Kuan-Chieh Tseng

The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 plant species. To explore regulatory landscapes, genomic locations of TFBSs have been captured from 662 public ChIP-seq samples using standard data processing. A total of 1 233 999 regulatory linkages were identified from 99 regulatory factors (TFs, histones and other DNA-binding proteins) and their target genes across seven species. Additionally, this new version added 2449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. In addition to integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events, including (i) 1107 experimentally verified TF matrices from the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures of TFs and TF-DNA complexes and (iv) condition-specific co-expression networks of TFs and their target genes extended to four species. The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF-targets under specific conditions.

Diverse soil microbial community is determinant for sustainable agriculture. Rich microbial diversity has presumably improved soil health for economic crops to grow. In this work, the benefits of paddy-upland rotation on soil microbial diversity and specific microbes are thus intensively explored. The microbiome from multiple factor experiment (three fertilizations coupled with two rotation systems) were investigated by novel enrichment and co-occurrence analysis in a field well maintained for 25 years. Using next-generation sequencing technique, we firstly present explicit evidence that different rotation systems rather than fertilizations mightily governed the soil microbiome. Paddy-upland rotation (R1) obviously increase more microbial diversity than upland rotation (R2) whether organic (OF), chemical (CF) or integrated fertilizers (IF) were concomitantly applied. Besides, the specific bacterial composition dominated in OF soil is more similar to that of R1 than to CF, suggesting that paddy-upland rotation might be the best option for sustainable agriculture if chemical fertilizer is still required. Interestingly, the pot bioassay verified clearly the novel analysis prediction, illustrating that greater microbial diversity and specific microbial composition correlated significantly with disease resistance. This finding highlights the eminence of paddy-upland rotation in promoting microbial diversity and specific microbial compositions, preserving soil health for sustainable agriculture.

Extreme resistance (ER) is a type of R-gene-mediated resistance that rapidly induces a symptomless resistance phenotype, which is different from the phenotypical R-resistance manifested by the programmed cell death, accumulation of reactive oxygen species, and hypersensitive response. The Rsv3 gene in soybean cultivar L29 is responsible for ER against the avirulent strain G5H of soybean mosaic virus (SMV), but is ineffective against the virulent strain G7H. Rsv3-mediated ER is achieved through the rapid accumulation of callose, which arrests SMV-G5H at the point of infection. Callose accumulation, however, may not be the lone mechanism of this ER. Analyses of RNA-seq data obtained from infected soybean plants revealed a rapid induction of the abscisic acid pathway at 8 h post infection (hpi) in response to G5H but not to G7H, which resulted in the down-regulation of transcripts encoding β-1,3 glucanases that degrade callose in G5H-infected but not G7H-infected plants. In addition, parts of the autophagy and the small interfering (si) RNA pathways were temporally up-regulated at 24 hpi in response to G5H but not in response to G7H. The jasmonic acid (JA) pathway and many WRKY factors were clearly up-regulated only in G7H-infected plants. These results suggest that ER against SMV-G5H is achieved through the quick and temporary induction of ABA, autophagy, and the siRNA pathways, which rapidly eliminate G5H. The results also suggest that suppression of the JA pathway in the case of G5H is important for the Rsv3-mediated ER.

Abstract Motivation MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants. A systematic approach to determine novel miRNAs without reference sequences is thus necessary. Results In this study, an effective method was developed to identify miRNAs from non-model plants based only on NGS datasets. The miRNA prediction model was trained with several duplex structure-related features of mature miRNAs and their passenger strands using a support vector machine algorithm. The accuracy of the independent test reached 96.61% and 93.04% for dicots (Arabidopsis) and monocots (rice), respectively. Furthermore, true small RNA sequencing data from orchids was tested in this study. Twenty-one predicted orchid miRNAs were selected and experimentally validated. Significantly, 18 of them were confirmed in the qRT-PCR experiment. This novel approach was also compiled as a user-friendly program called microRPM (miRNA Prediction Model). Availability and implementation This resource is freely available at http://microRPM.itps.ncku.edu.tw. Supplementary information Supplementary data are available at Bioinformatics online.

Chloroplast movement is important for plants to avoid photodamage and to perform efficient photosynthesis. Phototropins are blue light receptors in plants that function in chloroplast movement, phototropism, stomatal opening, and they also affect plant growth and development. In this study, full-length cDNAs of two PHOTOTROPIN genes, PaPHOT1 and PaPHOT2, were cloned from a moth orchid Phalaenopsis aphrodite, and their functions in chloroplast movement were investigated. Phylogenetic analysis showed that PaPHOT1 and PaPHOT2 orthologs were highly similar to PHOT1 and PHOT2 of the close relative Phalaenopsis equestris, respectively, and clustered with monocots PHOT1 and PHOT2 orthologs, respectively. Phalaenopsis aphrodite expressed a moderate level of PaPHOT1 under low blue light of 5 μmol�m-2�s-1 (BL5) and a high levels of PaPHOT1 at >BL100. However, PaPHOT2 was expressed at low levels at <BL50 but expressed at high levels at > BL100. Analysis of light-induced chloroplast movements using the SPAD method indicated that orchid accumulated chloroplasts at <BL10. The chloroplast avoidance response was detectable at >BL25 and significant chloroplast avoidance movement was observed at >BL100. Virus-induced gene silencing of PaPHOTs in orchids showed decreased gene expression of PaPHOTs and reduced both chloroplast accumulation and avoidance responses. Heterologous expression of PaPHOT1 in Arabidopsis phot1phot2 double mutant recovered chloroplast accumulation response at BL5, but neither PaPHOT1 nor PaPHOT2 was able to restore mutant chloroplast avoidance at BL100. Overall, this study showed that phototropins mediate chloroplast movement in Phalaenopsis orchid is blue light-dependent but their function is slightly different from Arabidopsis which might be due to gene evolution.