Apple ring rot and Botryosphaeria canker are severe diseases affecting apple production in China, but there is confusion regarding which pathogens cause these diseases and their similarity to other diseases, such as white rot of apple, and ring rot and Botryosphaeria canker of pear. In this study, the pathogen of apple ring rot in China was compared with the pathogen of apple ring rot in Japan and Korea, the pathogen of Botryosphaeria canker of apple and pear in China, the pathogen of pear ring rot in China, and the pathogen of white rot of apple in the United States. Comparisons were based on morphology, pathogenicity on branches and fruit, and sequences of rDNA in the internal transcribed spacer region and of the β-tubulin and actin genes. Results showed that the causal agent of apple ring rot and Botryosphaeria canker of apple in China was Botryosphaeria dothidea, which has also been reported to be the pathogen of apple ring rot in Korea and Japan. Pathogenicity tests showed that B. dothidea infection on apple and pear branches may induce wart or canker symptoms depending on the conditions. These results are consistent with the hypothesis that the same pathogen causes the wart symptom of apple ring rot and the Botryosphaeria canker symptom on apple branches in China. The results also suggest that apple ring rot and white rot are the same disease and are caused by B. dothidea. Finally, B. dothidea isolates from pear and other fruit or forest trees may serve as inoculum for apple ring rot.

Summary Late blight caused by the plant pathogenic oomycete Phytophthora infestans is known as one of the most destructive potato diseases. Plant breeders tend to employ NB‐LRR‐based resistance for introducing genetically controlled late blight resistance in their breeding lines. However, P. infestans is able to rapidly escape this type of resistance, and hence, NB‐LRR‐based resistance in potato cultivars is often not durable. Previously, we identified a novel type of Phytophthora resistance in Arabidopsis. This resistance is mediated by the cell surface receptor LecRK‐I.9, which belongs to the family of L‐type lectin receptor kinases. In this study, we report that expression of the Arabidopsis LecRK‐I.9 gene in potato and Nicotiana benthamiana results in significantly enhanced late blight resistance. Transcriptional profiling showed strong reduction in salicylic acid (SA)‐mediated defence gene expression in LecRK‐I.9 transgenic potato lines (TPLs). In contrast, transcripts of two protease inhibitor genes accumulated to extreme high levels, suggesting that LecRK‐I.9‐mediated late blight resistance is relying on a defence response that includes activation of protease inhibitors. These results demonstrate that the functionality of LecRK‐I.9 in Phytophthora resistance is maintained after interfamily transfer to potato and N. benthamiana and suggest that this novel type of LecRK‐based resistance can be exploited in breeding strategies to improve durable late blight resistance in Solanaceous crops.

BackgroundIn recent years, the genus Pestalotiopsis is receiving increasing attention, not only because of its economic impact as a plant pathogen but also as a commonly isolated endophyte which is an important source of bioactive natural products. Pestalotiopsis fici Steyaert W106-1/CGMCC3.15140 as an endophyte of tea produces numerous novel secondary metabolites, including chloropupukeananin, a derivative of chlorinated pupukeanane that is first discovered in fungi. Some of them might be important as the drug leads for future pharmaceutics.ResultsHere, we report the genome sequence of the endophytic fungus of tea Pestalotiopsis fici W106-1/CGMCC3.15140. The abundant carbohydrate-active enzymes especially significantly expanding pectinases allow the fungus to utilize the limited intercellular nutrients within the host plants, suggesting adaptation of the fungus to endophytic lifestyle. The P. fici genome encodes a rich set of secondary metabolite synthesis genes, including 27 polyketide synthases (PKSs), 12 non-ribosomal peptide synthases (NRPSs), five dimethylallyl tryptophan synthases, four putative PKS-like enzymes, 15 putative NRPS-like enzymes, 15 terpenoid synthases, seven terpenoid cyclases, seven fatty-acid synthases, and five hybrids of PKS-NRPS. The majority of these core enzymes distributed into 74 secondary metabolite clusters. The putative Diels-Alderase genes have undergone expansion.ConclusionThe significant expansion of pectinase encoding genes provides essential insight in the life strategy of endophytes, and richness of gene clusters for secondary metabolites reveals high potential of natural products of endophytic fungi.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-014-1190-9) contains supplementary material, which is available to authorized users.

One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the Ia haplotype in the 1930s.

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Background Ophiocordyceps sinensis, which is only naturally found in the high-elevation extreme environment of the Tibetan Plateau, has been used in traditional Chinese medicine. Information concerning the evolutionary and geologic context of O. sinensis remains limited, however. Methods We constructed the high-quality genome of O. sinensis and provided insight into the evolution and ecology of O. sinensis using comparative genomics. Results We mapped the whole genome of the anamorph/asexual form Hirsutella of O. sinensis using Illumina and PacBio sequencing technologies and obtained a well assembled genome of 119.2 Mbp size. Long-read Single Molecule Real Time (SMRT) sequencing technology generated an assembly with more accurate representation of repeat sequence abundances and placement. Evolutionary analyses indicated that O. sinensis diverged from other fungi 65.9 Mya in the Upper Cretaceous, during the uplift of the Tibetan Plateau. Gene family expansions and contractions in addition to genome inflation via long terminal repeat (LTR) retrotransposon insertions were implicated as an important driver of O. sinensis divergence. The insertion rate of LTR sequences into the O. sinensis genome peaked ~ 30–40 Mya, when the Tibetan Plateau rose rapidly. Gene Ontology (GO) enrichment analysis suggested that O. sinensis contained more genes related to ice binding compared to other closely related fungi, which may aid in their adaptability to the cold Tibetan Plateau. Further, heavy metal resistance genes were in low abundance in the O. sinensis genome, which may help to explain previous observations that O. sinensis tissues contain high levels of heavy metals. Conclusions Our results reveal the evolutionary, geological, and ecological context for the evolution of the O. sinensis genome and the factors that have contributed to the environmental adaptability of this valuable fungus. These findings suggest that genome inflation via LTR retrotransposon insertions in O. sinensis coincided with the uplift of the Tibetan Plateau. LTRs and the specific genetic mechanisms of O. sinensis contributed to its adaptation to the environment on the plateau.

Carotenoids are natural pigments found in plants and microorganisms. These important nutrients play significant roles in animal health. In contrast to plant production, the advantages of microbial fermentation of carotenoids are the lower media costs, fast growth rate of microorganisms, and the ease of culture condition control. In this study, a colony of red pigment-producing yeast, Rhodotorula sp. RY1801, was isolated from the sediment of marine environment with the potential to produce carotenoids. Optimization of carotenoid production in Rhodotorula sp. RY1801 was also discussed. The optimum conditions found for carotenoid production were as follows: temperature, 28 °C; pH 5.0; carbon source, 10 g/L glucose, nitrogen source, 10 g/L yeast extract, maximum concentration of 987 µg/L of total carotenoids was obtained. The results of this study show that the isolated yeast strain Rhodotorula sp. RY1801 can potentially be used in future as a promising microorganism for the commercial production of carotenoids.

In this paper, the basic components, nutrient composition, and processing characteristics of cassava flour were determined. In addition, the effects of xanthan gum and inulin on the pasting properties, microstructure, and thermal properties of cassava flour were studied. Biscuits were prepared using cassava flour as the main raw material and the optimal technology and formula for the biscuits were determined by single‐factor and orthogonal tests. The effects of xanthan gum and inulin on the quality of cassava flour short biscuits were also investigated, and volatile components in the biscuits were determined using electronic nose technique. The addition of xanthan gum improved the pasting properties and microstructure of cassava flour, and improved the taste and increased hardness and brittleness of the biscuits, making their quality similar to that of commercially available short biscuits. The addition of inulin inhibited the setback of starch and improved starch gelatinization. However, inulin was not suitable for processing of cassava flour biscuits as it decreased their hardness, brittleness, and taste. The optimal formula and baking conditions of cassava flour short biscuits were as follows: cassava flour 100 g, water 24 g, shortening 25 g, sugar 30 g, baking powder 0.6 g, salt 1 g, and egg 25 g; the surface fire and primer fire temperatures were 180°C, and the baking time was 9 min. In addition, although the main aroma volatile components present in cassava flour and low gluten wheat flour short biscuits were similar, the proportions of each component were different.