsp. nov. is hereby proposed. [ABSTRACT FROM AUTHOR]

Developments in genetic engineering technology have led to an increase in number of food products that contain genetically engineered crops in the global market. However, due to lack of scientific studies, the presence of genetically modified organisms (GMOs) in the Kuwaiti food market is currently ambiguous. Foods both for human and animal consumption are being imported from countries that are known to produce GM food. Therefore, an attempt has been made to screen foods sold in the Kuwaiti market to detect GMOs in the food. For this purpose, samples collected from various markets in Kuwait have been screened by SYBR green-based real time polymerase chain reaction (RT-PCR) method. Further confirmation and GMO quantification was performed by TaqMan-based RT-PCR. Results indicated that a significant number of food commodities sold in Kuwait were tested positive for the presence of GMO. Interestingly, certain processed foods were tested positive for more than one transgenic events showing complex nature of GMOs in food samples. Results of this study clearly indicate the need for well-defined legislations and regulations on the marketing of approved GM food and its labeling to protect consumer's rights. [ABSTRACT FROM AUTHOR]

Prophage-encoded genes can provide a variety of benefits for their bacterial hosts. These beneficial genes are often contained within "moron" elements. Morons, thus termed as the insertion of the DNA encoding them adds "more on" the genome in which they are found, are independent transcriptional units disseminated among phage genomes through horizontal gene transfer. Morons have been identified in the majority of phage genomes and they have been found to play diverse roles in bacterial physiology. At present, we are only beginning to ascribe functions to the many proteins encoded within these ubiquitous genetic elements. Recently, we discovered that the first described moron-encoded protein, gp15 of phage HK97, is expressed from the HK97 prophage and functions as a superinfection exclusion protein, protecting its host from genome injection by other phages. This work and the growing body of data pertaining to other morons challenges the traditional view of phages as purely parasites of bacteria and emphasizes the symbiotic relationship between bacteria and prophages. [ABSTRACT FROM AUTHOR]

The DNA packaging motors of double-stranded DNA phages are models for analysis of all multi-molecular motors and for analysis of several fundamental aspects of biology, including early evolution, relationship of in vivo to in vitro biochemistry and targets for anti-virals. Work on phage DNA packaging motors both has produced and is producing dualities in the interpretation of data obtained by use of both traditional techniques and the more recently developed procedures of single-molecule analysis. The dualities include (1) reductive vs. accretive evolution, (2) rotation vs. stasis of sub-assemblies of the motor, (3) thermal ratcheting vs. power stroking in generating force, (4) complete motor vs. spark plug role for the packaging ATPase, (5) use of previously isolated vs. new intermediates for analysis of the intermediate states of the motor and (6) a motor with one cycle vs. a motor with two cycles. We provide background for these dualities, some of which are under-emphasized in the literature. We suggest directions for future research. [ABSTRACT FROM AUTHOR]

Comparative morphological investigations and molecular analyses of rbcL data are used to critically reassess the genus Symphyocladia and to examine phylogenetic relationships with the type species, 5. marchantioides. Specimens collected from the type locality in New Zealand confirm that S. marchantioides can be identified by the presence of numerous apical cells on the growing margin producing axial systems that remain congenitally laterally attached, branched trichoblasts arising marginally and close to dormant apical cells, six to eight pericentral cells, and lacking cortication. Symphyocladia jejuinsula sp. nov is newly described for samples from the southern coast of Korea, and is characterized by thin and flat thalli to 10 cm in height, 8-10 pericentral cells, lack of trichoblasts, 10 segments of congenital fusions, cortication in the lower part of branches, and determinate branches each with a sharply pointed apical cell. Molecular analysis of the rbcL gene reveals sufficient sequence divergence to warrant species recognition of six distinct species within Symphyocladia, and the presence of two clusters of species that form sister clades in the phylogenetic tree. The monophyly of Symphyocladia is strongly supported and the genus is clearly separated from Pterosiphonia. These two genera belong in the tribe Pterosiphonieae, having an alternate-distichous branching pattern as their diagnostic character. [ABSTRACT FROM AUTHOR]

Detailed comparative karyotype analyses have proved to be an important tool for taxonomy and for understanding chromosome evolution. The basic principle of cytotaxonomy is that closely related species share a more similar karyotype than less related ones. However, phylogenetic studies have demonstrated that some karyotype features are more often recurrent than previously thought, meaning that similarity is not all. Two other criticisms to the cytotaxonomical interpretation are intraspecific variation, traditionally neglected, and the interpretation of chromosomal alterations based only on classical structural changes, without any investigative support. Chromosome numbers and nuclear DNA content are among the most reliable and practical characters for cytotaxonomical analyses involving a large number of species, whereas chromosome mapping with molecular probes is more recommended for a restricted number of species. In both cases, a robust phylogenetic tree is necessary to understand the relationships between species and their karyotype evolution. Evolutionary inferences based only on putative karyological trends are no longer sustainable. [ABSTRACT FROM AUTHOR]

B chromosomes (Bs) can be described as “selfish chromosomes”, a term that has been used for the repetitive DNA which comprises the bulk of the genome in large genome species, except that Bs have a life of their own as independent chromosomes. They can accumulate in number by various processes of mitotic or meiotic drive, especially in the gametophyte phase of the life cycle of flowering plants. This parasitic property of drive ensures their survival and spread in natural populations, even against a gradient of harmful effects on the host plant phenotype. B chromosomes are inhabitants of the nucleus and they are subject to control by “genes” in the A chromosome (As) complement. This interaction with the As, together with the balance between drive and harmful effects makes a dynamic system in the life of a Bs. In this review, we concentrate mainly on recent developments in the Bs of rye and maize, two of the species currently receiving most attention. We focus on their population dynamics and on the molecular basis of their structural organisation and mechanisms of drive, as well as on their mode of origin and potential applications in plant biotechnology. [ABSTRACT FROM AUTHOR]

Two new species of Hypocrea are added here to the European funga. Hypocrea britdaniae, a fungus with unknown anamorph and large, conspicuous stromata resembling basidiomata of a corticiaceous fungus, is a sister species to the Longibrachiatum clade, while H. foliicola, a leaf-dwelling species that forms pulvinate stromata, is recognized as an additional member of the pachybasium core group. Hypocrea foliicola sporulates in culture in a reduced verticillium-like manner, while it produces a white, typical pachybasium-like anamorph in nature. Ecologically H. foliicola is remarkable in inhabiting leaves a substrate rarely recorded for Hypocrea. M1 relevant morphological teleomorphic and anamorphic traits are given. The phylogenetic placement of the new species within Hypocrea/Trichoderma was determined with combined analyses of rpb2 and tef1 exon sequences. [ABSTRACT FROM AUTHOR]

In North America, one of the most important root diseases of Poa and Festuca turf is summer patch, caused by Magnaporthe poae. Detection and identification of M. poae in infected roots by conventional culture-based methods is difficult and time consuming, typically taking 3 wk or longer to accomplish. In this study, a culture-independent, TaqMan real-time PCR assay was developed for the detection of M. poae from the roots of fungicide-treated and non-treated Kentucky bluegrass (Poa pratensis) turf. The assay was validated with the target pathogen, closely related fungal species and a number of other microorganisms that inhabit the same host and soil environment. This assay was more sensitive (could detect as little as 3.88 pg genomic DNA of M. poae), rapid and accurate compared to direct microscopic observation and isolation on a selective medium. The real-time PCR detection results corresponded closely to visual assessments of disease severity in the field. Utilization of this assay in diagnostic laboratories will enable turfgrass managers to more quickly and effectively detect and potentially reduce fungicide usage through early and accurate identification of the pathogen. [ABSTRACT FROM AUTHOR]

A rust specimen with macroscopic similarities to the cereal stem rusts was collected on Elymus sp. from Gansu province, China. Phylogenetic analyses of ITS and COI DNA sequences indicated the fungus was closely related but distinct as a strongly supported sister taxon to the Puccinia graminis species complex. Microscopic examination revealed diagnostic teliospore characteristics, differentiating it from P. graminis and other morphologically similar rusts. Herein, we designate a name for this new lineage, Puccinia chunjii sp. nov. [ABSTRACT FROM AUTHOR]

The three subgenera of alder (Alnusroman Clethropsis and Alnobetula) are taxonomically distinctive, but how does their pollen match up with their gross morphology? This study links pollen characters with the taxonomic divisions of the genus alder based on nrDNA ITS sequence data. The value of the study is in the breadth of the taxonomic coverage of the three subgenera, as the samples per species only range from 1 to 6. From 29 Alnus species, the authors studied pollen from 59 modern reference collections (prepared by acetolysis) and recorded the number and type of apertures (pores), thickness of the arci, pollen size and polar arci. Tallies of the number of pores on the pollen grains in a reference collection typically have a range of ± 1 or 2. Exceptions are presumed hybrid collections in Alnus rugosa with a range of ± 5, which have malformed pollen cells suggesting infertility. The presumed hybrids show a greater range of both pore number and size of pollen grains. The dominant pore number is a key feature that separates the subgenus Alnobetula (= Alnaster) from the other two subgenera by consistently having predominantly 5-, 6- or 7-pored pollen grains, while all other Alnus taxa sampled have pollen with predominantly 4- or 5-pored pollen. The dominant pore number is a consistent feature within the subgenus Alnobetula (10 species), but is inconsistent in 3 out of 16 species of the subgenus Alnus and within the subgenus Clethropsis (3 species). Thickenings of the pore lip, aspidate (protruding) and vestibulate pores are important features of Alnus pollen on a species level. Alnus-like pollen morphology occurs occasionally in certain other betulaceous genera (Betula and Carpinus). Differences in character or thickness of arci (band-like thickenings on the pollen wall between pores) tend to be somewhat consistent within a species and vary within subgenera. Two Alnobetula species in the Alnus viridis complex (Alnus crispa and Alnus sinuata) have arci that are weakly developed or appear as simple folds; walls are fragile and pores are typically less aspidate. Pollen sizes in different species overlap greatly, may be partly influenced by processing methods and do not seem to be generally helpful in characterizing species. Circular doughnut-shaped arci thickenings on the polar area of pollen grains are a common feature (16–40%) in two closely related East Asian taxa of subgenus Alnobetula with large pollen (‘Clade A’: Alnus firma and Alnus sieboldii). These ‘Clade A’ features have been reported from Miocene collections of Alnus pollen from Alaska, and support megafossil evidence in determining the biogeography of this group along the Pacific Rim in the Neogene. The Miocene appearance of subgenus Alnobetula megafossils in both Alaska and Japan can only have occurred via a Bering Land Bridge. This relation is now confirmed by Reinink-Smith's Miocene ‘Clade-A-type’ pollen data of Alaska. These taxa had Pacific Rim distributions, similar fruiting carposamaras and now correspond to a DNA ITS subgroup within Alnobetula. Depending on the geographic location with limited number of local alder species, certain Holocene identifications are possible based on pore structure and arci thickness, e.g. the Alnus crispa-type in eastern Canada and the Alnus sinuata-type in the Pacific northwest. [ABSTRACT FROM AUTHOR]

Nine isolates of Alternaria causing black rot of ‘Fortune’ mandarin were obtained from a commercial orchard in the Murcia region of south-east Spain. The isolates, according to their morphological and physiological characteristics, were identified as A. alternata. Analysis of DNA sequences of the internal transcribed spacers 1 (ITS1) and 2 (ITS2) of the ribosomal DNA corroborated the morphological identification. In this work, we evaluated the pathogenicity of each of the nine isolates on fruits and leaves as well as fruit susceptibility to the pathogen at different growth stages. Studies were performed on both wounded and unwounded fruits and leaves. Disease development was faster in wounded than in unwounded organs, one and two days after inoculation, respectively. Differences in pathogenicity were observed among the A. alternata isolates, depending on the plant organ. Immature fruits were more susceptible; fruit infection tolerance increased with maturity, for both wounded and unwounded fruits. These findings could contribute to more-successful phytosanitary management of the disease. [ABSTRACT FROM AUTHOR]

As museums are increasingly solicited for destructive sampling for DNA research, the potential effect that past and present conservation treatments may have on research results needs to be understood. To date, research on DNA damage has focused on mechanisms experienced by living cells or within an archaeological burial context. Relatively little research has been undertaken on the possible effects of preparation and conservation treatments, as well as the storage conditions, on DNA in artefacts and specimens within a museum environment. Conservation treatments may cause DNA damage, potentially in a variety of forms, and may also confound DNA research by contributing contaminating or inhibiting substances. The focus of this article is to provide a conservation-based perspective on understanding DNA as a material, its deterioration and analysis, as well as the potential effects of treatments on DNA research in general. The possible effects of some treatments that have been used on basketry are discussed in a brief case study. [ABSTRACT FROM AUTHOR]

The author comments on his career in botany. The author states that, he did Bachelor of Science (B.Sc.) and Master of Science (M.Sc.) (botany) programs in 1957 and 1959 respectively from the University of Lucknow in Lucknow, Uttar Pradesh, India. The author states that, during his student days there were several important topics which were being taught including, DNA double helix and Calvin cycle in photosynthesis.