Identification and analysis of in planta expressed genes of Magnaporthe oryzae

<p>Abstract</p> <p>Background</p> <p>Infection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. We have employed expressed sequence tag (EST) analysis to identify rice genes involved in defense responses against infection by the blast fungus <it>Magnaporthe oryzae </it>and fungal genes involved in infectious growth within the host during a compatible interaction.</p> <p>Results</p> <p>A cDNA library was constructed with RNA from rice leaves (<it>Oryza sativa </it>cv. Hwacheong) infected with <it>M. oryzae </it>strain KJ201. To enrich for fungal genes, subtraction library using PCR-based suppression subtractive hybridization was constructed with RNA from infected rice leaves as a tester and that from uninfected rice leaves as the driver. A total of 4,148 clones from two libraries were sequenced to generate 2,302 non-redundant ESTs. Of these, 712 and 1,562 ESTs could be identified to encode fungal and rice genes, respectively. To predict gene function, Gene Ontology (GO) analysis was applied, with 31% and 32% of rice and fungal ESTs being assigned to GO terms, respectively. One hundred uniESTs were found to be specific to fungal infection EST. More than 80 full-length fungal cDNA sequences were used to validate <it>ab initio</it> annotated gene model of <it>M. oryzae</it> genome sequence.</p> <p>Conclusion</p> <p>This study shows the power of ESTs to refine genome annotation and functional characterization. Results of this work have advanced our understanding of the molecular mechanisms underpinning fungal-plant interactions and formed the basis for new hypothesis.</p

Perspectives Provided by Leopard and Other Cat Genomes: How Diet Determined the Evolutionary History of Carnivores, Omnivores, and Herbivores

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment

Determination of Fire Blight Susceptibility on Wild Rosaceae Plants in Korea by Artificial Inoculation

The fire blight caused by Erwinia amylovora (Ea) is a devastating disease of Rosaceae plants, including commercially important apple and pear trees. Since the first report in Korea in May 2015, it has been spreading to neighboring regions gradually. Host plants can be infected by pollinators like bees, rainfall accompanied by wind, and cultural practices such as pruning. Many studies have revealed that wild Rosaceae plants such as Cotoneaster spp., Crataegus spp., Pyracantha spp., Prunus spp., and Sorbus spp. can be reservoirs of Ea in nature. However, wild Rosaceae plants in Korea have not been examined yet whether they are susceptible to fire blight. Therefore, the susceptibility to fire blight was examined with 25 species in 10 genera of wild Rosaceae plants, which were collected during 2020–2022, by artificial inoculation. Bacterial suspension (108 cfu/ml) of Ea type strain TS3128 was inoculated artificially in flowers, leaves, stems, and fruits of each plant species, and development of disease symptoms were monitored. Moreover, the presence of Ea bacteria from inoculated samples were checked by conventional polymerase chain reaction. Total 14 species of wild Rosaceae plants showed disease symptoms of fire blight, and Ea bacteria were detected inside of inoculated plant parts. These results suggest that wild Rosaceae plants growing nearby commercial apple and pear orchards in Korea can be Ea reservoirs, and thus they should be monitored regularly to minimize the damage by Ea infection and spreading

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

Abstract: Background: Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. Results: Here, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identify common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems, such as loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems that are convergent with other nocturnal avian orders. Additionally, we find that a suite of genes associated with vision and circadian rhythm are differentially expressed in blood tissue between nocturnal and diurnal raptors, possibly indicating adaptive expression change during the transition to nocturnality. Conclusions: Overall, raptor genomes show genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators

Analysis of clinical and genomic profiles of therapy-related myeloid neoplasm in Korea

Background Therapy-related myeloid neoplasm (T-MN) rarely occurs among cancer survivors, and wascharacterized by poor prognosis. T-MN has germline predisposition in a considerable proportion. Here, clinical characteristics and germline/somatic variant profiles in T-MN patients were investigated, and the findings were compared with those of previous studies. Methods A review of medical records, cytogenetic study, targeted sequencing by next-generation sequencing, and survival analysis were performed on 53 patients with T-MN at a single institution in Korea. Results The patients were relatively younger compared to T-MN patients in other studies. Our T-MN patients showed ahigh frequency of complex karyotypes, −5/del(5q), and −7/del(7q), which was similar to the Japanese study group but higher than the Australian study group. The most common primary disease was non-Hodgkin lymphoma, followed by breast cancer. The detailed distributions of primary diseases were different across study groups. Seven patients (13.2%) harbored deleterious presumed/potential germline variants in cancer predisposition genes (CPG) such as BRIP1, CEBPA, DDX41, FANCM, NBN, NF1, and RUNX1. In the somatic variant profile, TP53 was the most frequently mutated gene, which was consistent with the previous studies about T-MN. However, the somatic variant frequency in our study group was lower than in other studies. Adverse factors for overall survival were male sex, older age, history of previous radiotherapy, previous longer cytotoxic therapy, and −5/del(5q). Conclusion The findings of our study corroborate important information about T-MN patients. As well as a considerable predisposition to CPG, the clinical characteristics and somatic variant profile showed distinctive patterns. Germline variant testing should be recommended for T-MN patients. If the T-MN patients harbor pathogenic germline variants, the family members for stem cell donation should be screened for carrier status through germline variant testing to avoid donor-derived myeloid neoplasm. For the prediction of the prognosis in T-MN patients, sex, age, past treatment history, and cytogenetic findings can be considered.This work was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korean government (MSIT) (NRF-2017R1A2A1A17069780 and NRF-2020R1A3B3079653) and a Grant from the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI) funded by the Ministry of Health & Welfare, Republic of Korea (Grant No. HR14C0003)

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.

BACKGROUND: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. RESULTS: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. CONCLUSIONS: Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research

Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus

Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via MoCRZ1, a Magnaporthe oryzae C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. MoCRZ1 itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen

A Novel Pathogenicity Gene Is Required in the Rice Blast Fungus to Suppress the Basal Defenses of the Host

For successful colonization and further reproduction in host plants, pathogens need to overcome the innate defenses of the plant. We demonstrate that a novel pathogenicity gene, DES1, in Magnaporthe oryzae regulates counter-defenses against host basal resistance. The DES1 gene was identified by screening for pathogenicity-defective mutants in a T-DNA insertional mutant library. Bioinformatic analysis revealed that this gene encodes a serine-rich protein that has unknown biochemical properties, and its homologs are strictly conserved in filamentous Ascomycetes. Targeted gene deletion of DES1 had no apparent effect on developmental morphogenesis, including vegetative growth, conidial germination, appressorium formation, and appressorium-mediated penetration. Conidial size of the mutant became smaller than that of the wild type, but the mutant displayed no defects on cell wall integrity. The Δdes1 mutant was hypersensitive to exogenous oxidative stress and the activity and transcription level of extracellular enzymes including peroxidases and laccases were severely decreased in the mutant. In addition, ferrous ion leakage was observed in the Δdes1 mutant. In the interaction with a susceptible rice cultivar, rice cells inoculated with the Δdes1 mutant exhibited strong defense responses accompanied by brown granules in primary infected cells, the accumulation of reactive oxygen species (ROS), the generation of autofluorescent materials, and PR gene induction in neighboring tissues. The Δdes1 mutant displayed a significant reduction in infectious hyphal extension, which caused a decrease in pathogenicity. Notably, the suppression of ROS generation by treatment with diphenyleneiodonium (DPI), an inhibitor of NADPH oxidases, resulted in a significant reduction in the defense responses in plant tissues challenged with the Δdes1 mutant. Furthermore, the Δdes1 mutant recovered its normal infectious growth in DPI-treated plant tissues. These results suggest that DES1 functions as a novel pathogenicity gene that regulates the activity of fungal proteins, compromising ROS-mediated plant defense

Taxonomic Study on Six Yeast Species Unlisted in the National Species List of Korea

More than five hundreds of yeast species (including 9 variants) encompassing 142 genera and 48 classes of 2 phyla exist in Korea. However, only 173 species have been cataloged in the National Species List of Korea (NSLK), the backbone reference to claim sovereign rights over biological resources, as of December 2021, due to the lack of taxonomic descriptions, although some of these species are extensively used in industry. The present pilot study investigated the taxonomy of strains belonging to the six most widely used or frequently isolated yeast species (Meyeromyma guilliermondii, Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Wickerhamomyces anomalus, Candida tropicalis, and Papiliotrema flavescens) to include these species in the NSLK. Strains with diverse habitats and geographic origins were retrieved from the National Institute of Biological Resources culture collection. These strains clustered in the same clade as the type strains of the designated species according to phylogenetic analysis of the D1/D2 sequences. Moreover, we described the cell morphology and physiological characteristics of representative strains of each species. This study suggests that these six species are indigenous to Korea and can be accordingly listed in the NSLK