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The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust. In the present study, two loci for adult plant resistance (APR), QYrSM155.1 and QYrSM155.2, were identified in the Chinese wheat breeding line Shaanmai 155. QYrSM155.1 was mapped to a 3.0-cM interval between the single-nucleotide polymorphism (SNP) markers AX-109583610 and AX-110907562 on chromosome arm 2BL. QYrSM155.2 was mapped to a 2.1-cM interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7AS. A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines. Thirteen and 11 SNPs were significantly associated with QYrSM155.1 and QYrSM155.2, respectively, corresponding to physical intervals of 653.75–655.52 Mb on 2BL and 81.63–83.93 Mb on 7AS. To characterize the haplotype variation and the distribution of these QTL, haplotype analysis was performed based on these SNPs in an independent panel of 1,101 worldwide wheat accessions. Three major haplotypes (2B_h1, 2B_h2, and 2B_h3) for QYrSM155.1 and four major haplotypes (7A_h1, 7A_h2, 7A_h3, and 7A_h4) for QYrSM155.2 were identified. Accessions individually harboring QYrSM155.1_h1 and QYrSM155.2_h1 haplotypes and their combination displayed resistance. Additional assays of 1,306 current Chinese cultivars and breeding lines using markers flanking QYrSM155.1 and QYrSM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45% and 14.16% of lines. Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.

An unidentified diatom species belonging in the genus Nitzschia isolated from samples in the Omani coastal region of the Arabian Sea is the focus of the present study. This species has been successfully cultivated in the laboratory and DNA was harvested and sequenced. Light microscopy (LM) and scanning electron microscopy (SEM) examination of the strain revealed some distinct features, of which the ultrastructure of canal raphe and the absence of central nodule are the most remarkable ones. In terms of morphology, the strain being studied resembles taxa belonging in Nitzschia sect. Lanceolatae. However, our phylogenetic tree based on a three-gene dataset, comprising concatenated nuclear-encoded small-subunit ribosomal DNAs (SSU) and chloroplast encoded (rbcL and psbC) shows that our strain is sister to N. filiformis, which belongs in Nitzschia sect. Obtusae. This species that we have named Nitzschia omanensis, is thus far only known from the harsh coastal waters of Oman, which are characterized by very high daily temperatures and extremely low precipitation.

To protect above-ground plant organs from excessive water loss, their surfaces are coated by waxes. The genes involved in wax formation have been investigated in detail in Arabidopsis but scarcely in crop species. Here, we aimed to isolate and characterize a CER1 enzyme responsible for formation of the very long-chain alkanes present in high concentrations especially during late stages of wheat development. On the basis of comparative wax and transcriptome analyses of various wheat organs, we selected TaCER1-1A as a primary candidate and demonstrated that it was located to the endoplasmic reticulum, the subcellular compartment for wax biosynthesis. A wheat nullisomic-tetrasomic substitution line lacking TaCER1-1A had significantly reduced amounts of C33 alkane, whereas rice plants overexpressing TaCER1-1A showed substantial increases of C25 -C33 alkanes relative to wild type control. Similarly, heterologous expression of TaCER1-1A in Arabidopsis wild type and the cer1 mutant resulted in increased levels of unbranched alkanes, iso-branched alkanes and alkenes. Finally, the expression of TaCER1-1A was found activated by abiotic stresses and abscisic acid treatment, resulting in increased production of alkanes in wheat. Taken together, our results demonstrate that TaCER1-1A plays an important role in wheat wax alkane biosynthesis and involved in responding to drought and other environmental stresses.

Background and aims – The diatom genus Simonsenia has been considered for some time a minor taxon, limited in its distribution to fresh and slightly brackish waters. Recently, knowledge of its diversity and geographic distribution has been enhanced with new species described from brackish-marine waters of the southern Iberian Peninsula and from inland freshwaters of South China, and here we report novel Simonsenia from fully marine waters. Methods – New isolates of Simonsenia species were obtained from marine waters, the littoral zone of the Korean Yellow Sea coast and the Gulf of Mexico in Corpus Christi (Texas), and documented in LM, SEM and with DNA sequence data (plastid-encoded rbcL and psbC). Phylogenetic trees of raphid diatoms were constructed to assess the relationships of the new species and of the genus as a whole. Key results and conclusions – Two novel species of Simonsenia (S. eileencoxiae and S. paucistriata) are described and a further putative taxon is characterized morphologically. The molecular phylogeny of the new Simonsenia species and previously sequenced species supports both the monophyly of the genus and its place within the Bacillariaceae. The Simonsenia clade clusters with clades composed of Cylindrotheca, Denticula and some Nitzschia spp. (including N. amphibia, N. frustulum, N. inconspicua). Hence Simonsenia is firmly positioned within the Bacillariaceae by molecular phylogenies, confirming its position within this group based on the possession of a canal raphe and its ultrastructure, and rejecting its classification within the Surirellaceae. Morphological data from the new Simonsenia species is typical for the genus, with a “simonsenioid” canal raphe type supported over the valve face with fenestral braces, alar canals connecting the canal raphe with the cell lumen, and the presence of fenestrae between the alar canals externally. Our results indicate unequivocally that the biogeography and the biodiversity of Simonsenia remain highly underestimated. info:eu-repo/semantics/publishedVersion

Ethnopharmacological relevance Essential oils (EOs) are important active ingredients in Chinese herbal medicine. Cymbopogon citratus (DC.) Stapf, Cinnamomum cassia (L.) Presl, Salvia japonica Thunb., and Rosa rugosa Thunb. are used in local and traditional medicine to treat inflammation-related diseases. While the constituents and bioactivities of EOs of the above four Chinese herbals have been reported previously, but their anti-inflammatory and antioxidant activities have not been systematically evaluated. Aim of the study The purpose of this study was to research the chemical constituents, anti-inflammatory activities, and antioxidant activities of EOs of four Chinese herbal medicines. Materials and methods Fresh plant materials were collected both in August 2018. The compositions of EOs were determined by the gas chromatography-mass spectrometry (GC-MS) method. TPA (12-O-tetradecylphophenol-13-acetate)-induced mouse ear model was evaluated the anti-inflammatory activities of EOs. The reduction of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), cyclooxygenase-2 (COX-2) and RelA protein of the nuclear factor kappa-B (NF-κB) in the signal pathway (P65) were measured. The antioxidant activities of EOs from four plants were determined by using 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging method. Results A total of 217 compounds were separated and identified from four EOs, mainly including trans-cinnamylaldehyde (68.75%), citronellal (38.16%), linalool (1.02–33.73%), geraniol (19.39%) and citronellol (17.18%). All four EOs reduced the damage of the ear tissue and had certain anti-inflammatory effects, and the EOs of C. citratus (CyCEOs) and S. japonica (SJEOs) had the best anti-inflammatory activities among others, even better than ibuprofen. The four EOs exhibited different DPPH radical-scavenging activities (IC50, 0.101–1.017%), where most of them were much lower than that of EOs of C. citratus (CiCEOs) (IC50, 0.101%) and EOs of R. rugosa (RREOs) (IC50, 0.142%). Conclusions The main components determine diverse propertise of these four EOs, our results suggested that four EOs presented anti-inflammatory and antioxidant effect via reducing the expression of TNF-a, IL-6, COX-2, and NF-κB p65, which may provide a new approach for development of new anti-inflammatory drugs.

Suberin is a complex hydrophobic polymer of aliphatic and phenolic compounds which controls the movement of gases, water, and solutes and protects plants from environmental stresses and pathogenic infection. The synthesis and regulatory pathways of suberin remain unknown in Brachypodium distachyon. Here we describe the identification of a B. distachyon gene, BdFAR4, encoding a fatty acyl-coenzyme A reductase (FAR) by a reverse genetic approach, and investigate the molecular relevance of BdFAR4 in the root suberin synthesis of B. distachyon. BdFAR4 is specifically expressed throughout root development. Heterologous expression of BdFAR4 in yeast (Saccharomyces cerevisiae) afforded the production of C20:0 and C22:0 fatty alcohols. The loss-of-function knockout of BdFAR4 by CRISPR/Cas9-mediated gene editing significantly reduced the content of C20:0 and C22:0 fatty alcohols associated with root suberin. In contrast, overexpression of BdFAR4 in B. distachyon and tomato (Solanum lycopersicum) resulted in the accumulation of root suberin-associated C20:0 and C22:0 fatty alcohols, suggesting that BdFAR4 preferentially accepts C20:0 and C22:0 fatty acyl-CoAs as substrates. The BdFAR4 protein was localized to the endoplasmic reticulum in Arabidopsis thaliana protoplasts and Nicotiana benthamiana leaf epidermal cells. BdFAR4 transcript levels can be increased by abiotic stresses and abscisic acid treatment. Furthermore, yeast one-hybrid, dual-luciferase activity, and electrophoretic mobility shift assays indicated that the R2R3-MYB transcription factor BdMYB41 directly binds to the promoter of BdFAR4. Taken together, these results imply that BdFAR4 is essential for the production of root suberin-associated fatty alcohols, especially under stress conditions, and that its activity is transcriptionally regulated by the BdMYB41 transcription factor.

Stomata are valves on the leaf surface controlling carbon dioxide (CO2) influx for photosynthesis and water loss by transpiration. Thus, plants have to evolve elaborate mechanisms controlling stomatal aperture to allow efficient photosynthesis while avoid excessive water loss. Light is not only the energy source for photosynthesis but also an important signal regulating stomatal movement during dark-to-light transition. Our knowledge concerning blue and red light signaling and light-induced metabolite changes that contribute to stomatal opening are accumulating. This review summarizes recent advances on the signaling components that lie between the perception of blue/red light and activation of the PM H+-ATPases, and on the negative regulation of stomatal opening by red light-activated phyB signaling and ultraviolet (UV-B and UV-A) irradiation. Besides, light-regulated guard cell (GC)-specific metabolic levels, mesophyll-derived sucrose, and CO2 concentration within GCs also play dual roles in stomatal opening. Thus, light-induced stomatal opening is tightly accompanied by brake mechanisms, allowing plants to coordinate carbon gain and water loss. Knowledge on the mechanisms regulating the trade-off between stomatal opening and closure may have potential applications toward generating superior crops with improved water use efficiency (CO2 gain vs. water loss).

International audience; Madagascar is an isolated oceanic island characterized by high degrees of endemism at all taxonomic levels. The waters surrounding Madagascar are still poorly studied for benthic marine diatom assemblages. The aim of our study was to analyse the taxonomic biodiversity and molecular phylogeny of the diatom assemblages of the Nosy Be archipelago in terms of their ubiquity/rarity. A total of 65 samples from 14 sampling sites were collected from the Nosy Be and Nosy Tanikely islands in June/July 2014. Diatom identification, based on light and electron microscopic examination, revealed 332 diatom taxa. From those, ∼90 strains were isolated and successfully cultured. So far, DNA has been extracted and one chloroplast gene (rbcL) sequenced from 21 strains in order to reconstruct their single gene phylogeny. Taxa selected for sequencing and the preliminary phylogeny are from genera considered common benthic and planktonic forms in the marine littoral: Bellerochea, Melosira, Paralia, Triceratium, Navicula, Hippodonta, Auricula, Nitzschia, Cocconeis, and some araphids. For each site, Shannon and Simpson biodiversity indices were calculated. Diatom assemblages of Nosy Be were characterized by high biodiversity. The most abundant species was Cocconeis scutellum. Whereas some of the cultured taxa seem to represent cosmopolitan or zonal forms: e.g., Bellerochea malleus, Triceratium dubium, Melosira lineata, Paralia crawfordii, or Nitzschia inconspicua, most of the taxa isolated in culture and sequenced have not been observed in earlier works based on use of molecular markers. The dominant taxa were generally those with broad geographic distribution with global/Indo-Pacific affinities. Amongst all 332 taxa, only 35% have been identified to the species level. Many of the taxa identified to the generic level may turn out to represent taxa new to science after further SEM examination and DNA sequencing.

Two genes controlling the purple pericarp trait in wheat, TaPpm1 and TaPpb1, are identified and the mechanism by which they co-regulate anthocyanin synthesis is proposed., Purple pericarps of bread wheat (Triticum aestivum L.) are a useful source of dietary anthocyanins. Previous mapping results indicated that the purple pericarp trait is controlled by two complementary genes located on chromosomes 7D and 2A. However, the identity of the genes and the mechanisms by which they regulate the trait are unknown. In this study, two transcription factors were characterised as anthocyanin activators in purple pericarps: TaPpm1 (purple pericarp-MYB 1) and TaPpb1 (purple pericarp-bHLH 1). Three non-functional variants were detected in the coding sequence of TaPpm1 from non-purple seed lines, in which the function of TaPpm1 was destroyed either by insertion-induced frame shifts or truncated peptides. There were six 261-bp tandem repeats in the promoter region of TaPpb1 in the purple-grained varieties, while there was only one repeat unit present in the non-purple varieties. Furthermore, using yeast two-hybrid, dual luciferase, yeast one-hybrid, and transient assays, we were able to demonstrate that the interaction of TaPpm1 and TaPpb1 co-regulates the synthesis of anthocyanin. Overall, our results provide a better understanding of the molecular basis of anthocyanin synthesis in the wheat pericarp and indicate the existence of an integrated regulatory mechanism that controls production.

Wheat (Triticum aestivum L.) dough strength and extensibility are mainly determined by the polymerization of glutenin. The number of high-molecular-weight glutenin subunits (HMW-GS) differs in various wheat varieties due to the silencing of some genes. The effects of Ax1 or Dx2 subunit absence on glutenin polymerization, dough mixing properties and gluten micro structure were investigated with two groups of near-isogenic lines. The results showed that Ax1 or Dx2 absence decreased the accumulation rate of glutenin polymers and thus delayed the rapid increase period for glutenin polymerization by at least ten days, which led to lower percentage of polymeric protein in mature grain. Ax1 or Dx2 absence significantly decreased the dough development time and dough stability, but increased the uniformity of micro structure. Lacunarity, derived from quantitative analysis of gluten network, is suggested as a new indicator for wheat quality.

We report the chloroplast genome sequence of Nanofrustulum shiloi, a tiny araphid pennate diatom collected from the Adriatic Sea. The 160,994-bp N. shiloi genome displays a quadripartite structure and its gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located in the inverted repeat, psbY is duplicated. A gene-poor region in the large single-copy region contains multiple ORFs sharing sequence similarities with plasmids and chloroplast ORFs found in other diatom species. The genome features a single intron, a group II intron in petB. Phylogenomic analysis identified N. shiloi at a basal position within the araphid 2 clade.

Leaf rust, caused by Puccinia triticina, is an important fungal disease of wheat (Triticum aestivum L.) and causes significant yield losses worldwide. To determine quantitative trait loci (QTLs) responsible for leaf rust resistance, a recombinant inbred line (RIL) population developed from a cross of Ning7840 × Clark was evaluated for leaf rust severity, and was genotyped for single nucleotide polymorphisms (SNPs) using 9K Illumina chips, and with simple sequence repeat (SSR) markers. Two major QTLs on chromosome arms 7DS and 3BS, and two minor QTLs on chromosomes 5AS and 6AS showed a significant effect on leaf rust severity. The 7DS QTL from Ning7840 and the 3BS QTL from Clark explained, respectively, about 35% and 18% of the phenotypic variation for leaf rust resistance. The QTL on 7DS was confirmed to be Lr34. The QTL on 3BS, QLr.hwwg-3B.1, was associated with adult plant resistance and was provisionally identified as Lr74. QLr.hwwg-5AS and QLr.hwwg-6AS from Ning7840 and Clark, respectively, may correspond to previously described QTLs. Lr34, QLr.hwwg-3BS.1, and QLr.hwwg-6AS had an additive effect on leaf rust severity. RILs with all three favorable alleles showed the highest resistance to leaf rust and the RILs with none of them showed the lowest resistance.

The focus of this paper is the sexual reproduction and phylogeny of Schizostauron Grunow, which were studied using clonal cultures isolated from the Indian Ocean coast of Mozambique near Tofo and Bazaruto. Taxa of Schizostauron were characterized by light and electron microscopy and a phylogeny derived from three genes (rbcL, psbC and short subunit). Schizostauron was established in the second half of the 19th century, then forgotten, with its taxa included in Cocconeis or Achnanthes sensu lato. Schizostauron, together with Astartiella and perhaps also Kolbesia and Karayevia, seems to form a third lineage of monoraphid diatoms, which are related to biraphid diatoms belonging to the Stauroneidaceae and Parlibellus, but not to the two other lineages of monoraphids (Achnanthes and the Achnanthidiaceae–Cocconeidaceae group). In culture, size reduction was followed by release of gametes and auxosporulation in mixtures of clones. Despite some morphological differences, four clones from the Bazaruto po...

Cuticular wax accumulation and composition affects drought resistance in plants. Brachypodium distachyon plants subjected to water deficit and polyethylene glycol treatments resulted in a significant increase in total wax load, in which very-long-chain (VLC) alkanes were more sensitive to these treatments than other wax compounds, implying that VLC alkanes biosynthesis plays a more important role in drought resistance in B. distachyon. ECERIFERUM1 (CER1) has been reported to encode a core enzyme involved in VLC alkanes biosynthesis in Arabidopsis (Arabidopsis thaliana), but few corresponding genes are investigated in B. distachyon. Here, we identified eight CER1 homologous genes in B. distachyon, namely BdCER1-1 to BdCER1-8, and then analyzed their sequences feature, expression patterns, stress induction, and biochemical activities. These genes had similar protein structure to other reported CER1 and CER1-like genes, but displayed closer phylogenetic relationship to the rice OsGL1 genes. They were further found to exhibit various tissue expression patterns after being induced by abiotic stresses. Among them, BdCER1-8 gene showed extremely high expression in leaves. Heterologous introduction of BdCER1-8 into the Arabidopsis cer1 mutant rescued VLC alkanes biosynthesis. These results indicate that BdCER1 genes are likely to be involved in VLC alkanes biosynthesis of B. distachyon. Taken together, BdCER1-8 seems to play an explicit and predominant role in VLC alkanes biosynthesis in leaf. Our work provides important clues for further characterizing function of CER1 homologous genes in B. distachyon and also an option to improve drought resistance of cereal crops.

Although previous phylogenetic analyses suggested that the araphid diatom family Plagiogrammaceae is monophyletic, there is still not a clear understanding of relationships among the genera, and the taxonomy of several genera--Dimeregramma and Plagiogramma--remains questionable in light of paraphyly for both genera using molecular and morphological data. We have expanded the available DNA for molecular work for dozens of plagiogrammacean clones and analyzed 29 morphological characters from plagiogrammarian taxa and closely related genera, to increase understanding of the evolutionary history and systematics of the family and re-evaluate the current taxonomical classification of plagiogrammacean genera. The addition of more taxa and more data confirm the results from previous molecular phylogenies: most plagiogrammacean genera are monophyletic, except for Dimeregramma and Plagiogramma. Interestingly, the morphological analysis resolves only Talaroneis and Glyphodesmis as monophyletic. Given these results, we feel there is limited support for retaining Dimeregramma and Plagiogramma as distinct genera, and formally propose amending Plagiogramma and transferring six Dimeregramma species. As the Plagiogrammaceae is also one of the first-diverging clades of pennate diatoms, we also used these molecular data to estimate the age of the family, based on multiple calibration points derived from fossil taxa within or close to the Plagiogrammaceae. The results indicated that the Plagiogrammaceae evolved more than 114 million year ago and its diversification appears to correspond to a time of climate cooling. Additionally, we described a new monotypic genus (Coccinelloidea) with one new species C. gracilis, and five new species within established genera, e.g. Plagiogramma marginalis, Plagiogramma harenae, Plagiogramma porcipellis, Neofragilaria montgomeryii and Psammogramma anacarae.

Detailed morphological documentation is provided for established Proschkinia taxa, including the generitype, P. bulnheimii, and P. complanata, P. complanatula, P. complanatoides and P. hyalosirella, and six new species. All established taxa are characterized from original material from historical collections. The new species described in this paper (P. luticola, P. staurospeciosa, P. impar, P. modesta, P. fistulispectabilis, and P. rosowskii) were isolated from the Western Pacific (Yellow Sea coast of Korea) and the Atlantic (Scottish and Texas coasts). Thorough documentation of the frustule, valve and protoplast architecture revealed the combination of characters diagnostic of the genus Proschkinia: a single‐lobed chloroplast; a broad girdle composed of U‐shaped, perforated bands; the position of the conopeate raphe‐sternum relative to the external and internal valve surface; and the presence of an occluded process through the valve, termed the “fistula”. Seven strains of Proschkinia were grown in culture and five of these were sequenced for nuclear ribosomal SSU and plastid‐encoded rbcL. Phylogenetic analysis recovered a clade of Proschkinia with Fistulifera, another fistula‐bearing diatom genus, and together these were sister to a clade formed of the Stauroneidaceae; in turn, all of these were sister to a clade composed of Parlibellus and two monoraphid genera Astartiella and Schizostauron. Despite morphological similarities between Proschkinia and the Naviculaceae, these two taxa are distant in our analysis. We document the variation in the morphology of Proschkinia, including significant variability in the fistula, suggesting that fistula ultrastructure might be one of the key features for species identification within the genus. info:eu-repo/semantics/acceptedVersion

The Bacillariaceae is a very species-rich family of raphid diatoms and includes the large and taxonomically difficult genus Nitzschia, whose species are often small-celled and finely structured and have few discrete morphological characters visible in the light microscope. The classification of Nitzschia is still mostly based on one developed in the second half of the 19th century by Grunow, who separated the genus into a series of sections largely on cell shape and symmetry, the position of the raphe, transverse extension of the fibulae, and folding of the valve. We assembled and analysed single-gene and concatenated alignments of nSSU, nLSU, rbcL, psbC and cox1 to test Grunow’s and subsequent classifications and to examine selected morphological characters for their potential to help define monophyletic groups. The maximum likelihood trees were equivocal as to monophyly of the family itself but showed good support for each of eight main clades of Bacillariaceae, three of which corresponded more or less to existing genera (Hantzschia, Cylindrotheca and Bacillaria). The other five main clades and some subclades comprised groups of Nitzschia species or assemblies of Nitzschia species with other genera (Pseudo-nitzschia, Fragilariopsis, Neodenticula, Tryblionella, Psammodictyon). Relationships between most of the eight main clades were not resolved robustly but all analyses recovered Nitzschia as non-monophyletic. The Grunowian classification of Nitzschia into sections was not supported, though in some respects (e.g. treatment of sigmoid species) it is better than subsequent reclassifications. Several of the main clades and subclades are cryptic (lacking morphological synapomorphies) and homoplasy is common in both light microscopical and ultrastructural characters (to the extent that organisms initially assigned to the same species sometimes prove to belong to a different main clade). Nevertheless, some characters, including the structure of the raphe canal and girdle, seem to be sufficiently conservative evolutionarily to give a provisional estimate of relationships if molecular data are unavailable. No new formal classifications are proposed but various options are explored and research needs identified. info:eu-repo/semantics/acceptedVersion

Diatoms are important contributors to the benthic microeukaryote flora. This manuscript lays the foundation for future metagenomic and environmental sequencing projects off coastal China by curating diatom DNA sequences from the Yantai region of the Bohai and Yellow Seas (Northeast China). These studies are based on cultures established from samples collected in different seasons from marine littoral and supralittoral zones in 2013 and 2014. Thirty- six diatom strains were cultured successfully and identification of these clones was determined by light and scanning electron microscopy(LM and SEM) and DNA sequencing of the nuclear-encoded small subunit ribosomal RNA (SSU)and chloroplast-encoded rbcL and psbC genes. The strains primarily represent raphid pennate genera, such as Amphora, Amphora (Oxyamphora), Caloneis, Diploneis, Halamphora, Navicula, Nitzschia, Parlibellus, Pleurosigma, Surirella and Tryblionella. When the DNA markers from these strains were analysed in a multi-gene phylogeny, we found that some clones-particularly within the genera Amphora, Navicula and Nitzschia—show greater than expected genetic diversity despite their very similar morphology and morphometrics. We also compared the molecular and morphological identities of several seemingly ubiquitous marine littoral taxa in the genera Amphora and Nitzschia from the Indian Ocean and Atlantic Ocean, the Red Sea and Adriatic Sea to their Yellow Sea counterparts.

In many marine littoral and sublittoral benthic habitats, we find small diatoms with few features resolvable with light microscopy (LM) other than internal costae across their valves. While classically those internal costae have defined their identification and classification, the use of electron microscopy and of molecular data have started to reveal the true diversity of unrelated forms and genera (e.g., Anaulus, Eunotogramma, Hustedtiella, or Plagiogramma) which possess these structures. Here we describe the new genus Ambo, in an attempt to clarify some of the polyphyly of taxa with internal costa by formally transferring Anaulus balticus, Anaulus simonsenii, and Plagiogramma tenuissimum as well as Ambo gallaeciae, described here. Related to this, we attempt to document and characterize the genus Anaulus itself, which was formally described by Ehrenberg with an illustration. A search by LM of mica designated by Ehrenberg as the holotype of Anaulus scalaris, the generitype of Anaulus, failed to recover a specimen which adequately describes the genus to the exclusion of other genera with internal costa. We also present morphological and molecular data for Anaulus creticus and suggest a new genus-Ceratanaulus-to reflect the distinct morphological and molecular characters we documented.

Fatty acyl-CoA reductase (FAR) is involved in the biosynthesis of primary alcohols, which are waxy constituents that play an important role in plant stress. Previous studies have shown that primary alcohol is the most important component in the wheat seeding stage and accounts for more than 80% of the total composition. To date, eight FAR genes have been identified in wheat, but there has not been a systematic analysis. In this study, a comprehensive overview of the TaFAR gene family was performed, including analyses of the phylogenetic relationship, the multiple sequence alignment, the conserved motif distribution and the expression pattern. The result showed that a total of 41 wheat FAR genes were identified and designated TaFAR1-A–TaFAR22-D; all FAR genes were divided into six classes according to their phylogenetic relationship, and most of the FAR genes might be related to wheat cuticular wax synthesis. The analysis of the promoter binding site showed that TaFAR genes could be regulated by the MYB transcription factor and could be used as target genes for hormone regulation under adverse conditions, especially during a drought. This study provides a basis for further analyses of the TaFAR gene function and of upstream regulatory genes.

Background The cuticle covers the surface of the polysaccharide cell wall of leaf epidermal cells and forms an essential diffusion barrier between the plant and the environment. The cuticle is composed of cutin and wax. Cuticular wax plays an important role in the survival of plants by serving as the interface between plants and their biotic and abiotic environments, especially restricting nonstomatal water loss. Leaf cuticular waxes of hexaploid wheat at the seedling stage mainly consist of primary alcohols, aldehydes, fatty acids, alkane and esters. Primary alcohols account for more than 80% of the total wax load. Therefore, we cloned several genes encoding fatty acyl-coenzyme A reductases from wheat and analyzed their function in yeast and plants. We propose the potential use of these genes in wheat genetic breeding. Results We reported the cloning and characterization of three TaFARs, namely TaFAR6, TaFAR7 and TaFAR8, encoding fatty acyl-coenzyme A reductases (FAR) in wheat leaf cuticle. Expression analysis revealed that TaFAR6, TaFAR7 and TaFAR8 were expressed at the higher levels in the seedling leaf blades, and were expressed moderately or weakly in stamen, glumes, peduncle, flag leaf blade, sheath, spike, and pistil. The heterologous expression of three TaFARs in yeast (Saccharomyces cerevisiae) led to the production of C24:0 and C26:0 primary alcohols. Transgenic expression of the three TaFARs in tomato (Solanum lycopersicum) and rice (Oryza sativa) led to increased accumulation of C24:0–C30:0 primary alcohols. Transient expression of GFP protein-tagged TaFARs revealed that the three TaFAR proteins were localized to the endoplasmic reticulum (ER), the site of wax biosynthesis. The three TaFAR genes were transcriptionally induced by drought, cold, heat, powdery mildew (Blumeria graminis) infection, abscisic acid (ABA) and methyl jasmonate (MeJa) treatments. Conclusions These results indicated that wheat TaFAR6, TaFAR7 and TaFAR8 are involved in biosynthesis of very-long-chain primary alcohols in hexaploid wheat and in response to multiple environmental stresses. Electronic supplementary material The online version of this article (10.1186/s12870-018-1256-y) contains supplementary material, which is available to authorized users.

Wheat (Triticum aestivum L.) morphological and adaptation-related traits that are controlled by quantitative trait loci (QTLs) help define potential growing areas of a wheat cultivar. To dissect QTLs for heading date, lodging, shattering (SH), cold tolerance, plant height, spike length, spike compactness, awn length (AL) and chaff color (CC), a high-density genetic map with single nucleotide polymorphism and simple sequence repeat markers were developed using recombinant inbred lines (RILs) derived from ‘Ning7840’ × ‘Clark’. The RILs were evaluated in eight Oklahoma environments from 2001 to 2004. A total of 31 QTLs with additive effects on different traits were mapped on most wheat chromosomes except for 1D, 3A, 3D, 4D, 6D, and 7B. Six chromosome regions showed either tightly linked QTLs or QTLs with pleiotropic effects for two to three traits. Five QTL pairs showed additive × additive effects (AA). Ten additive QTLs were involved in additive × environment (AE) effects, and one epistatic QTL was involved in AAE effects. Among nine traits evaluated only three (SH, AL, and CC) were controlled by single genes in this biparental population. Seven traits were conditioned by multiple QTLs. A total of 127 markers were tightly linked to the QTLs. The findings shed light on the inheritance of wheat morphological and adaptation-related traits and provide DNA markers for manipulating these important traits to improve wheat production.

Continuous improvement in grain yield is one of the major challenges for wheat (Triticum aestivum L.) breeding worldwide. This study characterized quantitative trait loci (QTL) underlying wheat grain yield and its components using a high-density genetic linkage map developed from a recombinant inbred line (RIL) population derived from ‘Ning7840’ × ‘Clark’. The map consisted of 594 single nucleotide polymorphism and 404 simple sequence repeat markers covering a genetic distance of 4225.7 cM. The RIL population was evaluated for grain yield (GY), spike number per m2 (SNPM), kernel number per spike (KNPS), and thousand-kernel weight (TKW) in three Oklahoma locations from 2001 to 2003. A total of 29 additive QTL (eight for GY, two for SNPM, five for KNPS, and 14 for TKW) were mapped on 13 chromosomes. Eight pairs of epistatic QTL were detected for different yield components: four for GY, two for KNPS, and two for TKW. Four additive QTL, including two for GY and two for KNPS, showed additive × environment interactions. QTL that were repeatable in multiple environments were identified for all traits except SNPM. Positive alleles were dispersed between the two parents for all traits, with ‘Clark’ contributing slightly more. Seven pleiotropic loci were co-localized for at least two traits. Interestingly, all co-localized loci overlapped for TKW, and four of them overlapped for GY. Thus, selecting QTL for TKW may simultaneously select for or against yield or other yield components in breeding.

The frequency of toxic cyanobacterial blooms has increased in recent decades, but the factors that regulate the dominance of toxin-producing cyanobacteria over non-toxin-producing strains of one species are still obscure. This study examined the effects of temperature, light intensity, nitrate and phosphate on the dominance of MC-producing and non-MC-producing strains of Microcystis aeruginosa in monoculture and co-culture experiments. In the monoculture experiments, growth rates of the non-MC-producing strain were higher than those of the MC-producing strain under the same growth conditions. However, at the end of the co-culture experiments, the MC-producing strain became surprisingly dominant in all treatments except when treated with extreme low phosphate concentrations. Higher temperatures and nutrient levels can shift the dominance more quickly towards the toxic strain. The dominance may be explained by allelopathic interactions through allelochemicals and other secondary metabolites, but not MC. Environmental factors such as extremely low phosphate content may exert an indirect effect on strain dominance by changing the production of allelochemicals. Our findings highlight the complications in predicting competitive outcome for cyanobacterial strains in natural environments.

A waxy cuticle that serves as a protective barrier against non-stomatal water loss and environmental damage coats the aerial surfaces of land plants. It comprises a cutin polymer matrix and waxes. Cuticular waxes are complex mixtures of very long chain fatty acids (VLCFAs) and their derivatives. Results show that primary alcohols are the major components of bread wheat (Triticum aestivum L.) leaf blade cuticular waxes. Here, the characterization of TaFAR5 from wheat cv Xinong 2718, which is allelic to TAA1b, an anther-specific gene, is reported. Evidence is presented for a new function for TaFAR5 in the biosynthesis of primary alcohols of leaf blade cuticular wax in wheat. Expression of TaFAR5 cDNA in yeast (Saccharomyces cerevisiae) led to production of C22:0 primary alcohol. The transgenic expression of TaFAR5 in tomato (Solanum lycopersicum) cv MicroTom leaves resulted in the accumulation of C26:0, C28:0, and C30:0 primary alcohols. TaFAR5 encodes an alcohol-forming fatty acyl-coenzyme A reductase (FAR). Expression analysis revealed that TaFAR5 was expressed at high levels in the leaf blades, anthers, pistils, and seeds. Fully functional green fluorescent protein-tagged TaFAR5 protein was localized to the endoplasmic reticulum (ER), the site of primary alcohol biosynthesis. SDS-PAGE analysis indicated that the TaFAR5 protein possessed a molecular mass of 58.4kDa, and it was also shown that TaFAR5 transcript levels were regulated in response to drought, cold, and abscisic acid (ABA). Overall, these data suggest that TaFAR5 plays an important role in the synthesis of primary alcohols in wheat leaf blade.

Plant cuticular wax is a heterogeneous mixture of very long chain fatty acids (VLCFAs) and their derivatives. Primary alcohols are the dominant wax components throughout leaf development of Brachypodium distachyon (Brachypodium). However, the genes involved in primary alcohol biosynthesis have not been investigated and their exact biological function remains unclear in Brachypodium to date. Here, we monitored the leaf wax profile and crystal morphology during Brachypodium leaf morphogenesis, and isolated three Brachypodium fatty acyl-CoA reductase (FAR) genes, named BdFAR1, BdFAR2 and BdFAR3, then analyzed their biochemical activities, substrate specificities, expression patterns, subcellular localization and stress induction. Transgenic expression of BdFAR genes in yeast (Saccharomyces cerevisiae), tomato (Solanum lycopersicum), Arabidopsis (Arabidopsis thaliana) and Brachypodium increased the production of primary alcohols. The three BdFAR genes were preferentially expressed in Brachypodium aerial tissues, consistent with known sites of wax primary alcohol deposition, and localized in the endoplasmic reticulum (ER) in Arabidopsis protoplasts. Finally, expression of the BdFAR genes was induced by drought, cold and ABA treatments, and drought stress significantly increased cuticular wax accumulation in Brachypodium. Taken together, these results indicate that the three BdFAR genes encode active FARs involved in the biosynthesis of Brachypodium wax primary alcohols and respond to abiotic stresses.

The diploid Aegilops tauschii (Ae. tauschii) is the D-genome donor to hexaploid wheat (Triticum aestivum) and represents a potential source for genetic study in common wheat. The ubiquitous wax covering the aerial parts of plants plays an important role in protecting plants against nonstomatal water loss. Cuticular waxes are complex mixtures of very long-chain fatty acids, alkanes, primary and/or secondary alcohols, aldehydes, ketones, esters, triterpenes, sterols, and flavonoids. In the present work, primary alcohols were identified as the major components of leaf cuticular wax in Ae. tauschii, with C26:0-OH being the dominant primary alcohol. Analysis by scanning electron microscope (SEM) revealed that dense platelet-shaped wax crystals were deposited on leaf surfaces of Ae. tauschii. Ten putative wax biosynthetic genes encoding fatty acyl-coenzyme A reductase (FAR) were identified in the genome of Ae. tauschii. Five of these genes, Ae.tFAR1, Ae.tFAR2, Ae.tFAR3, Ae.tFAR4 and Ae.tFAR6, were found expressed in the leaf blades. Heterologous expression of the five Ae.tFARs in yeast (Saccharomyces cerevisiae) showed that Ae.tFAR1, Ae.tFAR2, Ae.tFAR3, Ae.tFAR4 and Ae.tFAR6 were predominantly responsible for the accumulation of C16:0, C18:0, C26:0, C24:0 and C28:0 primary alcohols, respectively. In addition, nine Ae.tFAR paralogous genes were located on D chromosome of wheat and the wheat nullisomic–tetrasomic lines with the loss of Ae.tFAR3 and Ae.tFAR4 paralogous genes had significantly reduced levels of primary alcohols in the leaf blades. Collectively, these data suggest that Ae.tFAR1, Ae.tFAR2, Ae.tFAR3, Ae.tFAR4 and Ae.tFAR6 encode alcohol-forming FARs involved in the biosynthesis of primary alcohols in the leaf blades of Ae. tauschii. The information obtained in Ae. tauschii enables us to better understand wax biosynthesis in common wheat.

The family Cymatosiraceae, composed of two subfamilies (Cymatosiroideae and Extubocelluloideae), are elongate, non-pennate diatoms and are commonly reported in marine planktonic and benthic assemblages all over the world. The combination of the gross bilateral symmetry of the frustule and radial symmetry of the valve poration, distinct pore fields at the valve apices and DNA sequence data place this family in the controversial diatom class Mediophyceae, sister to the pennate diatoms. The relationships of the Cymatosiraceae within the Mediophyceae, and the monophyly of the two cymatosiroid subfamilies, have become less stable with the addition of new DNA sequence data. In this paper, we examine 24 cymatosiraceaen strains, including the new taxa Lambertocellus africana (Dąbek & Witkowski) Dąbek, Witkowski & Ashworth comb. nov., Leyanella probus Ashworth, Dąbek & Witkowski sp. nov., and Leyanella pauciporis Ashworth, Dąbek & Park sp. nov. to create the most complete molecular phylogeny of the Cymatosiraceae to date, using a three-gene (SSU, rbcL and psbC) dataset. The results of the phylogenetic analysis support the monophyly of the Cymatosiraceae, but not the monophyly of the subfamilies Cymatosiroideae and Extubocelluloideae. The phylogenetic analysis also suggests a close relationship of the Cymatosiraceae to the family Eupodiscaceae. The phylogenetic results have lead us to re-evaluate the taxonomy of Lambertocellus africana, which is sister to Cymatosira lorenziana rather than Minutocellus as suggested in the original description. This article is protected by copyright. All rights reserved.

Segregation distortion is a widespread phenomenon in plant and animal genomes and significantly affects linkage map construction and identification of quantitative trait loci (QTLs). To study segregation distortion in wheat, a high-density consensus map was constructed using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers by merging two genetic maps developed from two recombinant-inbred line (RIL) populations, Ning7840 × Clark and Heyne × Lakin. Chromosome regions with obvious segregation distortion were identified in the map. A total of 3541 SNPs and 145 SSRs were mapped, and the map covered 3258.7 cM in genetic distance with an average interval of 0.88 cM. The number of markers that showed distorted segregation was 490 (18.5%) in the Ning7840 × Clark population and 225 (10.4%) in the Heyne × Lakin population. Most of the distorted markers (630) were mapped in the consensus map, which accounted for 17.1% of mapped markers. The majority of the distorted markers clustered in the segregation distortion regions (SDRs) on chromosomes 1B, 2A, 2B, 3A, 3B, 4B, 5A, 5B, 5D, 6B, 7A, and 7D. All of the markers in a given SDR skewed toward one of the parents, suggesting that gametophytic competition during zygote formation was most likely one of the causes for segregation distortion in the populations.

The genus Simonsenia is reviewed and S. aveniformis described as new for science by light and electron microscopy. The new species originated from estuarine environments in southern Iberia (Atlantic coast) and was isolated into culture. In LM, Simonsenia resembles Nitzschia, with bridges (fibulae) beneath the raphe, which is marginal. It is only electron microscope (EM) examination that reveals the true structure of the raphe system, which consists of a raphe canal raised on a keel (wing), supported by rib like braces (fenestral bars) and tube-like portulae; between the portulae the keel is perforated by open windows (fenestrae). Based on the presence of portulae and a fenestrated keel, Simonsenia has been proposed to be intermediate between Bacillariaceae and Surirellaceae. However, an rbcL phylogeny revealed that Simonsenia belongs firmly in the Bacillariaceae, with which it shares a similar chloroplast arrangement, rather than in the Surirellaceae. Lack of homology between the surirelloid and simonsenioid keels is reflected in subtle differences in the morphology and ontogeny of the portulae and fenestrae. The diversity of Simonsenia has probably been underestimated, particularly in the marine environment.

Here we present a formal description of Biremis panamae Barka, Witkowski et Weisenborn sp. nov., which was isolated from the marine littoral environment of the Pacific Ocean coast of Panama. The description is based on morphology (light and electron microscopy) and the rbcL, psbC and SSU sequences of one clone of this species. The new species is included in Biremis due to its morphological features; i.e. two marginal rows of foramina, chambered striae, and girdle composed of numerous punctate copulae. The new species also possesses a striated valve face which is not seen in most known representatives of marine littoral Biremis species. In this study we also present the relationship of Biremis to other taxa using morphology, DNA sequence data and observations of auxosporulation. Our results based on these three sources point to an evolutionary relationship between Biremis, Neidium and Scoliopleura. The unusual silicified incunabular caps present in them are known otherwise only in Muelleria, which is probably related to the Neidiaceae and Scoliotropidaceae. We also discuss the relationship between Biremis and the recently described Labellicula and Olifantiella. info:eu-repo/semantics/publishedVersion

Based on an improved multi-population genetic algorithm, a new fast flexible docking program, GAsDock, was developed. The docking accuracy, screening efficiency, and docking speed of GAsDock were evaluated by the docking results of thymidine kinase (TK) and HIV-1 reverse transcriptase (RT) enzyme with 10 available inhibitors of each protein and 990 randomly selected ligands. Nine of the ten known inhibitors of TK were accurately docked into the protein active site, the root-mean-square deviation (RMSD) values between the docking and X-ray crystal structures are less than 1.7 A; binding poses (conformation and orientation) of 9 of the 10 known inhibitors of RT were reproduced by GAsDock with RMSD values less than 2.0 A. The docking time is approximately in proportion to the number of rotatable bonds of ligands; GAsDock can finish a docking simulation within 60 s for a ligand with no more than 20 rotatable bonds. Results indicate that GAsDock is an accurate and remarkably faster docking program in comparison with other docking programs, which is applausive in the application of virtual screening.

Plant microRNAs (miRNAs), a class of small non-coding regulatory RNAs, are canonically 20–24 nucleotides (nt) in length and bind to complementary target RNA sequences, guiding target attenuation via mRNA degradation or translation inhibition. Of the annotated miRNA families, evolutionarily conserved families have been well known to extensively regulate analogous targets and play critical roles in plant development and adaptation to adverse environments. By contrast, majority of these families that are merely present in a specific lineage or in a few closely related species have not been well functionally explored until recently. The fast-growing progresses being made in the actions of non-conserved miRNAs nowadays in diverse plant species may represent a highly promising research field in future. This review thereby summarizes the emerging advances in our understanding of the biogenesis, associated effectors, modes to targets, and biological functions of plant non-conserved miRNAs. In addition, it outlines the regulatory units recently discovered between conserved miRNAs and their alternative targets.

The glossy varieties (A14 and Jing 2001) and glaucous varieties (Fanmai 5 and Shanken 99) of wheat (Triticum aestivum L.) were selected for evaluation of developmental changes in the composition and morphology of cuticular waxes on leaves and spikes. The results provide us with two different wax development patterns between leaf and spike. The general accumulation trend of the total wax load on leaf and spike surfaces is first to increase and then decrease during the development growth period, but these changes were caused by different compound classes between leaf and spike. Developmental changes of leaf waxes were mainly the result of variations in composition of alcohols and alkanes. In addition, diketones were the third important contributor to the leaf wax changes in the glaucous varieties. Alkanes and diketones were the two major compound classes that caused the developmental changes of spike waxes. For leaf waxes, β- and OH-β-diketones were first detected in flag leaves from 200-day-old plants, and the amounts of β- and OH-β-diketones were significantly higher in glaucous varieties compared with glossy varieties. In spike waxes, β-diketone existed in all varieties, but OH-β-diketone was detectable only in the glaucous varieties. Unexpectedly, the glaucous variety Fanmai 5 yielded large amounts of OH-β-diketone. There was a significant shift in the chain length distribution of alkanes between early stage leaf and flag leaf. Unlike C28 alcohol being the dominant chain length in leaf waxes, the dominant alcohol chain length of spikes was C24 or C26 depending on varieties. Epicuticular wax crystals on wheat leaf and glume were comprised of platelets and tubules, and the crystal morphology changed constantly throughout plant growth, especially the abaxial leaf crystals. Moreover, our results suggested that platelets and tubules on glume surfaces could be formed rapidly within a few days.

Wheat (Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci (QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content (GPC); test weight (TW); single kernel characterization system (SKCS)-estimated kernel weight (SKW); kernel diameter (KD); kernel hardness measured by near-infrared reflectance spectroscopy (NIRS) hardness index (NHI); and SKCS-hardness index (SHI), a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers was developed using recombinant inbred lines (RILs) derived from Ning7840 × Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes, excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic effects on two to four traits. Ten pairs of QTL showed additive × additive effects (AA), four QTL were involved in additive × environment (AE) effects, and one was involved in AAE effects. Two to eleven QTL for each of the six traits and 139 tightly linked markers to these QTL were identified. The findings shed light on the inheritance of wheat grain quality traits and provide DNA markers for manipulating these important traits to improve quality of new wheat cultivars.