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)

Jasmonic acid (JA) and its precursors and dervatives, referred as jasmonates (JAs) are important molecules in the regulation of many physiological processes in plant growth and development, and especially the mediation of plant responses to biotic and abiotic stresses. JAs biosynthesis, perception, transport, signal transduction and action have been extensively investigated. In this review, we will discuss the initiation of JA signaling with a focus on environmental signal perception and transduction, JA biosynthesis and metabolism, transport of signaling molecules (local transmission, vascular bundle transmission, and airborne transportation), and biological function (JA signal receptors, regulated transcription factors, and biological processes involved).

https://www.mdpi.com/1422-0067/20/10/2479/pdf

Jasmonic Acid Signaling Pathway in Plants

The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance

MYB transcription factors (TFs), as one of the largest gene families in plants, play important roles in multiple biological processes, such as plant growth and development, cell morphology and pattern building, physiological activity metabolism, primary and secondary metabolic reactions, and responses to environmental stresses. The function of MYB TFs in crops has been widely studied, but few studies have been done on medicinal plants. In this review, we summarized the MYB TFs that play important roles in secondary metabolism and emphasized the possible mechanisms underlying how MYB TFs are regulated at the protein, posttranscriptional, and transcriptional levels, as well as how they regulate the downstream target gene networks related to secondary metabolism in plants, especially in medicinal plants.

https://www.mdpi.com/2079-7737/9/3/61/pdf

MYB Transcription Factors as Regulators of Secondary Metabolism in Plants.

Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots

Summary
Little is known about the molecular mechanism of the R2R3-MYB transcriptional repressors involved in plant phenylpropanoid metabolism. Here, we describe one R2R3-type MYB repressor, FtMYB11 from Fagopyrum tataricum. It contains the SID-like motif GGDFNFDL and it is regulated by both the importin protein ‘Sensitive to ABA and Drought 2’ (SAD2) and the jasmonates signalling cascade repressor JAZ protein.
Yeast two hybrid and bimolecular fluorescence complementation assays demonstrated that FtMYB11 interacts with SAD2 and FtJAZ1. Protoplast transactivation assays demonstrated that FtMYB11 acts synergistically with FtSAD2 or FtJAZ1 and directly represses its target genes via the MYB-core element AATAGTT.
Changing the Asp122 residue to Asn in the SID-like motif results in cytoplasmic localization of FtMYB11 because of loss of interaction with SAD2, while changing the Asp126 residue to Asn results in the loss of interaction with FtJAZ1. Overexpression of FtMYB11or FtMYB11D126N in F. tataricum hairy roots resulted in reduced accumulation of rutin, while overexpression of FtMYB11D122N in hairy roots did not lead to such a change.
The results indicate that FtMYB11 acts as a regulator via interacting with FtSAD2 or FtJAZ1 to repress phenylpropanoid biosynthesis, and this repression depends on two conserved Asp residues of its SID-like motif.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.14692

FtSAD2 and FtJAZ1 regulate activity of the FtMYB11 transcription repressor of the phenylpropanoid pathway in Fagopyrum tataricum.

Buckwheat is a nutritional and economically crop belonging to Polygonaceae, Fagopyrum. To better understand the mutation patterns and evolution trend in the chloroplast (cp) genome of buckwheat, and found sufficient number of variable regions to explore the phylogenetic relationships of this genus, two complete cp genomes of buckwheat including Fagopyrum dibotrys (F. dibotrys) and Fagopyrum luojishanense (F. luojishanense) were sequenced, and other two Fagopyrum cp genomes were used for comparative analysis. After morphological analysis, the main difference among these buckwheat were height, leaf shape, seeds and flower type. F. luojishanense was distinguishable from the cultivated species easily. Although the F. dibotrys and two cultivated species has some similarity, they different in habit and component contents. The cp genome of F. dibotrys was 159,320 bp while the F. luojishanense was 159,265 bp. 48 and 61 SSRs were found in F. dibotrys and F. luojishanense respectively. Meanwhile, 10 highly variable regions among these buckwheat species were located precisely. The phylogenetic relationships among four Fagopyrum species based on complete cp genomes was showed. The results suggested that F. dibotrys is more closely related to Fagopyrum tataricum. These data provided valuable genetic information for Fagopyrum species identification, taxonomy, phylogenetic study and molecular breeding.

/pdf/comparative-analysis-of-four-buckwheat-species-based-on-3s769w3zio.pdf

Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences.

The history of Chinese buckwheat cultivation goes back to 1st and 2nd centuries BC. After thousands of years of cultivation and evolution, cultivated buckwheat is not only widely spread in China, but has also formed a number of varieties. Southwest China especially has plentiful resources of wild-type buckwheat, which has drawn the attention of the wider world. Until now, 27 buckwheat species have been named and reported in China, including 2 cultivated species and 25 wild species. They are widely distributed in Sichuan, Yunnan, Guizhou, and Tibet, in the southwest of China, because of the complicated geographical environments of these regions, which have been described as the treasure of plant resources. In the future, the relationship between buckwheat species and their genetic diversity will be further clarified, and there will be a sizable breakthrough in the area of breeding new varieties and exploiting new buckwheat resources.

Germplasm Resources of Buckwheat in China

Fagopyrum longzhoushanense (Polygonaceae) is here described and illustrated as a new species from Longzhoushan (Puge County, Sichuan Province, China) on the basis of morphological, caryological and molecular analyses. The new species is morphologically similar to F. gracilipes from which it differs in having densely pubescent or villose parts, thicker and red-brown stems and branches, dense nodes, rugulose and small postulate leaf blade on the surface, stamens longer than pistils. Another similar species is F. densovillosum from which F. longzhoushanense differs by the winged and greater achenes, and the stamens which are longer than the pistils. From the caryioogical point of view F. longzhoushanense is a diploid species with 2n=2x=16 and a karyotype of 16 metacentric chromosomes, while F. gracilipes is tetraploid, 4n=4x=32, with a karyotype of 30 metacentric and 2 submetacentric chromosomes. The results of molecular marker analysis ( matK ) also highlight the distinction of the new species.

Fagopyrum longzhoushanense , a new species of Polygonaceae from Sichuan, China

Buckwheat accumulates abundant flavonoids, which exhibit excellent health-promoting value. Flavonoids biosynthesis is mediated by a variety of phytohormones, among which jasmonates (JAs) induce numerous transcription factors, taking part in regulation of flavonoids biosynthesis genes. However, some transcriptional repressors appeared also induced by JAs. How these transcriptional repressors coordinately participate in JA signaling remains unclear. Here, we found that the disruption of the GCC-box in FtF3H promoter was associated with flavonoids accumulation in Tartary buckwheat. Further, our study illustrated that the nucleus-localized FtERF-EAR3 could inhibit FtF3H expression and flavonoids biosynthesis through binding the GCC-box in the promoter of FtF3H. The JA induced FtERF-EAR3 gene expression while facilitating FtERF-EAR3 protein degradation via the FtBPM3-dependent 26S proteasome pathway. Overall, these results illustrate a precise modulation mechanism of JA-responsive transcription suppressor participating in flavonoid biosynthesis, and will further help to improve the efficiency of flavonoids biosynthesis in Tartary buckwheat.

Mengqi Ding

Papers

FtSAD2 and FtJAZ1 regulate activity of the FtMYB11 transcription repressor of the phenylpropanoid pathway in Fagopyrum tataricum.

Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences.

Germplasm Resources of Buckwheat in China

Fagopyrum longzhoushanense , a new species of Polygonaceae from Sichuan, China

JA-induced FtBPM3 accumulation promotes FtERF-EAR3 degradation and rutin biosynthesis in Tartary buckwheat.