MicroRNA482/2118 is lineage-specifically involved in gibberellin signalling via the regulation of GID1 expression by targeting noncoding PHAS genes and subsequently instigated phasiRNAs.

MicroRNA482/2118 (miR482/2118) is a 22-nt miRNA superfamily, with conserved functions in disease resistance and plant development. It usually instigates the production of phased small interfering RNAs (phasiRNAs) from its targets to expand or reinforce its silencing effect. Using a new high-quality reference genome sequence and comprehensive small RNA profiling, we characterized a newly evolved regulatory pathway of miR482/2118 in litchi. In this pathway, miR482/2118 cleaved a novel noncoding trans-acting gene (LcTASL1) and triggered phasiRNAs to regulate the expression of gibberellin (GA) receptor gene GIBBERELLIN INSENSITIVE DWARF1 (GID1) in trans; another trans-acting gene LcTASL2, targeted by LcTASL1-derived phasiRNAs, produced phasiRNAs as well to target LcGID1 to reinforce the silencing effect of LcTASL1. We found this miR482/2118-TASL-GID1 pathway was likely involved in fruit development, especially the seed development in litchi. In vivo construction of the miR482a-TASL-GID1 pathway in Arabidopsis could lead to defects in flower and silique development, analogous to the phenotype of gid1 mutants. Finally, we found that a GA-responsive transcription factor, LcGAMYB33, could regulate LcMIR482/2118 as a feedback mechanism of the sRNA-silencing pathway. Our results deciphered a lineage-specifically evolved regulatory module of miR482/2118, demonstrating the high dynamics of miR482/2118 function in plants.

sRNAminer: A multifunctional toolkit for next-generation sequencing small RNA data mining in plants.

Small RNAs (sRNAs), found extensively in plants, play an essential role in plant growth and development. Although various sRNA analysis tools have been developed for plants, the use of most of them depends on programming and command-line environments, which is a challenge for many wet-lab biologists. Furthermore, current sRNA analysis tools mostly focus on the analysis of certain type of sRNAs and are resource-intensive, normally demanding an immense amount of time and effort to learn the use of numerous tools or scripts and assemble them into a workable pipeline to get the final results. Here, we present sRNAminer, a powerful stand-alone toolkit with a user-friendly interface that integrates all common functions for the analysis of three major types of plant sRNAs: microRNAs (miRNAs), phased small interfering RNAs (phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). We constructed a curated or "golden" set of MIRNA and PHAS loci, which was used to assess the performance of sRNAminer in comparison to other existing tools. The results showed that sRNAminer outperformed these tools in multiple aspects, highlighting its functionality. In addition, to enable an efficient evaluation of sRNA annotation results, we developed Integrative Genomics Viewer (IGV)-sRNA, a modified genome browser optimized from IGV and we incorporated it as a functional module in sRNAminer. IGV-sRNA can display a wealth of sRNA-specific features, enabling a more comprehensive understanding of sRNA data. sRNAminer and IGV-sRNA are both platform-independent software that can be run under all operating systems. They are now freely available at https://github.com/kli28/sRNAminer and https://gitee.com/CJchen/IGV-sRNA.

Laccase Directed Lignification Is One of the Major Processes Associated With the Defense Response Against Pythium ultimum Infection in Apple Roots.

Apple replant disease (ARD), incited by a pathogen complex including Pythium ultimum, causes stunted growth or death of newly planted trees at replant sites. Development and deployment of resistant or tolerant rootstocks offers a cost-effective, ecologically friendly, and durable approach for ARD management. Maximized exploitation of natural resistance requires integrated efforts to identify key regulatory mechanisms underlying resistance traits in apple. In this study, miRNA profiling and degradome sequencing identified major miRNA pathways and candidate genes using six apple rootstock genotypes with contrasting phenotypes to P. ultimum infection. The comprehensive RNA-seq dataset offered an expansive view of post-transcriptional regulation of apple root defense activation in response to infection from P. ultimum. Several pairs of miRNA families and their corresponding targets were identified for their roles in defense response in apple roots, including miR397-laccase, miR398-superoxide dismutase, miR10986-polyphenol oxidase, miR482-resistance genes, and miR160-auxin response factor. Of these families, the genotype-specific expression patterns of miR397 indicated its fundamental role in developing defense response patterns to P. ultimum infection. Combined with other identified copper proteins, the importance of cellular fortification, such as lignification of root tissues by the action of laccase, may critically contribute to genotype-specific resistance traits. Our findings suggest that quick and enhanced lignification of apple roots may significantly impede pathogen penetration and minimize the disruption of effective defense activation in roots of resistant genotypes. The identified target miRNA species and target genes consist of a valuable resource for subsequent functional analysis of their roles during interaction between apple roots and P. ultimum.

sRNAanno-a database repository of uniformly annotated small RNAs in plants.

Small RNAs (sRNAs) are essential regulatory molecules, and there are three major sRNA classes in plants: microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Excluding miRNAs, the other two classes are not well annotated or available in public databases for most sequenced plant genomes. We performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly available. The results are available via an online repository called sRNAanno ( www.plantsRNAs.org ). Compared with other public plant sRNA databases, we obtained was much more miRNA annotations, which are more complete and reliable because of the consistent and highly stringent criteria used in our miRNA annotations. sRNAanno also provides free access to genomic information for >22,721 PHAS loci and >22 million hc-siRNA loci annotated from these 143 plant species. Both miRNA and PHAS loci can be easily browsed to view their main features, and a collection of archetypal trans-acting siRNA 3 (TAS3) genes were annotated separately for quick access. To facilitate the ease of sRNA annotation, sRNAanno provides free service for sRNA annotations to the community. In summary, the sRNAanno database is a great resource to facilitate genomic and genetic research on plant small RNAs.

Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.).

The CRISPR/Cas9 system is an efficient genome editing tool that possesses the outstanding advantages of simplicity and high efficiency. Genome-wide identification and specificity analysis of editing sites is an effective approach for mitigating the risk of off-target effects of CRISPR/Cas9 and has been applied in several plant species but has not yet been reported in pepper. In present study, we first identified genome-wide CRISPR/Cas9 editing sites based on the 'Zunla-1' reference genome and then evaluated the specificity of CRISPR/Cas9 editing sites through whole-genome alignment. Results showed that a total of 603,202,314 CRISPR/Cas9 editing sites, including 229,909,837 (~38.11%) NGG-PAM sites and 373,292,477 (~61.89%) NAG-PAM sites, were detectable in the pepper genome, and the systematic characterization of their composition and distribution was performed. Furthermore, 29,623,855 highly specific NGG-PAM sites were identified through whole-genome alignment analysis. There were 26,699,38 (~90.13%) highly specific NGG-PAM sites located in intergenic regions, which was 9.13 times of the number in genic regions, but the average density in genic regions was higher than that in intergenic regions. More importantly, 34,251 (~96.93%) out of 35,336 annotated genes exhibited at least one highly specific NGG-PAM site in their exons, and 90.50% of the annotated genes exhibited at least 4 highly specific NGG- PAM sites, indicating that the set of highly specific CRISPR/Cas9 editing sites identified in this study was widely applicable and conducive to the minimization of the off-target effects of CRISPR/Cas9 in pepper.

Transport and percolation theory in weighted networks.

We study the distribution P(sigma) of the equivalent conductance sigma for Erdös-Rényi (ER) and scale-free (SF) weighted resistor networks with N nodes. Each link has conductance g triple bond e-ax, where x is a random number taken from a uniform distribution between 0 and 1 and the parameter a represents the strength of the disorder. We provide an iterative fast algorithm to obtain P(sigma) and compare it with the traditional algorithm of solving Kirchhoff equations. We find, both analytically and numerically, that P(sigma) for ER networks exhibits two regimes: (i) A low conductance regime for sigmae-apc in which we find that P(sigma) has strong N dependence and scales as P(sigma) approximately f(sigma,apc/N1/3) . For SF networks with degree distribution P(k) approximately k-lambda, kmin

[A novel catalysis kinetics fluorimetry system for the determination of eliminating ratio of Chinese traditional medicine for *OH].

Benzoic acid with weak fluorescence may react on *OH, and then products with intense fluorescence are made. Extractives of Chinese traditional medicine may eliminate *OH in solution, and reduce the amounts of the products. Then, the increased level of fluorescence of the products in solution will be lowered. Based on this principle, a novel catalysis kinetics fluorimetry system for the determination of eliminating ratio of Chinese traditional medicine for *OH was developed. When the concentration of traditional Chinese herbal drugs was 4.0 mg (dry weight) x mL(-1), the eliminating ratios of Viola yedoensis, Atrctylodes chinensis and Paeonia veitchii were 60.8%, 40.1% and 94.3%, respectively. The results obtained by this method are in good agreement with those obtained by spectrophotometry.

[Synthesis and luminescence spectrum of trinuclear copper(I) complex].

The novel luminescent trinuclear copper( I ) complex [Cu3 (dppm)3 (NO3) (OH)] (NO3) has been obtained by treating binuclear copper(I) [Cu(dppm) (NO3)]2 with sodium tetraphenyl boron (dppm = Ph2 PCH2 PPh2). The complex was characterized by physico-chemical and spectroscopic methods. The title complex exhibits photoluminescence behavior at room temperature.