Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Long-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes constitute one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is NLR gene-rich. Here, toward identification of the Xo1 gene, we combined Nanopore and Illumina reads and generated a high-quality Carolina Gold Select genome assembly. We identified 529 complete or partial NLR genes and discovered, relative to Nipponbare, an expansion of NLR genes at the Xo1 locus. One of these has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain, and the repeats within each protein are nearly perfect. Across diverse Oryzeae, we identified two sub-clades of NLR genes with these features, varying in the presence of the zfBED domain and the number of repeats. The Carolina Gold Select genome assembly also uncovered at the Xo1 locus a rice blast resistance gene and a gene encoding a polyphenol oxidase (PPO). PPO activity has been used as a marker for blast resistance at the locus in some varieties; however, the Carolina Gold Select sequence revealed a loss-of-function mutation in the PPO gene that breaks this association. Our results demonstrate that whole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Finally, the Carolina Gold Select genome assembly will facilitate identification of other useful traits in this historically important variety. Author summary Plants lack adaptive immunity, and instead contain repeat-rich, disease resistance genes that evolve rapidly through duplication, recombination, and transposition. The number, variation, and often clustered arrangement of these genes make them challenging to sequence and catalog. The US heirloom rice variety Carolina Gold Select has resistance to two important bacterial diseases. Toward identifying the responsible gene(s), we combined long- and short-read sequencing technologies to assemble the whole genome and identify the resistance gene repertoire. We previously narrowed the location of the gene(s) to a region on chromosome four. The region in Carolina Gold Select is larger than in the rice reference genome (Nipponbare) and contains twice as many resistance genes. One shares unusual features with a known bacterial disease resistance gene, suggesting that it confers the resistance. Across diverse varieties and related species, we identified two widely-distributed groups of such genes. The results are an important step toward mechanistic characterization and deployment of the bacterial disease resistance. The genome assembly also identified a resistance gene for a fungal disease and predicted a marker phenotype used in breeding for resistance. Thus, the Carolina Gold Select genome assembly can be expected to aid in the identification and deployment of other valuable traits

Нефтяное загрязнение берегов Севастополя

Приводятся результаты изучения загрязнения береговых структур при низких уровнях нефтяных углеводородов в морской воде. В прибрежных водах и берегах на границе с морем нефтяные углеводороды в концентрациях, не достигающих поражающего уровня для морской биоты вступают в сложные взаимодействия с гидробионтами. Первым этапом этого процесса является накопление или поверхностное загрязнение морских организмов-обрастателей. Такие данные являются составной частью мониторинга прибрежных акваторий и первым этапом изучения роли биопотоков нефтяных углеводородов в общем потоке нефтяного загрязнения у морских берегов.Наводяться результати вивчення забруднення берегових структур при низьких рівнях нафтових вуглеводнів в морській воді. У прибережних водах і берегах на кордоні з морем нафтові вуглеводні в концентраціях, що не досягають вражаючого рівня для морської біоти вступають в складні взаємодії з гідробіонтами. Першим етапом цього процесу є накопичення або поверхневе забруднення морських організмів-обрастателей. Такі дані є складовою частиною моніторингу прибережних акваторій і першим етапом вивчення ролі біопотоков нафтових вуглеводнів в загальному потоці нафтового забруднення морських берегів.The results of the study of coastal structures pollution at low levels of oil hydrocarbons in the sea water are given. Oil hydrocarbons at concentrations that do not reach damaging levels for marine biota enter into complex interactions with marine life in coastal waters and sea shores. The first step of this process is the accumulation or surface contamination of marine fouling organisms. These data are a part of the monitoring of coastal waters and the first step in studying the role of oil hydrocarbons bioflows in the general flow of the oil pollution at sea coast

Rice Galaxy: An open resource for plant science

Background: Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non−computer savvy rice researchers. Findings: The Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented. Conclusions: Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science

Evidence for the h_b(1P) meson in the decay Upsilon(3S) --> pi0 h_b(1P)

Using a sample of 122 million Upsilon(3S) events recorded with the BaBar detector at the PEP-II asymmetric-energy e+e- collider at SLAC, we search for the $h_b(1P)$ spin-singlet partner of the P-wave chi_{bJ}(1P) states in the sequential decay Upsilon(3S) --> pi0 h_b(1P), h_b(1P) --> gamma eta_b(1S). We observe an excess of events above background in the distribution of the recoil mass against the pi0 at mass 9902 +/- 4(stat.) +/- 2(syst.) MeV/c^2. The width of the observed signal is consistent with experimental resolution, and its significance is 3.1sigma, including systematic uncertainties. We obtain the value (4.3 +/- 1.1(stat.) +/- 0.9(syst.)) x 10^{-4} for the product branching fraction BF(Upsilon(3S)-->pi0 h_b) x BF(h_b-->gamma eta_b).Comment: 8 pages, 4 postscript figures, submitted to Phys. Rev. D (Rapid Communications

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN

Drons col·laboratius

La robòtica col·laborativa és senzillament robots dissenyats per dur a terme treballs de col·laboració amb els humans. Els robots col·laboratius o cobots són cada cop més utilitzats a les indústries. La robòtica col·laborativa és un dels àmbits d'actualitat en aquests moments. Però també és un dels més interessants en més d'un sentit. Com es comuniquen dos drons autònoms que col·laboren per fer una tasca? Com són aquests missatges que s'envien? Que poden fer que no podrien fer sols? Aquestes són algunes de les preguntes que ens volem respondre en aquest projecte. En aquest treball es presenta un disseny i implementació de dos drons terrestres que es comuniquen per col·laborar entre ells per resoldre una tasca.Collaborative robotics is simply robots designed to perform collaborative work with humans. Collaborative robots or cobots are increasingly used in industries. Collaborative robotics is one of the current topics now. But it is also one of the most interesting in more ways than one. How do two autonomous drones that collaborate to perform a task communicate? How are these messages sent? What can they do that they could not do alone? These are some of the questions we want to answer in this project. This work presents a design and implementation of two ground drones that communicate to collaborate with each other to solve a task.La robótica colaborativa es sencillamente robots diseñados para llevar a cabo trabajos de colaboración con los humanos. Los robots colaborativos o cobots son cada vez más utilizados en las industrias. La robótica colaborativa es uno de los ámbitos de actualidad. Pero también es uno de los más interesantes en más de un sentido. ¿Cómo se comunican drones autónomos que colaboran para hacer una tarea? ¿Cómo son estos mensajes que es envían? ¿Qué pueden hacer que no lo podrían hacer solos? Estas son algunas de las preguntas que queremos responder con este proyecto. En este trabajo se presenta un diseño e implementación de dos drones terrestres que se comunican para colaborar entre ellos para resolver una tarea

Survey of Toxin–Antitoxin Systems in <i>Erwinia amylovora</i> Reveals Insights into Diversity and Functional Specificity

Toxin&#8211;antitoxin (TA) systems are diverse genetic modules with demonstrated roles in plasmid stability, stress management, biofilm formation and antibiotic persistence. However, relatively little is known about their functional significance in plant pathogens. In this study we characterize type II and IV TA systems in the economically important plant pathogen Erwinia amylovora. Hidden Markov Model (HMM) and BLAST-based programs were used to predict the identity and distribution of putative TA systems among sequenced genomes of E. amylovora and other plant-associated Erwinia spp. Of six conserved TA systems tested for function from E. amylovora, three (CbtA/CbeA, ParE/RHH and Doc/PhD) were validated as functional. CbtA was toxic to E. amylovora, but not to Escherichia coli. While the E. coli homolog of CbtA elicits the formation of lemon-shaped cells upon overexpression and targets cytoskeletal proteins FtsZ and MreB, E. amylovora CbtA led to cell elongation and did not interact with these cytoskeletal proteins. Phylogenetic analysis revealed that E. amylovora CbtA belongs to a distinct clade from the CbtA of pathogenic E. coli. This study expands the repertoire of experimentally validated TA systems in plant pathogenic bacteria, and suggests that the E. amylovora homolog of CbtA is functionally distinct from that of E. coli

Regulation of Effector Delivery by Type III Secretion Chaperone Proteins in Erwinia amylovora

Type III secretion (TTS) chaperones are critical for the delivery of many effector proteins from Gram-negative bacterial pathogens into host cells, functioning in the stabilization and hierarchical delivery of the effectors to the type III secretion system (TTSS). The plant pathogen Erwinia amylovora secretes at least four TTS effector proteins: DspE, Eop1, Eop3, and Eop4. DspE specifically interacts with the TTS chaperone protein DspF, which stabilizes the effector protein in the cytoplasm and promotes its efficient translocation through the TTSS. However, the role of E. amylovora chaperones in regulating the delivery of other secreted effectors is unknown. In this study, we identified functional interactions between the effector proteins DspE, Eop1, and Eop3 with the TTS chaperones DspF, Esc1 and Esc3 in yeast. Using site-directed mutagenesis, secretion, and translocation assays, we demonstrated that the three TTS chaperones have additive roles for the secretion and translocation of DspE into plant cells whereas DspF negatively affects the translocation of Eop1 and Eop3. Collectively, these results indicate that TTS chaperone proteins exhibit a cooperative behavior to orchestrate the effector secretion and translocation dynamics in E. amylovora

Dominance of Ciliophora and Chlorophyta Among Phyllosphere Protists of Solanaceous Plants

Phyllosphere microbiota play an important role in shaping plant health and function but most research has focused only on bacterial and fungal communities. As a result, little is known about the composition of diverse microeukaryotes in the phyllosphere, including protist predators and algae, or how they are affected by host species or cooccurring bacteria. Using universal eukaryotic primers and a peptide nucleic acid clamp to block amplification of the plant 18S ribosomal RNA gene, we profiled the phyllosphere and rhizosphere microbiomes of five solanaceous crop species grown in a field plot in Connecticut, United States. Phyllosphere communities of protists, like those of bacteria, were far less diverse and more variable than those of the rhizosphere. Phyllosphere samples contained hundreds of protist sequence variants from at least seven major eukaryotic lineages, of which one-fifth were not observed in bulk soil or rhizosphere samples. Phyllosphere samples were highly enriched for a few specific sequence variants representing green algae (Chlorophyta order Chlamydomonales) and ciliates (Ciliophora class Colpodea), while rhizospheres were dominated by protists from the phylum Cercozoa. Correlation analysis identified Sphingomonas spp. bacteria as central network hubs positively associated with protists in the phyllosphere and rhizosphere. These findings indicate that, although leaf surfaces host a highly variable protist community of limited diversity, certain ciliates and green algae may be well adapted for the phyllosphere habitat