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A new emerging disease of quinoa, quinoa basal stem rot (QBSR), has been recorded in Shanxi Province, China. Observed during the inflorescence emergence stage, the pathogen causes wilting, foliar chlorosis, leaf abscission and eventual death of quinoa. In this study, isolates were identified as Fusarium solani using morphology, molecular and phylogenetic analysis (using sequences of calmodulin, rDNA internal transcribed spacer region, RNA polymerase II B‐subunits RPB1 RPB1 and RPB2 RPB2, and translation elongation factor 1‐α), and pathogenicity analysis. Twenty‐seven isolates were classified into two different groups according to their morphological characteristics, and the mycelial growth rate of Group 2 was higher than that of Group 1 on six different media. The optimum growth temperature for both groups was 30°C and the highest mycelial growth rates were 9.2 and 10.0 mm/day, for Groups 1 and 2, respectively. The sporodochial conidia (SC) and aerial conidia (AC) germinated normally at 15–25°C and 10–40°C, respectively, and the width of SC and AC germ tubes were 1.4 and 2.2 μm. The lethal temperature for AC was 51°C for 20 min, and SC stopped germinating at 45°C. Pathogenicity tests of representative isolates showed that mycelia or conidia caused typical symptoms of QBSR on wounded basal stems of Chenopodium quinoa at 6 days postinoculation. The optimum temperature for the onset of QBSR was 30°C for both groups of isolates, and lesion lengths ranged from 5.4 to 5.9 cm. Knowledge of this pathogen will provide useful information for effective disease management to prevent its spread. [ABSTRACT FROM AUTHOR]

Choanephora rot of Chenopodium plants (CRC) was observed at the flowering stages in seven plantations of Shanxi Province, China. CRC had caused leaf, stem, and panicle neck rot of C. quinoa, panicle neck and stem rot of C. formosanum, and stem rot of C. album. Typical symptoms included water-soaked, rapid soft rotting, and abundant sporulation on the whole panicle necks, stems, and leaves. Based on morphological characteristics, phylogenetic analyses, and pathogenicity tests, the pathogens were identified as Choanephoraceae cucurbitarum. Sporangiola and sporangiospore of C. cucurbitarum germinated at 30 °C and were able to germinate by two h post-inoculation (hpi). The germination rates of sporangiola and sporangiospore significantly increased at 3 to 4 hpi, and the germination rates ranged from 91.53 to 97.67%. The temperature had a significant effect on the pathogenicity of C. cucurbitarum the optimum pathogenic temperatures for stems of C. quinoa, C. formosanum and C. album were 30 °C after one day post-inoculation. Choanephoraceae cucurbitarum could infect white and red quinoa panicle necks between 20 and 30 °C, and the average lesion lengths were 0.21 to 3.62 cm. Among the five tested fungicides (boscalid, dimethomorph, isopyrazam, propiconazole, and tebuconazole), isopyrazam showed higher sensitivity to sporangiola germination of C. cucurbitarum, with an EC50 value of 0.6550 μg/mL. Isopyrazam and tebuconazole strongly inhibited the sporangiospore germination of C. cucurbitarum, which showed EC50 values of 0.4406 and 0.3857 μg/mL. To our knowledge, the present study found for the first time that C. cucurbitarum is a pathogen causing panicle neck of C. formosanum and stem rot of C. formosanum and C. album, while CRC first appeared in the quinoa panicle necks, and gradually expanded to stems and leaves. [ABSTRACT FROM AUTHOR]

Quinoa panicle rot (QPR) is a novel disease that poses a significant threat to quinoa production in China. Typical symptoms on panicles include a film of pale pink, grey‐white, or dark brown mould on the grains during the grain‐filling stage. Furthermore, QPR causes quinoa grain discolouration, unfilling, and malformation. In total, 37 isolates were identified as belonging to three species: Trichothecium roseum (nine isolates), Alternaria alternata (12), and Fusarium citri (16) based on morphology, and phylogenetic and pathogenicity characterization. The present study shows for the first time that T. roseum, A. alternata, and F. citri are the pathogens responsible for QPR. An evaluation of the growth and germination rates revealed a significant difference among the three species, with T. roseum and F. citri isolates having higher fitness in warmer (25–30℃) and humid conditions (water activity ≥0.98). However, A. alternata preferred cooler (20–25℃) and more arid conditions, and germinated in a wide range of water activities (water activity of 0.90–1.00). Among the three species, T. roseum and F. citri are probably responsible for the pink and grey diseased grains in humid regions, and A. alternata for the black‐brown diseased grains in arid regions. Pathogenicity tests showed that all three species could infect the quinoa panicles. The results of this study provide a basis for the recognition and management of QPR. [ABSTRACT FROM AUTHOR]

Background: Shotgun metagenomics has been used clinically for diagnosing infectious diseases. However, most technical assessments have been limited to individual sets of reference standards, experimental workflows, and laboratories., Methods: A reference panel and performance metrics were designed and used to examine the performance of shotgun metagenomics at 17 laboratories in a coordinated collaborative study. We comprehensively assessed the reliability, key performance determinants, reproducibility, and quantitative potential., Findings: Assay performance varied significantly across sites and microbial classes, with a read depth of 20 millions as a generally cost-efficient assay setting. Results of mapped reads by shotgun metagenomics could indicate relative and intra-site (but not absolute or inter-site) microbial abundance., Interpretation: Assay performance was significantly impacted by the microbial type, the host context, and read depth, which emphasizes the importance of these factors when designing reference reagents and benchmarking studies. Across sites, workflows and platforms, false positive reporting and considerable site/library effects were common challenges to the assay's accuracy and quantifiability. Our study also suggested that laboratory-developed shotgun metagenomics tests for pathogen detection should aim to detect microbes at 500 CFU/mL (or copies/mL) in a clinically relevant host context (10^5 human cells/mL) within a 24h turn-around time, and with an efficient read depth of 20M., Funding: This work was supported by National Science and Technology Major Project of China (2018ZX10102001)., Competing Interests: Declaration of Competing Interest SM Xie, WJ Chen, JY Zhao, YL Wu, XF Meng, C Ouyang, Z Jiang, ZK Liang, HQ Tan, Y Fang, N Qin, YL Guan, and W Gai were employed by Vision Medicals Center for Infectious Diseases, BGI PathoGenesis Pharmaceutical Technology, Dalian GenTalker Clinical Laboratory, Guangzhou Sagene Biotech Co., Ltd., Guangzhou Kingmed Diagnostics, Hangzhou MatriDx Biotechnology Co., Ltd, Genskey Medical Technology, Co., Ltd., Guangzhou Darui Biotechnology, Co., Ltd., Hangzhou IngeniGen XunMinKang Biotechnology Co., Ltd., Dinfectome Inc, Realbio Genomics Institute, Hugobiotech Co., Ltd., WillingMed Technology (Beijing) Co., Ltd., respectively, outside the submitted work. WL Xing was employed by School of Medicine Tsinghua University and CapitalBio Technology Co., Ltd., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)