Study of gene expression in Chromolaena odorata cuttings using a combination of RNA-seq and digital gene expression analysis
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ABSTRACT:
ORGANISM(S): Chromolaena odorata
SUBMITTER: Haiwang He
PROVIDER: E-GEOD-42283 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The genomes of three major mosquito vectors of human diseases, including Anopheles gambiae, Aedes aegypti, and Culex pipiens quinquefasciatus, have been previously sequenced. C. p. quinquefasciatus has the largest number of predicted protein-coding genes, which partially results from the expansion of three detoxification gene families: cytochrome P450 monooxygenases (P450), glutathione S-transferases (GST), and carboxylcholinesterases (CCE). However, unlike A. gambiae and A. aegypti, which have large amounts of gene expression data, C. p. quinquefasciatus has limited transcriptomic resources. Knowledge of complete gene expression information is very important for the exploration of the functions of genes involved in specific biological processes. In the present study, the three detoxification gene families of C. p. quinquefasciatus were analyzed for phylogenetic classification and compared with those of three other dipteran insects. Gene expression during various developmental stages and the differential expression responsible for parathion resistance were profiled using the digital gene expression (DGE) technique. Results: A total of 291 detoxification genes were found in C. p. quinquefasciatus, including 70 CCE, 186 P450, and 35 GST genes. Compared with three other dipteran species, gene expansion in Culex mainly occurred in the CCE and P450 families, where the genes of M-NM-1-esterases, juvenile hormone esterases, and CYP325 of the CYP4 subfamily showed the most pronounced expansion on the genome. A total of 13314 genes were expressed in five DGE libraries. Genes with signal transduction and odorant binding functions were prominently expressed during egg development. Genes involved in proteolysis, glycosphingolipid biosynthesis, and purine metabolism were preferentially expressed at the larval stage. Seventy five percent of the detoxification genes were found to be expressed. One fourth of the CCE and P450 genes were expressed at unique stages, indicating their developmentally regulated expression. Fifteen detoxification genes, including 2 CCEs, 6 GSTs, and 7 P450s, were expressed at higher levels in a parathion-resistant strain than in a susceptible strain. Conclusion: The results of the present study provide new insights into the functions and evolution of three detoxification gene families in mosquitoes and comprehensive transcriptomic resources for C. p. quinquefasciatus, which will facilitate the elucidation of molecular mechanisms underlying the different biological characteristics of the three major mosquito vectors. Raw data were deposited in SRA and assigned accession number SRA049959: http://www.ncbi.nlm.nih.gov/sra?term=SRA049959 Five DGE libraries were sequenced: the egg, third instar larval, pupal, and adult stages of the SG strain, and the third instar larval stage of the S-lab strain.
2012-12-30 | E-GEOD-35744 | biostudies-arrayexpress
Project description:A genome-wide transcriptome analysis showed that altering ZmPIN1a expression led to wide-ranging gene expression changes. When comparing overexpression lines A17 with the WT, 2975 genes were differentially expressed with 793 up-regulated and 2182 down-regulated in the leaves, and 2129 genes were differentially expressed with 938 up-regulated and 1191 down-regulated in the roots. GO analysis indicated that these differentially expressed genes participate in multiple biological processes from hormone signaling to metabolism. The local biosynthesis, PAT and signaling of auxin were altered; some was directly employed in plant developments such as AUX/IAA, ARFs and genes related to PAT. The genes involved in ethylene, GA, BR CK and ABA metabolism and signaling were altered as well. These phytohormones were also confirmed as key regulators in plant development and abiotic stress responses. Some of the differentially expressed genes between A17 and WT were identified as Arabidopsis root morphology and development mutant genes. These mutants were abnormal in their plant hormone synthesis and signaling, calcium-mediated signaling, MAP kinase signaling, transcription factors, membrane transporters etc. This finding suggested that ZmPIN1a overexpression led to a change of the auxin signaling transduction and even the metabolism of auxin and the metabolism and signaling of other hormones. These events led to changes in the expression of numerous genes and resulted in the modification of plant morphology, especially the root architecture. Maize (Zea mays L.) inbred line DH4866, its ZmPIN1a sense transgenic lines A17 and antisense transgenic lines a55 were used in this study. The transcriptome by altering ZmPIN1a expression was done by comparing the transcriptome of WT and transgenic lines both in root and leaf of V3 stage plants.
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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.
2011-11-08 | E-GEOD-28001 | biostudies-arrayexpress
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
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Project description:Purpose: AURKA plays an important role in breast cancer development. Exploring the gene expression profiles regulated by AURKA will facilitate to understand the mechanism which is responsible for AURKA induced breast cancer development. Results: We found that 350 genes were significantly up-regulated during AURKA overexpression in MCF-10A cells, 346 genes were significantly down-regulated during AURKA overexpression in MCF-10A cells. Conclusions: Our study indicated that 696 differentially expressed genes might contribute to AURKA induced breast cancer development. MCF-10A cells overexpressed AURKA or the empty vector were subjected to RNA extraction. The resulted RNA samples were performed RNA-sequencing analyses of gene expression profiles.
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