The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The NON EXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and related NPR1-like proteins are a functionally similar, yet surprisingly diverse family of transcription co-factors. Initially, NPR1 in Arabidopsis was identified as a positive regulator of systemic acquired resistance (SAR), paralogs NPR3 and NPR4 were later shown to be negative SAR regulators. The mechanisms involved have been the subject of extensive research and debate over the years, during which time a lot has been uncovered. The known roles of this protein family have extended to include influences over a broad range of systems including circadian rhythm, endoplasmic reticulum (ER) resident proteins and the development of lateral organs. Recently, important advances have been made in understanding the regulatory relationship between members of the NPR1-like protein family, providing new insight regarding their interactions, both with each other and other defense-related proteins. Most importantly the influence of salicylic acid (SA) on these interactions has become clearer with NPR1, NPR3 and NPR4 being considered bone fide SA receptors. Additionally, post-translational modification of NPR1 has garnered attention during the past years, adding to the growing regulatory complexity of this protein. Furthermore, growing interest in NPR1 overexpressing crops has provided new insights regarding the role of NPR1 in both biotic and abiotic stresses in several plant species. Given the wealth of information, this review aims to highlight and consolidate the most relevant and influential research in the field to date. In so doing, we attempt to provide insight into the mechanisms and interactions which underly the roles of the NPR1-like proteins in plant disease responses.

/pdf/the-nonexpressor-of-pathogenesis-related-genes-1-npr1-and-62yy1ecmez.pdf

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and related family: mechanistic insights in plant disease resistance.

The NPR1 (NONEXPRESSOR OF PATHOGENESIS RELATED GENES1) gene has a central role in the long-lasting, broad-spectrum defense response known as systemic acquired resistance (SAR). When overexpressed in a transgenic context in Arabidopsis thaliana, this gene enhances resistance to a number of biotic and abiotic stresses. Its position as a key regulator of defense across diverse plant species makes NPR1 a strong candidate gene for genetic engineering disease and stress tolerance into other crops. High-value horticultural crops face many new challenges from pests and pathogens, and their emergence exceeds the pace of traditional breeding, making the application of NPR1-based strategies potentially useful in fruit and vegetable crops. However, plants overexpressing NPR1 occasionally present detrimental morphological traits that make its application less attractive. The practical utility of NPR-based approaches will be a balance of resistance gains versus other losses. In this review, we summarize the progress on the understanding of NPR1-centered applications in horticultural and other crop plants. We also discuss the effect of the ectopic expression of the A. thaliana NPR1 gene and its orthologs in crop plants and outline the future challenges of using NPR1 in agricultural applications.

/pdf/npr1-as-a-transgenic-crop-protection-strategy-in-qwvigtnozu.pdf

NPR1 as a transgenic crop protection strategy in horticultural species

Termitomyces is a genus of edible mushrooms commonly consumed in Africa and Asia among the mushrooms collected from the wild. Termitomyces mushrooms grow as symbionts in the termite nests, where they produce various enzymes to help termites digest lignocellulosic substrates. Many species of Termitomyces are used by different ethnic groups with ethnomedicinal knowledge. Bioactive components that Termitomyces mushrooms contain have potential uses as antioxidants, immunomodulators, antitumors, and antimicrobials. Termitomyces also has a potential for treating neurodegenerative disorders. Here, we review the bioactive compounds from Termitomyces species that have been isolated and assayed in vitro and/or in vivo for their medicinal properties.

Medicinal components in Termitomyces mushrooms

Salicylic acid (SA) plays pivotal role in plant defense against biotrophic and hemibiotrophic pathogens. Tremendous progress has been made in the field of SA biosynthesis and SA signaling pathways over the past three decades. Among the key immune players in SA signaling pathway, NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) functions as a master regulator of SA-mediated plant defense. The function of NPR1 as an SA receptor has been controversial; however, after years of arguments among several laboratories, NPR1 has finally been proven as one of the SA receptors. The function of NPR1 is strictly regulated via post-translational modifications and transcriptional regulation that were recently found. More recent advances in NPR1 biology, including novel functions of NPR1 and the structure of SA receptor proteins, have brought this field forward immensely. Therefore, based on these recent discoveries, this review acts to provide a full picture of how NPR1 functions in plant immunity and how NPR1 gene and NPR1 protein are regulated at multiple levels. Finally, we also discuss potential challenges in future studies of SA signaling pathway.

Characterization of LhSorTGA2, a novel TGA2-like protein that interacts with LhSorNPR1 in oriental hybrid lily Sorbonne.

The non-expressor of the pathogenesis-related genes 1 (NPR1) is a master regulator in defense signaling of plants and plays a key role in basal and systemic acquired resistance. In this study, we isolated a NPR1-like gene from the oriental hybrid lily ‘Sorbonne’ (designated as LhSorNPR1) using rapid amplification of cDNA ends (RACE). The open reading frame of LhSorNPR1 consisted of 1854 bp, encoding a protein of 617 amino acids. Multiple sequence alignment revealed that LhSorNPR1 shares high similarity to NPR1-like proteins and characteristics of the BTB/POZ domain and ankyrin repeats. A comparison between the intron/exon organization of LhSorNPR1 and orthologs from other plant species demonstrated that NPR1 genomic fragments (including LhSorNPR1) are all composed of 4 exons and 3 introns. We also identified sequence motifs involved in hormone response and binding sites for RAV1 proteins and WRKY transcription factors through the prediction of cis-regulatory elements in the LhSorNPR1 promoter. Our gene expression analysis showed that LhSorNPR1 transcript levels significantly differed in various tissues, and that LhSorNPR1 expressions were induced by sodium salicylate, ethephon, and methyl jasmonate. Furthermore, we transformed LhSorNPR1 into Col-0 wild-type Arabidopsis to conduct function analysis, and we observed enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 in the Arabidopsis expressing LhSorNPR1 gene. The enhanced disease resistance of LhSorNPR1 expressing plants could correlate to elevated expression levels in pathogenesis-related genes (PR1, PR2, and PR5) in vivo.

Overexpression of LhSorNPR1, a NPR1-like gene from the oriental hybrid lily ‘Sorbonne’, conferred enhanced resistance to Pseudomonas syringae pv. tomato DC3000 in Arabidopsis

Ribes odoratum, commonly known as clove currant, is a perennial deciduous shrub noted for its long-lasting fragrant flowers and edible fruits. Owing to its ornamental values, this species has been widely used in city gardening and urban landscaping. Here, the complete cp genome of R. odoratum was de novo assembled for the first time. The plastome is 157,152 bp in length, with a GC content of 38.2%. The cp genome featured a typical quadripartite structure, consisting of a pair of inverted repeat regions of 25,961 bp, separated by a large single copy region of 86,896 bp, and a small single copy region of 18,333 bp. A total of 131 genes were annotated in the plastome, including 86 protein coding genes, 37 tRNA genes, and 8 rRNA genes. 56 SSRs were identified, among which, 82.35% were located in the intergenic regions. A strong A/T bias in base composition was observed in these cpSSRs. In addition, 49 repeats of different sizes and types were also found in the plastome. Through comparison, seven divergence hotspots were identified between the cp genomes of R. odoratum and R. fasciculatum var. chinense. Sequences of these divergent regions could be developed as potential markers for species delimitation in further studies. We re-investigated the relationship aomong 32 Saxifragales species through plastome-based phylogenywhich revealed that R. odoratum as a sister of R. fasciculatum var. chinense. Thus, our study provides genomic resources and valuable reference for marker development and phylogenomics in Ribes.

Sequencing and comparative analysis of the chloroplast genome of Ribes odoratum provide insights for marker development and phylogenetics in Ribes

Prunus triloba var plena, also known as flowering plum, is a perennial deciduous shrub admired for its brilliant pink-purple blooms Chloroplast (cp) DNA is highly conserved in structure and gene arrangement, making cp genomic data valuable resources for species delimitation and phylogenetics The cp genome of P triloba var plena was de novo assembled with the aim of developing cp-derived molecular markers and deepening the understanding of phylogenetic relationship among Prunus species The complete cp genome was 158,022 bp in length, with a GC content of 368% The plastome featured a typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions of 26,379 bp, separated by a large single copy (LSC) region of 86,242 bp, and a small single copy (SSC) region of 19,022 bp The cp genome encoded 134 genes, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes A total of 59 simple sequence repeat (SSR) were identified, 68% of which were located in the intergenic regions An obvious A/T bias was observed in the majority of SSRs detected Besides, 48 repeats in different sizes and types were detected These repeats, together with SSRs and the divergence hotspots detected, could serve as markers facilitating species discrimination and evolutionary research in Prunus Using plastome sequences, we re-investigated the phylogenetic relationship among 32 Prunus species These species explicitly clustered into three monophyletic clades, among which P triloba var plena was closely related to species in the subgenera Amygdalus and Prunus

The complete chloroplast genome of Prunus triloba var. plena and comparative analysis of Prunus species: genome structure, sequence divergence, and phylogenetic analysis

Sorbaria kirilowii is a deciduous perennial admired for its showy white blossoms. Though of importance for horticultural purposes, the plastomic study concerning this species is still lacking. Here, the plastome of S. kirilowii was de novo assembled using the high-throughput sequencing data. The complete plastome assembly of S. kirilowii was 160,810 bp in length, with a GC content of 36.03%. It featured a typical quadripartite structure, containing a pair of inverted repeats (IRs; 26,338 bp) separated by a large single-copy (LSC; 88,762 bp) and a small single-copy (SSC, 19,372 bp). In total, 132 genes were annotated in the plastome, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Furthermore, 63 SSRs, most of which were AT-rich, were identified in the cp genome of S. kirilowii. 71.7% of the cpSSRs were shown to be located in the intergenic regions. In addition, 49 repeats of varying sizes and types were also identified in the plastome. Through comparison, eight divergence hotspots were identified between the plastome of S. kirilowii and S. sorbifolia var. stellipila. These variable regions could potentially be developed into molecular markers for species delimitation or phylogenetics in future studies. We re-investigated the relationship among 17 Rosaceae species using the plastomic sequences, and S. kirilowii was shown to be a sister to S. sorbifolia var. stellipila. Overall, this study provides plastomic resources which could facilitate marker development and phylogenomics of Rosaceae.

The complete plastome of Sorbaria kirilowii: genome structure, comparative analysis, and phylogenetic implications.

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