Transcriptome of Endophyte-Positive and Endophyte-Free Tall Fescue Under Field Stresses

This article is a study that represents the first transcriptome analysis of E+ and E− Texoma tall fescue under freezing and chilling temperatures in the natural field environment

Real-time Visual-Inertial Odometry for Event Cameras using Keyframe-based Nonlinear Optimization

Polymorphic conserved simple sequence repeats (SSR) markers detected among the two lowland and an upland genotypes. (DOCX 15 kb

Transcriptional Programs and Regulators Underlying Age-Dependent and Dark-Induced Senescence in Medicago truncatula

Article presents a study that reveals the dynamics of transcriptomic responses to age- and dark-induced senescence in M. truncatula and identifies senescence-associated TFs that are attractive targets for future work to control senescence in forage legumes

Iron from coal combustion particles dissolves much faster than mineral dust under simulated atmospheric acid conditions

Mineral dust is the largest source of aerosol iron (Fe) to the offshore global ocean, but acidic processing of coal fly ash (CFA) in the atmosphere may result in a disproportionally higher contribution of bioavailable Fe. Here, we determined the Fe speciation and dissolution kinetics of CFA from Aberthaw (United Kingdom), Krakow (Poland), and Shandong (China) in solutions which simulate atmospheric acidic processing. In CFA-PM10 fractions, 8 %–21.5 % of the total Fe was as hematite and goethite (dithionite extracted Fe), 2 %–6.5  % as amorphous Fe (ascorbate extracted Fe), while magnetite (oxalate extracted Fe) varied from 3 %–22 %. The remaining 50 %–87  % of Fe was associated with aluminosilicates. High concentration of ammonium sulphate ((NH4)2SO4), often found in wet aerosols, increased Fe solubility of CFA up to 7 times at low pH (2–3). Our results showed a large variability in the effects of oxalate on the Fe dissolution rates at pH 2, from no impact in Shandong ash to doubled dissolution in Krakow ash. However, this enhancement was suppressed in the presence of high concentration of (NH4)2SO4. Dissolution of highly reactive Fe was insufficient to explain the high Fe solubility at low pH in CFA, and the modelled dissolution kinetics suggests that other Fe phases such as magnetite may also dissolve rapidly under acidic conditions. Overall, Fe in CFA dissolved up to 7 times faster than in Saharan dust samples at pH 2. Based on these laboratory data, we developed a new scheme for the proton- and oxalate- promoted Fe dissolution of CFA, which was implemented into the global atmospheric chemical transport model IMPACT. The revised model showed a better agreement with observations of surface concentration of dissolved Fe in aerosol particles over the Bay of Bengal, due to the rapid Fe release at the initial stage at highly acidic conditions. The improved model also enabled us to predict sensitivity to a more dynamic range of pH changes, particularly between anthropogenic combustion and biomass burning aerosols

Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses

Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes

A deep transcriptomic analysis of pod development in the vanilla orchid (<em>Vanilla planifolia</em>)

International audienceBackground: Pods of the vanilla orchid (Vanilla planifolia) accumulate large amounts of the flavor compound vanillin (3-methoxy, 4-hydroxy-benzaldehyde) as a glucoside during the later stages of their development. At earlier stages, the developing seeds within the pod synthesize a novel lignin polymer, catechyl (C) lignin, in their coats. Genomic resources for determining the biosynthetic routes to these compounds and other flavor components in V. planifolia are currently limited. Results: Using next-generation sequencing technologies, we have generated very large gene sequence datasets from vanilla pods at different times of development, and representing different tissue types, including the seeds, hairs, placental and mesocarp tissues. This developmental series was chosen as being the most informative for interrogation of pathways of vanillin and C-lignin biosynthesis in the pod and seed, respectively. The combined 454/Illumina RNA-seq platforms provide both deep sequence coverage and high quality de novo transcriptome assembly for this non-model crop species. Conclusions: The annotated sequence data provide a foundation for understanding multiple aspects of the biochemistry and development of the vanilla bean, as exemplified by the identification of candidate genes involved in lignin biosynthesis. Our transcriptome data indicate that C-lignin formation in the seed coat involves coordinate expression of monolignol biosynthetic genes with the exception of those encoding the caffeoyl coenzyme A 3-O-methyltransferase for conversion of caffeoyl to feruloyl moieties. This database provides a general resource for further studies on this important flavor species

Additional file 4: Table S3. of Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

SNPs in or near genes detected for K5 and VS16 against AP13 at ≥100x coverage and 5% minor allele frequency. (XLSX 91 kb

Additional file 2: Table S2. of Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency

Gene expression (upregulation) among AP13 (LL), K5 (LL), and VS16 (UL) switchgrass genotypes (LL = lowland ecotype, UP = upland ecotype, 4X = tetraploid). (XLSX 2247 kb