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Dickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae), causing soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deployable loop-mediated isothermal amplification (LAMP) assay using a unique genomic region, present exclusively in D. fangzhongdai. Multiple genomes of D. fangzhongdai, and other species of Dickeya, Pectobacterium and unrelated genera were used for comparative genomic analyses to identify an exclusive and conserved target sequence from the major facilitator superfamily (MFS) transporter gene region. This gene region had broad detection capability for D. fangzhongdai and thus was used to design primers for endpoint PCR and LAMP assays. In-silico validation showed high specificity with D. fangzhongdai genome sequences available in the NCBI GenBank genome database as well as the in-house sequenced genome. The specificity of the LAMP assay was determined with 96 strains that included all Dickeya species and Pectobacterium species as well as other closely related genera, and 5 hosts; no false positives or false negatives were detected. The detection limit of the assay was determined by performing four sensitivity assays with 10-fold serially diluted purified genomic DNA of D. fangzhongdai with and without the presence of crude host extract (taro, orchid, and onion). The detection limit for all sensitivity assays was 100 fg (18–20 genome copies) with no negative interference by host crude extracts. The assays were performed by five independent operators (blind test) and on three instruments (Rotor-Gene, thermocycler and dry bath); the assay results were concordant. The assay consistently detected the target pathogen from artificially inoculated and naturally infected host samples. The developed assay is highly specific for D. fangzhongdai and has applications in routine diagnostics, phytosanitary and seed certification programs, and epidemiological studies.

Colletotrichum scovillei is a virulent pathogen and the dominant species causing anthracnose of chili pepper in many Asian countries. Three strains of this pathogen, Coll-524, Coll-153 and Coll-365, show varied virulence on chili pepper fruit. Among the three strains, Coll-365 showed significant defects in growth and virulence. To decipher the genetic variations among these strains and identify genes contributing to growth and virulence, in this study, comparative genomic analysis and gene transformation to verify gene function were applied. The genomes of the three strains were sequenced and Coll-524 had 1.3% and 1.5% more genes than Coll-153 and Coll-365, respectively. Compared to Coll-524 and Coll-153, Coll-365 had numerous gene losses including 33 effector genes that are distributed in different scaffolds and a cluster of 14 genes in a 34-kb genomic fragment. Through gene transformation, three genes in the 34-kb fragment were identified to have functions in growth and/or virulence of C. scovillei. Gene 15019 encoding a protein related to phospholipase A2-activating protein enhanced the growth of Coll-365. A combination of 15019 with one transcription factor gene 15022 and one C6 zinc finger domain-containing protein gene 15029 was found to enhance the pathogenicity of Coll-365. Introduction of gene 15215, which encodes a LysM domain-containing protein, into Coll-365 caused a reduction in the germination rate of Coll-365. In conclusion, the higher virulent strain Coll-524 had more genes and encoded more pathogenicity related proteins and transposable elements than the other two strains, which may contribute to the high virulence of Coll-524. In addition, the absence of the 34-kb fragment plays a critical role in the defects of growth and virulence of strain Coll-365.Author SummaryColletotrichum scovillei is a highly virulent and dominant pathogen causing anthracnose of chili that leads to significant economic loss in chili production in many Asia countries. In this study we focus on finding the gene differences of three C. scovillei strains with different pathogenicity in chili pepper infection and verifying the function of some genes in the lowest virulence strain. We sequenced them and did gene annotation and genome comparison. We setup a simple mathematical method to identify gene variations between strong and weak virulence strains. Our results show that the lowest virulence strain has less pathogenicity-related genes. We also found that the absence of 14 genes in a compact genomic fragment was part of the reason of growth and virulence defect of the lowest virulence strain. We identified four genes that play roles on fungal growth and/or virulence on chili pepper. We also found a group of effector genes that specifically appear in species collected form infected chili in C. acutatum species complex. Our research provides detailed information for why the three strains have different virulence on chili pepper.

Transportation safety has been widely discussed for avoiding forward collisions. The broad concept of remote sensing can be applied to detect the front of vehicles without contact. The traditional Haar features use adjacent rectangular areas for many ordinary vehicle studies to detect the front vehicle images in practice. This paper focused on large vehicles using a front-installed digital video recorder (DVR) with a near-infrared (NIR) camera. The views of large and ordinary vehicles are different; thus, this study used a deep learning method to process progressive improvement in moving vehicle detection. This study proposed a You Only Look Once version 4 (YOLOv4) supplemented with the fence method, called YOLOv4(III), to enhance vehicle detection. This method had high detection accuracy and low false omission rates using the general DVR equipment, and it provided comparison results. There was no need to have a high specification front camera, and the proposed YOLOv4(III) was found to have competitive performance. YOLOv4(III) reduced false detection rates and had a more stable frame per second (FPS) performance than with Haar features. This improved detection method can give an alert for large vehicle drivers to avoid serious collisions, leading to a reduction in the waste of social resources.

Four new species of Coemansia from Taiwan are described. Three produce spirally twisted sporangiophores, and these new taxa increase the number of species in the Coemansia spiralis complex from three to six. Each new taxon is morphologically unique. Coemansia biformis, sp. nov., has two different asexual reproductive types on the same thallus; one is straight and the other has a spiral fertile region. Coemansia helicoidea, sp. nov., has stoloniferous sporangiophores with a helicoid fertile region. Coemansia pennisetoides, sp. nov., has a sporangiophore with a fertile region that resembles the inflorescence of the plant genus Pennisetum. Coemansia umbellata, sp. nov., has an umbellate sporangiophore branching pattern and a spirally twisted fertile region on the lowest branches. A dichotomous key was provided to identify the 23 accepted Coemansia species. Phylogenetic analysis based on a combined data set of D1-D2 domains of nuc 28S ribosomal RNA (rDNA) and partial nuc 18S rDNA identifies several independent evolutionary lineages within Coemansia and suggests that Spirodactylon aureum and Kickxella alabastrina may be nested within the genus Coemansia. Sequences of nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS] barcode) are also used to support the description of these new species of Coemansia.

Two new species of Ramicandelaber isolated from soil in Taiwan are described. Ramicandelaber fabisporus sp. nov. is characterized by having bean-shaped spores that are the smallest in the genus and also by the absence of lateral branches on the sporangiophores. Ramicandelaber taiwanensis sp. nov. is characterized by small, fusiform spores and it produces lateral branches that arise from the sporangiophores. Morphological characters and molecular phylogenetic analysis (D1/D2 domains of the LSU rRNA genes and ITS region) justify these new species of Ramicandelaber. A key is provided to the recognized species of Ramicandelaber.