Identification of Ochratoxigenic Aspergillus Section Nigri Isolated from Grapes by ITS‐5.8S rDNA Sequencing Analysis and In Silico RFLP

To characterize Aspergillus section Nigri strains involved in the ochratoxin A (OTA) contamination of Tunisian wine and table grapes, a total of 33 strains were analysed. A molecular characterization of the isolates was performed by the amplification of internal transcribed spacer (ITS1‐5.8S rDNA‐ITS2) region combined with amplicon sequencing. Analysis of similarity between the obtained sequences and those deposited in the GenBank database was performed. Twelve strains were confirmed to belong to the Aspergillus carbonarius species. Strains belonging to the Aspergillus niger aggregate group were classified by in silico RFLP assay into two patterns N and T, corresponding to A. niger and Aspergillus tubingensis. Among the 21 OTA producing isolates analysed, 13 showed the T‐type pattern and 8 showed the N‐type pattern. The presented method showed to be a reliable alternative to the classic RFLP method. Our findings unambiguously revealed that multiple aspergilli species isolated from wine and table grape in Tunisia are able to produce OTA.     

Collections from the mesophytic zone off Bermuda reveal three species of Kallymeniaceae (Gigartinales,Rhodophyta) in genera with transoceanic distributions

A molecular survey of red algae collected by technical divers and submersibles from 90 m in the mesophotic zone off the coast of Bermuda revealed three species assignable to the Kallymeniaceae. Two of the species are representative of recently described genera centered in the western Pacific in Australia and New Zealand, Austrokallymenia and Psaromenia and the third from the Mediterranean Sea and the eastern Atlantic, Nothokallymenia. A phylogenetic analysis of concatenated mitochondrial (COI‐5P) and chloroplast (rbcL) genes, as well as morphological characteristics, revealed that two are shown to be new species with distant closest relatives (N. erosa and Psaromenia septentrionalis), while the third represents a deep water western Atlantic species now moved to an Australasian genus (A. westii).     

Diploid hybrid origin of Hippophaë gyantsensis (Elaeagnaceae) in the western Qinghai–Tibet Plateau

Homoploid hybrid speciation, the origin of a hybrid species without change in chromosome number, is currently considered to be a rare form of speciation. In the present study, we examined the phylogenetic origin of Hippophaë gyantsensis, a diploid species occurring in the western Qinghai–Tibet Plateau. Some of its morphological and molecular traits suggest a close relationship to H. rhamnoides ssp. yunnanensis while others indicate H. neurocarpa. We conducted phylogenetic analyses of sequence data of two maternally inherited chloroplast (cp) DNA fragments and the bi‐parentally inherited nuclear ribosomal internal transcribed spacer (ITS) from 17 populations of H. gyantsensis, 15 populations of H. rhamnoides ssp. yunnanensis and 27 populations of H. neurocarpa across their distributional ranges, and modelled the niche differentiation of the three taxa. Multiple lines of evidence suggested that H. gyantsensis is a morphologically stable, genetically independent and ecologically distinct species. The inconsistent phylogenetic placements of the H. gyantsensis clade that comprised the dominant cpDNA haplotypes and ITS ribotypes suggested a probable diploid hybrid origin from multiple crosses between H. rhamnoides ssp. yunnanensis and H. neurocarpa. This tentative hypothesis is more parsimonious than alternative explanations according to the data available, although more evidence based on further testing is needed.     

A molecular evaluation of the Liagoraceae sensu lato (Nemaliales,Rhodophyta) in Bermuda including Liagora nesophila sp. nov. and Yamadaella grassyi sp. nov.

We have undertaken a comprehensive, molecular‐assisted alpha‐taxonomic examination of the rhodophyte family Liagoraceae sensu lato, a group that has not previously been targeted for molecular studies in the western Atlantic. Sequence data from three molecular markers indicate that in Bermuda alone there are 10 species in nine different genera. These include the addition of three genera to the flora — Hommersandiophycus, Trichogloeopsis, and Yamadaella. Liagora pectinata, a species with a type locality in Bermuda, is phylogenetically allied with Indo‐Pacific species of Hommersandiophycus, and the species historically reported as L. ceranoides for the islands is morphologically and genetically distinct from that taxon, and is herein described as L. nesophila sp. nov. Molecular sequence data have also uncovered the Indo‐Pacific L. mannarensis in Bermuda, a long‐distance new western Atlantic record. DNA sequences of Trichogloeopsis pedicellata from the type locality (Bahamas) match with local specimens demonstrating its presence in Bermuda. We described Yamadaella grassyi sp. nov. from Bermuda, a species phylogenetically and morphologically distinct from the generitype, Y. caenomyce of the Indo‐Pacific. Our data also indicated a single species each of Ganonema, Gloiocallis, Helminthocladia, Titanophycus, and Trichogloea in the flora.     

The monospecific genus Meredithia (Kallymeniaceae,Gigartinales) is species rich and geographically widespread with species from temperate Atlantic,Pacific, and Indian Oceans

Using sequences of 5′ region of the cytochrome oxidase subunit 1 gene, large subunit rDNA, and ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit gene as genetic markers to elucidate their phylogenetic positions, six unknown species from Western Australia, Tasmania, Lord Howe Is., and Norfolk Is. cluster with Meredithia in the Kallymeniaceae (Gigartinales), and are described as new members of this previously monospecific genus. Specimens from Bermuda referable to Kallymenia limminghei Mont. in the 20th century also clustered with this genetic grouping, not with the generitype of Kallymenia. The Bermudian specimens are further shown to be morphologically distinct from the type of K. limminghei (Guadeloupe, Caribbean Sea) and are described as a new species, Meredithia crenata. Using these Indo‐Pacific and Bermudian collections, our analyses further show that Psaromenia is closely related to Meredithia, and that Cirrulicarpus nanus sensu stricto should be returned to Meredithia.     

Identification of Colletotrichum Species Causing Bitter Rot of Apple and Pear in Croatia

Symptoms of bitter rot were observed on apple and pear fruits in the field and in storage in Croatia between 2009 and 2011. Fifteen Colletotrichum isolates from apple and two from pear were collected and identified by sequencing of the ITS1 and ITS2 regions of the ribosomal DNA. Phylogenetic analysis revealed that ten isolates from apple and two isolates from pear could be identified as Colletotrichum fioriniae, five isolates from apple were clustered in Colletotrichum clavatum, while one isolate was in the Colletotrichum acutatum A7 group. All isolates caused typical bitter rot symptoms when inoculated on apple and pear fruits.     

Quantification of Alternaria,Cladosporium, Fusarium and Penicillium verrucosum in Conventional and Organic Grains by qPCR

We analysed the levels of Alternaria, Cladosporium, Fusarium and Penicillium verrucosum in grain samples harvested in 2011 and 2012 from conventional and organic farms using qPCR. In general, both Alternaria and Cladosporium occurred in all cereal grains in the highest quantities, followed by P. verrucosum and Fusarium. Alternaria, Cladosporium and P. verrucosum had the highest levels in crop mixtures, barley and rye and lower levels in wheat, while Fusarium levels were the highest in crop mixtures and wheat. The levels of Alternaria and P. verrucosum were higher in organic rye and wheat than conventional grains. Although the level of Fusarium was higher in conventional than organic rye, opposite results were obtained for crop mixtures. A positive correlation was found between Alternaria, Cladosporium and P. verrucosum, indicating that similar factors might affect the distribution of these fungi in grains.     

Evidence for no sexual isolation between Drosophila albomicans and D. nasuta

Sexual isolation, the reduced tendency to mate, is one of the reproductive barriers that prevent gene flow between different species. Various species‐specific signals during courtship contribute to sexual isolation between species. Drosophila albomicans and D. nasuta are closely related species of the nasuta subgroup within the Drosophila immigrans group and are distributed in allopatry. We analyzed mating behavior and courtship as well as cuticular hydrocarbon profiles within and between species. Here, we report that these two species randomly mated with each other. We did not observe any sexual isolation between species or between strains within species by multiple‐choice tests. Significant difference in the courtship index was detected between these two species, but males and females of both species showed no discrimination against heterospecific partners. Significant quantitative variations in cuticular hydrocarbons between these two species were also found, but the cuticular hydrocarbons appear to play a negligible role in both courtship and sexual isolation between these two species. In contrast to the evident postzygotic isolation, the lack of sexual isolation between these two species suggests that the evolution of premating isolation may lag behind that of the intergenomic incompatibility, which might be driven by intragenomic conflicts.     

Glucose and Nitrogen Amendments Can Mitigate Wastewater‐Borne Bacteria Competition Effect Against Algal Growth in Wastewater‐Based Systems

The reuse of wastewater is important for reducing costs involved with algal lipid production. However, nutrient limitations, wastewater‐borne microbes, and mixotrophic growth can significantly affect biomass yields and lipid/biomass ratios. This research compared the growth performances of both Chlorella vulgaris and Pseudokirchneriella subcapitata on domestic wastewater effluent. The experiments were conducted in the presence and absence of wastewater‐borne bacteria, while additionally assessing the impact of distinct nitrate and glucose supplementations. When compared to the sterilized controls, the presence of wastewater‐borne bacteria in the effluent reduced C. vulgaris and P. subcapitata total biomass production by 37% and 46%, respectively. In the corresponding treatments supplemented with glucose and nitrate, total biomass production increased by 12% and 61%, respectively. The highest biomass production of 1.11 and 0.72 g · L^?1 was, however, observed in the sterilized treatments with both glucose and nitrate supplementations for C. vulgaris and P. subcapitata, respectively. Lipid to biomass ratios were, on average, threefold higher when only nitrate was introduced in the sterilized treatments for both species (0.4 and 0.5, respectively). Therefore, the combination of nitrate and glucose supplementation is shown to be an important strategy for enhancing algal lipid and biomass production when those algae are grown in the presence of wastewater‐borne bacteria. On the other hand, in the absence of wastewater‐borne bacteria, only nitrate supplementation can significantly improve lipid/biomass ratios.     

Down‐regulation of BnDA1, whose gene locus is associated with the seeds weight,improves the seeds weight and organ size in Brassica napus

Brassica napus L. is an important oil crop worldwide and is the main raw material for biofuel. Seed weight and seed size are the main contributors to seed yield. DA1 (DA means big in Chinese) is an ubiquitin receptor and negatively regulates seed size. Down‐regulation of AtDA1 in Arabidopsis leads to larger seeds and organs by increasing cell proliferation in integuments. In this study, BnDA1 was down‐regulated in B. napus by over expressed of AtDA1^R358K, which is a functional deficiency of DA1 with an arginine‐to‐lysine mutation at the 358th amino acid. The results showed that the biomass and size of the seeds, cotyledons, leaves, flowers and siliques of transgenic plants all increased significantly. In particular, the 1000 seed weight increased 21.23% and the seed yield per plant increased 13.22% in field condition. The transgenic plants had no negative traits related to yield. The candidate gene association analysis demonstrated that the BnDA1 locus was contributed to the seeds weight. Therefore, our study showed that regulation of DA1 in B. napus can increase the seed yield and biomass, and DA1 is a promising target for crop improvement.     

Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L.

Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single‐nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high‐density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora‐derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high‐density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.     

Etheliaceae fam. nov. (Gigartinales,Rhodophyta), with a clarification of the generitype of Ethelia and the addition of six novel species from warm waters

Based upon COI‐5P, LSU rDNA, and rbcL sequence data and morphological characteristics, six new members of the noncalcified crustose genus of red algae Ethelia are described in a new family, Etheliaceae (Gigartinales), sister to the recently described Ptilocladiopsidaceae. The novel species are described from subtropical to tropical Atlantic and Indo‐Pacific Ocean basins; E. mucronata sp. nov. and E. denizotii sp. nov. from southern and northern Western Australia respectively, E. wilcei sp. nov. from the Cocos (Keeling) Islands of Australia, E. suluensis sp. nov. from the Philippines, E. umbricola sp. nov. from Bermuda and E. kraftii sp. nov. from Lord Howe Island, Australia. The generitype, Ethelia biradiata, originally reported from the Seychelles, Indian Ocean, is added to the Western Australian flora.     

Rapid diagnosis of rice bakanae caused by Fusarium fujikuroi and F. proliferatum using loop‐mediated isothermal amplification assays

Rice bakanae is an important disease that causes serious rice production loss worldwide. We describe a new method for rapid diagnosis of rice bakanae caused by Fusarium fujikuroi and F. proliferatum, based on loop‐mediated isothermal amplification (LAMP) assays. After screening, primers were selected to target FusariumDNA sequences, that is, the intergenic spacer (IGS) region of the nuclear ribosomal operon and reductase‐coding region (RED1) in F. fujikuroi and F. proliferatum, respectively. Both LAMP assays efficiently amplified target genes in 70 min at 62°C. A colour change from purple to sky blue (visible to the unaided eye) was observed in the presence of the DNA of the targeted pathogens only, by adding hydroxynaphthol blue to the reaction system prior to amplification. The minimum of genomic DNA needed in the assays was 67 and 346 pg/μl for F. fujikuroi and F. proliferatum, respectively. Using the two assays described here, we successfully and rapidly diagnosed suspected diseased rice plant and seed samples collected from Jiangsu Province.