Transcriptomic analysis of fungus Penicillium oxalicum and its laeA deletion strains in 24h and 60h
ABSTRACT: The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), and laeA knockout strain (ΔlaeA) in different development phase. The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inΔlaeA. This study provides the information that laeA function are required in conidiation and hydrolase activity of P. oxalicum. Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and laeA knockout mutant strains in 24h and 60h in modified Czapek culture medium with 2% glucose as carbon resource. qRT–PCR validation was performed using SYBR Green assays.
Project description:Transcriptomic analysis of fungus Penicillium decumbens and brlA deletion strains in liquid medium and solid medium respectivelly Examination of differential gene expressions by Penicillium decumbens strains 114-2 and brlA deletion stains in liquid medium and solid medium
Project description:Transcriptomic analysis of LaeA-deletion and overexpression LaeB in LaeA deletion strains in fungus Beauveria bassiana Examination of differential gene expressions by Beauveria bassiana wild type, LaeA-deletion and overexpression LaeB in LaeA deletion strains in fungus Beauveria bassiana
Project description:The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), laeA knockout strain (ΔlaeA), creA knockout strain (ΔcreA), and double genes knockout strain (ΔlaeAΔcreA). The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inΔlaeA. The deletion of creA upregulated genes involved in hydrolase activity, acting on glycosyl bonds. Many genes involved in conidiation were drastically regulated inΔlaeAΔcreA. This study provides the information that combined laeA and creA function are required in conidiation and hydrolase activity of P. oxalicum. Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and three mutant strains (laeA knockout strain, creA knockout strain and double genes knockout strain). qRT–PCR validation was performed using SYBR Green assays.
Project description:We used RNA-Seq to compare transcriptional responses of M. anisopliae and M. acridum to infection of the optically clear hind wings of adult locusts and cockroaches. It was calculated that >82% of predicted M. anisopliae genes and >88% of predicted M. acridum genes were expressed during pre-penetration growth. Germination and growth by M. anisopliae and M. acridum on either insect triggered high level expression of genes associated with translation and post-translational modifications. Between 6 to 10% of the genes that were highly expressed by M. anisopliae and M. acridum on host cuticles encoded cell wall proteins. Consistent with early host recognition events being key to establishing specificity, M. acridum but not M. anisopliae transcribed different Pth11-like GPCRs on locust and cockroach cuticles, thus differential activation of different signaling pathways. Examination of gene differential expressions by two different Metarhizium speceis on two different insects cuticles
Project description:This experiment contains Phytophthora sojae samples and RNA-seq data from experiment E-GEOD-29561 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29651/) to understand gene expression during the P. sojae life cycle. The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 5 different developmental stages: mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY) and germinating cysts (GC); based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established.
Project description:The transcriptome of the oomycete plant pathogen Phytophthora sojae was profiled at 10 different developmental and infection stages based on a 3'-tag digital gene expression (DGE) protocol. More than 90 million clean sequence tags were generated and compared to the P. sojae genome and its 19,027 predicted genes. A total of 14,969 genes were detected, of which 10,044 were deemed reliable because they mapped to unambiguous tags. A comparison of the whole-library genes expression patterns suggested four groups: 1) mycelia and zoosporangia (MY and SP); 2) zoospores and cysts (ZO and CY); 3) germinating cysts (GC); 4) five infection site libraries (IF1.5 to IF24h). The libraries from the different groups showed major transitional shifts in gene expression. From the ten libraries, 722 gene expression pattern clusters were obtained and the top 16 ones, containing more than half of the genes, comprised enriched genes with different functions including protein localization, triphosphate metabolism, signaling process, and non-coding RNA metabolism. An evaluation of the average expression level of 30 pathogenesis related gene families revealed that most were infection induced, but with diverse expression patterns and levels. A web-based server named the Phytophthora Transcriptional Database (PTD) has been established. The five axenically grown stages were mycelia (MY), zoosporangia (SP), zoospores (ZO), cysts (CY), and germinating cysts (GC). The five infection stages, 1.5, 3, 6, 12 and 24 h after inoculation onto susceptible soybean leaf tissues (IF1.5h to IF24h).
Project description:Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been mainly depicted in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Over-expression of a microRNA166-resistant version of SlREV (35S::REVRis) not only resulted in vegetative abnormities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged out from the exodermises of pedicel AZs and ectopic carpels formed between the first and the second whorl of floral buds in 35S::REVRis plants. Therefore, we performed Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing methodTranscriptional data to dicover differential expressed genes in early buds (1-2 mm floral buds at stage 6-8) of overexpression line SlREVRis-1. The result suggests that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of flower pedicel abscission zone, and modulate genes in homodomain and MADS-box families and hormone pathways during fruit formation. These results reveal important roles of SlREV in tomato. 1-2 mm floral buds at stage 6-8 were sampled from three individual plants of 35S::REVRis-1 and corresponding WT control. Three aliquots of RNA from transgenic or WT plants were pooled. Then, the digital expression profile were generated by Illumina Cluster Station and Illumina HiSeq™ 2000 System (BGI Inc.).
Project description:4,392 differentially expressed genes were generated by DGE analysis, and 3,074 had good comparability with known gene sequences in existing species. 1,152 differentially expressed sequences were mapped to the reference canonical pathways in the KEGG database, and were assigned to 110 KEGG pathways, 11 pathways less then with the transcriptome database. Differentially expressed genes were classed according to their function, which includes phytohormones, growth and developmental processes, defense, peroxidase and P450-related genes. Pathway analysis also revealed that the principal secondary metabolites in the C. odorata cuttings were phytohormones and flavonoids. Examination of 2 different stage of adventitious root formation
Project description:Insect pathogenic fungus Beauveria bassiana in one of the best studied insect biocontrol fungus, which infects insects by cuticle penetration. After breaking the cuticles, the fungus will propagate in insect hemocoel and kill insect hosts. It has also been found that the mycelia of B. bassiana can penetrate plant tissues to reach insect inside plant, e.g. corn borer (Ostrinia furnacalis), but do not cause damage to plants. The mechanism of fungal physiological plasticity is poorly understood. To accompany our genome sequencing work of B. bassiana strain ARSEF 2860, fungal transcriptional responses to different niches were studied using an Illumina RNA_seq technique. To examine fungal response to insect cuticle, conidia were inoculated on locust hind wings for 24 hours before used for RNA extraction. To evaluate fungal adaptation to insect hemocole, the fifth instar larvae of cotton bollworms were injected with spore suspension and fungal cells isolated by centrifugation in a step gradient buffer. To unveil the mechanism of interaction with plants, the fungus was grown in corn root exudates for 24 hours. After RNA sequencing, around three million tags were acquired for each sample and fungal transcriptional profiles were compared. Unveiling gene differential expression patterns when the insect biocontrol fungus Beauveria bassiana grown in insect hemocoel, corn root exudates and on insect cuticles.
Project description:The RNA-Seq technique was used to investigate the differentially transcribed genes of the caterpillar fungus Cordyces militaris. It was calculated that >63% of total annotated genes were expressed, including >55% of putative pathogen-host interaction genes. Overall, the fruiting-body development and mycelium growth by C. militaris activated high expression levels of genes in association with translation and post-translational modifications. Otherwise, there were many differentially expressed genes when the fungus was grown on insect pupae to different stages or in liquid medium. In general, the transcriptional profiles were more similar with each other during fungal fruiting-body developmental stages than during growth in a liquid culture. Examination of differential gene expressions by Cordyceps militaris during fruiting-body developments on silkmoth pupae and growth in a liquid medium.