Additional file 6: Table S5. of Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews

TPM values of DEGs encoding putative secreted proteins and cluster numbers from clustering analyses. (XLSX 68 kb

Uso de inhibidores de tak1 en la prevención y tratamiento del fracaso de la membrana peritoneal

[EN] The invention relates to the use of TAKl inhibitors for the preparation of a drug for the prevention and treatment of peritoneal membrane failure, said use preventing and reversing the mesenchymal-epithelial transition experienced by the mesothelial cells of the peritoneum during peritoneal dialysis treatment. In addition, the invention relates to the use of a TAKl expression product or of its activity as a biomarker for determining peritoneal fibrosis. The invention further relates to the method for obtaining data that can be used in the diagnosis and/or prognosis of peritoneal fibrosis and to a method for predicting the progression ofperitoneal fibrosis. The invention also relates to the use of a kit comprising the sequence that codes for TAKl or the protein for the diagnosis of peritoneal fibrosis.[ES] La presente invención se refiere al uso de inhibidores de TAKl para la preparación de un medicamento para la prevención y tratamiento del fracaso de la membrana peritoneal. Donde dicho uso previene y revierte la transición epitelio mesénquima que sufren las células mesoteliales del peritoneo durante el tratamiento de diálisis peritoneal. También, al uso de un producto de expresión de TAKl o de su actividad como biomarcador para la detenninación de fibrosis peritoneal. Al método de obtención de datos útiles en el diagnóstico y/o pronóstico de la fibrosis peritoneal; un método para predecir la progresión de la fibrosis peritoneal. Así como el uso de un kit que comprende la secuencia que codifica para TAKl o la proteína para el diagnóstico de la fibrosis peritoneal.Peer reviewedCentro Nacional de Investigaciones Cardiovasculares, Consejo Superior de Investigaciones Científicas, Centro de Investigación Biomédica en Red:Enfermedades Hepáticas y DigestivasA2 Solicitud de patente sin informe sobre el estado de la técnic

Additional file 16: of Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews

RXLR-like genes predicted in genome of Sclerospora graminicola and their expression levels during infection. (XLSX 82 kb

MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice

<div><p>Advances in genome sequencing technologies have enabled researchers and breeders to rapidly associate phenotypic variation to genome sequence differences. We recently took advantage of next-generation sequencing technology to develop MutMap, a method that allows rapid identification of causal nucleotide changes of rice mutants by whole genome resequencing of pooled DNA of mutant F2 progeny derived from crosses made between candidate mutants and the parental line. Here we describe MutMap+, a versatile extension of MutMap, that identifies causal mutations by comparing SNP frequencies of bulked DNA of mutant and wild-type progeny of M3 generation derived from selfing of an M2 heterozygous individual. Notably, MutMap+ does not necessitate artificial crossing between mutants and the wild-type parental line. This method is therefore suitable for identifying mutations that cause early development lethality, sterility, or generally hamper crossing. Furthermore, MutMap+ is potentially useful for gene isolation in crops that are recalcitrant to artificial crosses.</p></div

RNA interference confirms that the Os01g0127300 mutation is responsible for Hit9188 developmental phenotypes.

<p>(<b>A</b>) Structure of Os01g0127300 (<i>OsNAP6</i>) and scheme of the construct used for RNAi analysis targeting the <i>OsNAP6</i> gene. (<b>B</b>) Results of real-time quantitative reverse transcription (RT)-PCR showing the relative expression level of <i>OsNAP6</i> in rice plants transformed with OsNAP6-RNAi construct (RNAi) and empty vector (Empty). <i>Asterisks</i> indicate significant differences (Student’s <i>t</i>-test, **<i>P</i><0.01). (<b>C</b>) Phenotype of leaf blade (top) and seedlings (bottom) of <i>OsNAP6</i> RNAi transgenic plants compared to the Hit9188 mutant and Hitomebore wild-type (WT) plants.</p

学生による授業評価の意義と課題(第7回月例研究会記録)

この論文は国立情報学研究所の学術雑誌公開支援事業により電子化されました

MutMap+ identifies the genomic region harboring the Hit11440 mutation.

<p>(<b>A</b>) Phenotype of wild-type (WT) and Hit11440 mutant seedlings at about 12 days after sowing. (<b>B</b>) Chromosome 8 SNP-index plots for mutant and wild-type (WT) bulks derived from DNA bulks of M3 progeny obtained from selfing of a heterozygous M2 plant, and the Δ(SNP-index) plot generated by subtracting the WT bulk SNP-indices from that of the mutant bulk. Points in the graphs represent SNPs, and red lines represent the sliding window average of 4 Mb interval with 10 Kb increment. Shaded areas correspond to the genomic region where SNP-indices of WT and mutant bulks show statistically significant (P<0.05) differences (i.e. Δ(SNP-index) >0). (<b>C</b>) Genomic location and structure of the candidate gene, Os08g0139100, harboring a nucleotide change in the Hit11440 mutant. Location of the mutated glutamine residue is indicted by a red triangle. (<b>D</b>) The predicted 299-amino acid sequence of the DAG protein encoded by Os08g0139100. The mutated glutamine (Q) residue is indicated in red. (<b>E</b>) Sanger sequencing confirms the candidate SNP identified by Illumina whole genome re-sequencing as indicated by peak chromatograms of the region spanning the Os08g0139100 mutation. The wild-type C in Hitomebore, the mutated T in mutant-bulk DNA, and the C/T mixture in wild-type (WT) bulk DNA are indicted by the black arrows.</p

MutMap+ identifies the causal mutation of the Hit9188 early stage lethality phenotype.

<p>(<b>A</b>) The Hit9188 mutant is characterized by seedlings with pale-green and dwarf phenotypes that eventually die out starting from about three weeks after germination. (<b>B</b>) Chromosome 1 SNP-index plot for mutant and wild-type (WT) bulks derived from a segregating Hit9188 M3 progeny that was obtained by selfing a heterozygous M2 plant, as well as the Δ(SNP-index) plot generated by subtraction of WT bulk from mutant bulk. Points in the graphs represent SNPs, and the red lines represent the sliding window average of 4 Mb interval with 10 Kb increment. Shaded areas correspond to the genomic region where SNP-indices of mutant bulk and wild-type bulk show statistically significant (<i>P</i><0.05) differences (<i>i.e.</i> Δ(SNP-index) >0). (<b>C</b>) Genomic location and structure of the Os01g0127300 gene harboring the Hit9188 mutant candidate nucleotide change, whose position within the gene together with the predicted amino acid change are indicated by a red triangle. (<b>D</b>) The deduced amino acid sequence of the protein encoded by Os01g0127300. The red font indicates the mutated alanine residue. (<b>E</b>) DNA sequencing peak chromatograms of the region spanning the Os01g0127300 mutation showing the wild-type G in Hitomebore, mutant A in mutant bulk, and the heterozygous G/A in wild-type (WT) bulk.</p

A simplified scheme of MutMap+.

<p>(<b>A</b>) Seeds harvested following EMS mutagenesis of rice at immature embryo stage are used to establish M1 generation, at which stage most of mutations incorporated by EMS are in the heterozygous state. (<b>B</b>) M2 progeny obtained from a self-fertilized M1 plant segregate for wild-type (indicated by green color) and mutant (brown color) phenotypes. Here we focus on wild-type heterozygous individuals. (<b>C</b>) Heterozygous M2 plant are selfed to obtain M3 progeny that segregate 3∶1 for wild-type and mutant phenotypes. Genomic DNA from 20–40 M3 mutant and wild-type M3 progeny are separately bulked, and subjected to whole-genome sequencing. The resulting short reads are aligned to reference sequence of the cultivar used for mutagenesis. (<b>D</b>) SNP-index is calculated for each SNP, and plots relating SNP-index and chromosome positions are obtained for both the mutant and wild-type M3 bulks separately. The two SNP-index plots are compared to identify the region with SNP-index = 1 that is specific to the mutant bulk. (<b>E</b>) We can also evaluate Δ(SNP-index) plot, which is obtained by subtracting SNP-index value of wild-type bulk from that of mutant bulk. Genomic region harboring the causal mutation should have positive Δ(SNP-index) values.</p

Additional file 3: Supplemental dataset S1. of Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

List of the 26,198 protein coding genes predicted in the D. rotundata genome. (XLSX 1480 kb