As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.
Animals ; Arabidopsis ; Brassica rapa ; Clone Cells ; Genome ; Methods ; Synteny*

A new species belonging to the genus Alternaria was isolated from the necrotic leaf spots of Brassica rapa subsp. pekinensis in Yuseong district, Daejeon, Korea. It is an occasional isolate, not an etiological agent, which is morphologically similar to A. broccoli-italicae, but differs in conidial size and conidiophore shape. Phylogenetic analysis using the sequence datasets of the internal transcribed spacer (ITS) region of the rDNA, glyceraldehyde-3-phosphate dehydrogenase (gpd), and plasma membrane ATPase genes showed that it is distantly related to A. broccoli-italicae and closely related to Alternaria species in the section Pseudoalternaria, which belonged to a clade basal to the section Infectoriae. Morphologically, the species is unique because it produces solitary conidia or conidial chains (two units), unlike the four members in the section Pseudoalternaria that produce conidia as short branched chains. It exhibits weak pathogenicity in the host plant. This report includes the description and illustration of A. brassicifolii as a new species.
Adenosine Triphosphatases ; Alternaria* ; Brassica rapa* ; Brassica* ; Brassicaceae ; Cell Membrane ; Dataset ; DNA, Ribosomal ; Korea* ; Oxidoreductases ; Plants ; Spores, Fungal ; Virulence

OBJECTIVETo explore the physical and behavioral, microscopic and chemical characteristic traits of Brassica rapa, and supply scientific bases for establishing its quality control standard.

METHODMicroscopic identification method was adopted to observe the microscopic characters of ten batches crude drugs, the contents of water, impurity, total ash, insoluble acid ash and extractives were detected based on Chinese Pharmacopoeia (2010) , and the oil constituents were analyzed by gas chromatography-mass spectrometry (GC-MS).

RESULTThe microscopic traits were cotyledon, palisade cells, non-glandular hairs and inner endosperm, while the palisade cells, cotyledon cells and non-glandular hairs existed in its powders. The results confirmed the contents of water, impurity, total ash and insoluble acid ash should be fewer than 6%, 4.5%, 6%, 0.7%, while the content of extractives should exceed 11%. The main oil compounds in it were erucic acid, oleic acid and gamma-sitosterol through the GC-MS analysis.

CONCLUSIONThe experimental methods were accurate and reliable, and the indexes and parameters may be thought as the quality standards for B. rapa.

Brassica rapa ; chemistry ; growth & development ; Drugs, Chinese Herbal ; analysis ; standards ; Quality Control ; Seeds ; chemistry ; growth & development

Under different red (R):blue (B) photon flux ratios, the growth performance of rapeseed (Brassica napus L.) is significantly different. Rapeseed under high R ratios shows shade response, while under high B ratios it shows sun-type morphology. Rapeseed under monochromatic red or blue light is seriously stressed. Transcriptomic and proteomic methods were used to analyze the metabolic pathway change of rapeseed (cv. "Zhongshuang 11") leaves under different R:B photon flux ratios (including 100R:0B%, 75R:25B%, 25R:75B%, and 0R:100B%), based on digital gene expression (DGE) and two-dimensional gel electrophoresis (2-DE). For DGE analysis, 2054 differentially expressed transcripts (|log₂(fold change)|≥1, q<0.005) were detected among the treatments. High R ratios (100R:0B% and 75R:25B%) enhanced the expression of cellular structural components, mainly the cell wall and cell membrane. These components participated in plant epidermis development and anatomical structure morphogenesis. This might be related to the shade response induced by red light. High B ratios (25R:75B% and 0R:100B%) promoted the expression of chloroplast-related components, which might be involved in the formation of sun-type chloroplast induced by blue light. For 2-DE analysis, 37 protein spots showed more than a 2-fold difference in expression among the treatments. Monochromatic light (ML; 100R:0B% and 0R:100B%) stimulated accumulation of proteins associated with antioxidation, photosystem II (PSII), DNA and ribosome repairs, while compound light (CL; 75R:25B% and 25R:75B%) accelerated accumulation of proteins associated with carbohydrate, nucleic acid, amino acid, vitamin, and xanthophyll metabolisms. These findings can be useful in understanding the response mechanisms of rapeseed leaves to different R:B photon flux ratios.
Brassica napus/radiation effects* ; Brassica rapa/radiation effects* ; Carbon/chemistry* ; Chloroplasts/radiation effects* ; Computational Biology ; Electrophoresis, Gel, Two-Dimensional ; Gene Expression Regulation, Plant/radiation effects* ; Image Processing, Computer-Assisted ; Light ; Mass Spectrometry ; Metabolic Networks and Pathways ; Nitrogen/chemistry* ; Photons ; Photosystem II Protein Complex/genetics* ; Plant Leaves/radiation effects* ; Plant Proteins/genetics* ; Proteome ; Ribosomes ; Transcription, Genetic ; Transcriptome

AIMTo investigate the effect of brassinolide, a plant growth modulator, on multidrug resistance (MDR) of human T lymphoblastoid cell line CCRF-VCR 1000 which was obtained by progressively addition of vincristine (VCR) to sensitive CCRF-CEM cells, and to explore preliminarily the mechanism of reversing action.

METHODSMTT method was used to detect the resistant factor of resistant cell line and the reversing fold after addition of brassinolide. The intracellular accumulation of rhodamine 123, a fluorescent dye transported by P-glycoprotein was detected by flow cytometry, the catalytic activity of topoisomerase II was assessed by Sulliven method to find the effect of brassinolide on resistance. The protein expression of p53 was measured using Western blotting in the sensitive cells and resistant cells to explore the effect of brassinolide.

RESULTSThe resistant factors of CCRF-VCR cells on adriamycin, VP-16 and VCR are respectively as 153.1, 55.9 and 8123.1 folds comparing to the sensitive cell line CCRF-CEM. After treatment of brassinolide under the concentration of 0.001 - 10.0 microg x mL(-1), the resistance of CCRF-VCR was reversed partly with the reversing folds respectively as 4.4 - 11.6. The intracellular accumulation of rhodamine 123 was significantly reduced in the resistant cells. After treatment of brassinolide, the accumulation increased, the level of fluorescent dye was situated between resistant cells and sensitive cells. No alteration of the catalytic activity of topoisomerase II was found among three groups. The level of protein expression of p53 in resistant cells was higher than that of sensitive cells. After brassinolide treatment, the expression of p53 in CCRF-VCR cells restored to the level of sensitive cells.

CONCLUSIONBrassinolide could effectively reverse the resistance of CCRF-VCR cells by inhibiting the effusion of drug transported by P-glucoprotein. To down regulate the abnormal expression of p53 maybe one of the mechanisms of reversing MDR for brassinolide.

Brassica rapa ; chemistry ; Brassinosteroids ; Cell Line, Tumor ; drug effects ; Cholestanols ; isolation & purification ; pharmacology ; Drug Resistance, Multiple ; drug effects ; Drug Resistance, Neoplasm ; drug effects ; Humans ; Leukemia, T-Cell ; metabolism ; pathology ; Plant Growth Regulators ; pharmacology ; Pollen ; chemistry ; Steroids, Heterocyclic ; isolation & purification ; pharmacology ; Tumor Suppressor Protein p53 ; metabolism