Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing

The most enriched pathways that were identified for the target genes. A total of 53 most enriched pathways of target gene annotated in this study. (XLS 41 kb

CgGCS, Encoding a Glucosylceramide Synthase, Is Required for Growth, Conidiation and Pathogenicity in Colletotrichum gloeosporioides

Fungal glucosylceramide plays important role in cell division, hyphal formation and growth, spore germination and the modulation of virulence and has recently been considered as target for small molecule inhibitors. In this study, we characterized CgGCS, a protein encoding a glucosylceramide synthase (GCS) in Colletotrichum gloeosporioides. Disruption of CgGCS resulted in a severe reduction of mycelial growth and defects in conidiogenesis. Sphingolipid profile analysis revealed large decreases in glucosylceramide production in the mutant strains. Pathogenicity assays indicated that the ability of the ΔCgGCS mutants to invade both tomato and mango hosts was almost lost. In addition, the expression levels of many genes, especially those related to metabolism, were shown to be affected by the mutation of CgGCS via transcriptome analysis. Overall, our results demonstrate that C. gloeosporioides glucosylceramide is an important regulatory factor in fungal growth, conidiation, and pathogenesis in hosts

Fusaric acid instigates the invasion of banana by Fusarium oxysporum f. sp. cubense TR4

CITATION: Liu, S. et al. 2020. Fusaric acid instigates the invasion of banana by Fusarium oxysporum f. sp. cubense TR4. New Phytologist, 225:913–929, doi:10.1111/nph.16193.The original publication is available at https://nph.onlinelibrary.wiley.comFusaric acid (FSA) is a phytotoxin produced by several Fusarium species and has been associated with plant disease development, although its role is still not well understood. Mutation of key genes in the FSA biosynthetic gene (FUB) cluster in Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) reduced the FSA production, and resulted in decreased disease symptoms and reduced fungal biomass in the host banana plants. When pretreated with FSA, both banana leaves and pseudostems exhibited increased sensitivity to Foc TR4 invasion. Banana embryogenic cell suspensions (ECSs) treated with FSA exhibited a lower rate of O2 uptake, loss of mitochondrial membrane potential, increased reactive oxygen species (ROS) accumulation, and greater nuclear condensation and cell death. Consistently, transcriptomic analysis of FSA-treated ECSs showed that FSA may induce plant cell death through regulating the expression of genes involved in mitochondrial functions. The results herein demonstrated that the FSA from Foc TR4 functions as a positive virulence factor and acts at the early stage of the disease development before the appearance of the fungal hyphae in the infected tissues.https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.16193Publisher's versio

NOA1 Functions in a Temperature-Dependent Manner to Regulate Chlorophyll Biosynthesis and Rubisco Formation in Rice

NITRIC OXIDE-ASSOCIATED1 (NOA1) encodes a circularly permuted GTPase (cGTPase) known to be essential for ribosome assembly in plants. While the reduced chlorophyll and Rubisco phenotypes were formerly noticed in both NOA1-supressed rice and Arabidopsis, a detailed insight is still necessary. In this study, by using RNAi transgenic rice, we further demonstrate that NOA1 functions in a temperature-dependent manner to regulate chlorophyll and Rubisco levels. When plants were grown at 30°C, the chlorophyll and Rubisco levels in OsNOA1-silenced plants were only slightly lower than those in WT. However, at 22°C, the silenced plants accumulated far less chlorophyll and Rubisco than WT. It was further revealed that the regulation of chlorophyll and Rubisco occurs at the anabolic level. Etiolated WT seedlings restored chlorophyll and Rubisco accumulations readily once returned to light, at either 30°C or 15°C. Etiolated OsNOA1-silenced plants accumulated chlorophyll and Rubisco to normal levels only at 30°C, and lost this ability at low temperature. On the other hand, de-etiolated OsNOA1-silenced seedlings maintained similar levels of chlorophyll and Rubisco as WT, even after being shifted to 15°C for various times. Further expression analyses identified several candidate genes, including OsPorA (NADPH: protochlorophyllide oxidoreductase A), OsrbcL (Rubisco large subunit), OsRALyase (Ribosomal RNA apurinic site specific lyase) and OsPuf4 (RNA-binding protein of the Puf family), which may be involved in OsNOA1-regulated chlorophyll biosynthesis and Rubisco formation. Overall, our results suggest OsNOA1 functions in a temperature-dependent manner to regulate chlorophyll biosynthesis, Rubisco formation and plastid development in rice

Progress in Protein Interactomics Technologies and Their Applications to Plants Research

Protein interactomics is a cutting-edge technology to identify and quantify the interaction of proteins with other metabolites or molecules like proteins, which has been an important part of plant systems biology and multi-omics research. In recent years, the rapid development of mass spectrometry-based omics technologies has facilitated great progress in methodologies for discovery and verification of the protein-metabolite interaction (PMI) and protein-protein interaction (PPI), which are the main protein interactomic technologies, showing great potential for applications in plant functional genomic and metabolomic studies gradually. Here, we present a systematic overview of the analysis strategies of different protein interactomics technologies (including PMI and PPI) in the past decade and analyze their advantages, disadvantages and specific applicable interaction types. The application progress and application strategies of protein interactomics technologies in plant research and the key technical bottlenecks that need to be overcome are also summarized. In the near future, the continuous development of interactomics technologies will further leverage the analysis of intracellular signal transduction and metabolic regulatory pathways in plants, and precise analysis of key interactions in signal networks will provide important information for the studies of the growth and development of plants and their adaptation to external environment

The Musa Marker Database: A Comprehensive Genomic Resource for the Improvement of the Musaceae Family

Molecular markers, including Simple Sequence Repeat (SSR), Single Nucleotide Polymorphism (SNP), and Intron Length Polymorphism (ILP), are widely utilized in crop improvement and population genetics studies. However, these marker resources remain insufficient for Musa species. In this study, we developed genome-wide SSR, SNP, and ILP markers from Musa and its sister species, creating a comprehensive molecular marker repository for the improvement of Musa species. This database contains 2,115,474 SSR, 63,588 SNP, and 91,547 ILP markers developed from thirteen Musa species and two of its relative species. We found that 77% of the SSR loci are suitable for marker development; 38% of SNP markers originated from the genic region, and transition mutations (C↔T; A↔G) were more frequent than transversion. The database is freely accessible and follows a ‘three-tier architecture,’ organizing marker information in MySQL tables. It has a user-friendly interface, written in JavaScript, PHP, and HTML code. Users can employ flexible search parameters, including marker location in the chromosome, transferability, polymorphism, and functional annotation, among others. These distinctive features distinguish the Musa Marker Database (MMdb) from existing marker databases by offering a novel approach that is tailored to the precise needs of the Musa research community. Despite being an in silico method, searching for markers based on various attributes holds promise for Musa research. These markers serve various purposes, including germplasm characterization, gene discovery, population structure analysis, and QTL mapping

A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops

Genome-wide Expression Profiling in Ponkan Infected by Candidatus Liberibacter asiaticus

Huanglongbing (HLB) is an economical and destructive disease of citrus in South China, such as in Guangdong, Guangxi that is caused by the bacterium Candidatus Liberibacter asiaticus. The interaction at mRNA level between pathogen and citrus (Ponkan, Citrus reticulata Blanco ) was primarily researched by Digital Gene Expression Tag Profiling. Ponkan leaves at 13 weeks and 26 weeks after HLB inoculation were used for analysis. The numbers of up-regulated genes were increased from 37% in 13 wpi (weeks post inoculation) to 64% in 26 wpi. The differentially expressed genes (DEGs) fold change increased more than 8 times from 16.7% to 87.3%. Gene ontology (GO) process molecular function enrichment analysis showed that the DEGs with oxidation reduction function increased from 4.41% to 8.48% and that DEGs responsive to stresses increased from 1.10% to 2.08%, but those related to defense responses decreased from 0.74% to 0.64%. However, those related to defense responses of down-regulated genes increased from 0.55% to 0.79%. Apparently, the expression level of resistance genes strengthened, while the defense ability of host declined along with enhanced stresses caused by HLB infection. Photosynthesis-related genes were down-regulated at both 13 wpi and 26 wpi, which indicated that HLB infection greatly reduced the citrus photosynthesis, perhaps via feedback regulation of the accumulated starches resulted from blockage of sieve tubes by the bacteria in the phloem tissue. RIN4,a negative regulator of plant immunity, was also found up-regulated by approximately 9-fold