Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.

Abstract Mitochondria participate in metabolism and signaling. They adapt to the requirements of various cell types. Publicly available expression data permit to study expression dynamics of genes with mitochondrial function (mito-genes) in various cell types, conditions and organisms. Yet, we lack an easy way of extracting these data for mito-genes. Here, we introduce the visual data mining platform mitoXplorer, which integrates expression and mutation data of mito-genes with a manually curated mitochondrial interactome containing ∼1200 genes grouped in 38 mitochondrial processes. User-friendly analysis and visualization tools allow to mine mitochondrial expression dynamics and mutations across various datasets from four model species including human. To test the predictive power of mitoXplorer, we quantify mito-gene expression dynamics in trisomy 21 cells, as mitochondrial defects are frequent in trisomy 21. We uncover remarkable differences in the regulation of the mitochondrial transcriptome and proteome in one of the trisomy 21 cell lines, caused by dysregulation of the mitochondrial ribosome and resulting in severe defects in oxidative phosphorylation. With the newly developed Fiji plugin mitoMorph, we identify mild changes in mitochondrial morphology in trisomy 21. Taken together, mitoXplorer (http://mitoxplorer.ibdm.univ-mrs.fr) is a user-friendly, web-based and freely accessible software, aiding experimental scientists to quantify mitochondrial expression dynamics.

Biological pathways have become the standard way to represent the coordinated reactions and actions of a series of molecules in a cell. A series of interconnected pathways is referred to as a biological network, which denotes a more holistic view on the entanglement of cellular reactions. Biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization. Here, we review a set of pathway and network visualization and analysis methods and take a look at potential future developments in the field.

40Background 41 Mitochondria produce cellular energy in the form of ATP and are involved in various 42 metabolic and signaling processes. However, the cellular requirements for 43 mitochondria are different depending on cell type, cell state or organism. Information 44 on the expression dynamics of genes with mitochondrial functions (mito-genes) is 45 embedded in publicly available transcriptomic or proteomic studies and the variety of 46 available datasets enables us to study the expression dynamics of mito-genes in many 47 different cell types, conditions and organisms. Yet, we lack an easy way of extracting 48 these data for gene groups such as mito-genes. 49 50 Results 51 Here, we introduce the web-based visual data mining platform mitoXplorer, which 52 systematically integrates expression and mutation data of mito-genes. The central part 53 of mitoXplorer is a manually curated mitochondrial interactome containing ~1200 54 genes, which we have annotated in 35 different mitochondrial processes. This 55 mitochondrial interactome can be integrated with publicly available transcriptomic, 56 proteomic or mutation data in a user-centric manner. A set of analysis and visualization 57 tools allows the mining and exploration of mitochondrial expression dynamics and 58 mutations across various datasets from different organisms and to quantify the 59 adaptation of mitochondrial dynamics to different conditions. We apply mitoXplorer to 60 quantify expression changes of mito-genes of a set of aneuploid cell lines that carry 61 an extra copy of chromosome 21. mitoXplorer uncovers remarkable differences in the 62 regulation of the mitochondrial transcriptome and proteome due to the dysregulation 63 of the mitochondrial ribosome in retinal pigment epithelial trisomy 21 cells which 64 results in severe defects in oxidative phosphorylation. 65 3 66Conclusions 67 We demonstrate the power of the visual data mining platform mitoXplorer to explore 68 expression data in a focused and detailed way to uncover underlying potential 69 mechanisms for further experimental studies. We validate the hypothesis-creating 70 power of mitoXplorer by testing predicted phenotypes in trisomy 21 model systems. 71 MitoXplorer is freely available at http://mitoxplorer.ibdm.univ-mrs.fr. MitoXplorer does 72 not require installation nor programming knowledge and is web-based. Therefore, 73 mitoXplorer is accessible to a wide audience of experimental experts studying 74 mitochondrial dynamics. 75 76 77 4

A new leaf blight disease of browntop millet (Brachiaria ramosa) was noticed during rainy season (Kharif) 2018 at small millet experimental field, University of Agricultural Sciences, Gandhi Krishi Vignana Kendra (GKVK), Bengaluru, India. To assess the disease severity, an intensive roving survey was conducted during the 2019 cropping season. Based on the morphological characterization, the causal agent of leaf blight disease was identified as Bipolaris spp. Further sequencing and combined gene analysis of ITS (internal transcribed spacer of rDNA), GAPDH (glyceraldehyde 3‐phosphate dehydrogenase) and LSU (large subunit) of all the nine isolates confirmed the pathogen as B. setariae. Pathogenicity study showed that all the isolates were pathogenic and caused leaf blight symptoms on browntop millet. The B. setariae isolates showed marked variability with respect to disease incidence on browntop millet (cv. Dundu korale) under artificial inoculation conditions. However, the host range was limited only to browntop millet and found non‐pathogenic to other six small millets examined. To our knowledge, this is the first completely described study on characterization of B. setariae causing leaf blight disease of browntop millet in India.

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Browntop millet (Brachiaria ramosa (L.) Stapf), which is native to the United States, was recently introduced into India as one of the small millet crop. In September 2018, leaf blight symptoms were observed on cv. Dundu Korale on the adaxial side of the leaves in a field at Bangalore, India (13.0784oN, 77.5793oE). Initial lesions were brown with small yellow halo that ranged from 1 to 5 mm and eventually enlarged exhibiting light brown centers. Afterwards, spots coalesced and leaves were blighted. About 75% of the plants were infected in the field of 0.5 ha. Samples of symptomatic and asymptomatic leaves were collected, and nine isolates were recovered from culture on potato dextrose agar (PDA). Single conidial isolation was performed. Colonies were grey to olive green with regular margins at 7 days when cultured on PDA at 27 ± 1oC and 16 h light and 8 h dark cycles. Conidiophores were single or in clusters from 4.92 to 6.04 μm in width. Conidia were fusoid, cylindrical to slightly curved ranging from 38.50 to 130 μm in length and from 8.30 to 17 μm in width, with 4 to 10 distosepta (n =100). Hilum was flat to inconspicuous or slightly protruded. Based on the morphology, the pathogen was identified as a Bipolaris species according to the genus standard descriptions of Helminthosporium (Alcorn 1988). Misra and Prakash (1972) reported that Helminthosporium setariae causing leaf spot on browntop millet in India, but they did not provide any morphological or molecular evidence of identification. For molecular identification, the genomic DNA of isolate BTMH3 was extracted and the internal transcribed spacer region (ITS) and glyceraldehyde-3-phosphate dehydrogenase gene (GPD) were amplified using the pairs of primers ITS1/ITS4 (White et al. 1990) and GPD1/GPD2 (Berbee et al. 1999), respectively. BLAST analysis of ITS (MT750301; 562 matching base pairs) and GPD (MT896702; 562 matching base pairs) sequences showed 99.82% of identity with sequences of Bipolaris setariae (Sawada) Shoemaker type strain CBS 141.31 (ITS: EF452444 and GPD: EF513206). Pathogenicity was proved by spraying 10 healthy 20-day-old browntop millet plants with conidial suspension (106 conidia/ml). Control plants were sprayed with distilled water. Plants were covered with transparent polythene bags in a greenhouse at 28 ± 2oC and high relative humidity of 90%. Symptoms were observed at five days post inoculation. The pathogen was re-isolated from infected areas using the same protocol as before, whereas the control plants were symptomless. The re-isolated pathogen was confirmed as B. setariae based on morphological characters and PCR assay. To the best of our knowledge, this is the first report of leaf blight on browntop millet caused by B. setariae in the southern peninsular region of India. Disease specimen was deposited in Herbarium Cryptogamae Indiae Orientalis (HCIO), New Delhi, India with accession number 52209. Grain yield losses caused by leaf blight on browntop millet remain to be determined, however our findings indicate that cultivar cv. Dundu Korale is susceptible to B. setariae.

Morphological and molecular diversity of Ganoderma species causing basal stem rot of coconut in Southern dry tracts of Karnataka, India was carried out during 2016-17. A total of 20 isolates were isolated from Chitradurga, Chikamagalore, Hassan and Tumkur districts of Karnataka and were identified based on morphological and molecular characteristics. Sporocarps and diseased root bits were found as good source for isolation of Ganoderma. In all the isolates there were high variability in cultural, morphological and molecular characteristics. The dendrogram generated from the cultural and morphological characteristics showed clear variations among Ganoderma isolates and formed two main clusters, one cluster consisted of 13 isolates and another cluster consisted of 7 isolates. Several isolates showed 100 per cent similarity in the morphological characters regardless of their geographical origin. All the Ganoderma isolates amplified a fragment of 650 bp with fungal universal primers (ITS1 and ITS4). The ITS gene sequences of five isolates viz., CG1 (MK 681870), CG7 (MK681871), CG11 (MK681872), CG14 (MK681873) and CG20 (MK681874) were deposited in NCBI gene bank. Taxonomic comparison of the isolates with NCBI database proved that the isolates were genetically related to Ganoderma spp. with 80-100 per cent identity. However, all the tested isolates could not amplify G. lucidum species specific markers which indicate its absence in the region. The phylogenetic analysis of the Ganoderma isolates (ITS1 and ITS4) of coconut with other known species of Ganoderma from GenBank emphasized the close relationship with India, China and Sri Lanka isolates. The isolate CG1 grouped with Ganoderma carnosum (KR 733545.1) with 98.97 per cent identity which is isolated from Sri Lanka and CG14 and CG20 grouped with G. applanatum (MF 072395.1) and G. gibbosum (OM 350473.1) with 98 to 99 per cent identity and CG7 and CG11 isolates of coconut grouped into distinct sub cluster and clearly indicated the species diversity in Ganoderma infecting coconut in Southern Karnataka.