scholarly journals Transcriptomic landscape of Dendrobium huoshanense and its genes related to polysaccharide biosynthesis

2018 ◽  
Vol 87 (1) ◽  
Author(s):  
Rongchun Han ◽  
Dongmei Xie ◽  
Xiaohui Tong ◽  
Wei Zhang ◽  
Gang Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Average Length ◽  
Cultivated Plants ◽  
Polysaccharide Biosynthesis ◽  
Fastq Format ◽  
Its Gene ◽  
Dendrobium Huoshanense ◽  
Morphological Differences ◽  
Illumina Hiseq4000

<em>Dendrobium huoshanense</em> has long been used to treat various diseases in oriental medicine. In order to study its gene expression profile, transcripts involved in the biosynthesis of precursors of polysaccharides, as well as mechanisms underlining morphological differences between wild and cultivated plants, three organs of both wild type and cultivated <em>D. huoshanense</em> were collected and sequenced by Illumina HiSeq4000 platform, yielding 919,409,540 raw reads in FASTQ format. After Trinity de novo assembly and quality control, 241,242 nonredundant contigs with the average length of 967.5 bp were generated. qRT-PCR experiment on the selected transcripts showed the transcriptomic data were reliable. BLASTx was conducted against NR, SwissProt, String, Pfam, and KEGG. Gene ontology annotation revealed more than 40,000 contigs assigned to catalytic activity and metabolic process, suggesting its dynamic physiological activities. By searching KEGG pathway, six genes potentially involved in mannose biosynthetic pathway were retrieved. Gene expression analysis for stems between wild and cultivated <em>D. huoshanense</em> resulted in 956 genes differentially expressed. Simple sequence repeats (SSRs) analysis revealed 143 SSRs with the unit size of 4 and 3,437 SSRs the size of 3. The obtained SSRs are the potential molecular markers for discriminating distinct cultivars of <em>D. huoshanense</em>.

Gene Expression Profile of Acute Myeloid Leukemia (AML) with t(8;16)(p11;p13) and MYST3/CREBBP Rearrangement.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2054-2054
Author(s):  
Mireia Camos ◽  
Jordi Esteve ◽  
Pedro Jares ◽  
Maria Rozman ◽  
Dolors Colomer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
De Novo ◽  
Normal Karyotype ◽  
Genetic Profile ◽  
Transferase Activity ◽  
Internal Tandem Duplication ◽  
Its Gene ◽  
Differential Expression Profile

Abstract Translocation t(8;16)(p11;p13) is an infrequent chromosomal abnormality in de novo and secondary AML cases, leading to the fusion of MYST3 (MOZ) and CREBBP (CBP) genes, both of them harboring histone lysine acetyl-transferase activity. This AML variety displays specific clinical and biological features, although its gene expression profile is currently unknown. In this study, the genetic signature of AML cases with MYST3/CREBBP rearrangement was compared with the genetic profile of other well-defined AML subtypes. Genotypic analyses using oligonucleotide U133A arrays (Affymetrix) were performed on RNA of 19 AML samples, including t(8;16)-AML (n=3), t(15;17) (n=3), t(8;21) (n=2), inv(16)/t(16;16) (n=3), t(9;11) with AF9/MLL rearrangement (n=2), 3 cases with normal karyotype and flt-3 internal tandem duplication (flt-3 ITD), the three remaining samples corresponding to monocytic cases (M4/M5) without MLL rearrangement nor flt-3 ITD. After unsupervised analysis, cases of AML with t(8;16) clustered together, displaying a differential expression profile. Supervised analysis allowed the identification of the top 53 up-regulated and 28 down-regulated genes. Among the set of genes overexpressed, genes involved in chromatin remodelling and transcription (HOXA9, HOXA10, MEIS1, CHD3, SATB1) and protooncogenes (RET, flt-3, LMO2) were identified. In contrast, CREBBP gene and several members of the JAK-STAT pathway (STAT3, STAT5B, JAK2) were underexpressed. Interestingly, overexpression of multiple homeobox genes was detected in flt-3 ITD cases, some of them as a distinctive finding (HOXA2, HOXA3, HOXB6), and others (HOXA9, HOXA10, MEIS1) were found to be highly expressed in MYST3/CREBBP and MLL-rearranged samples. In conclusion, AML with t(8;16) and MYST3/CREBBP rearrangement shows a distinctive gene expression profile, with some similarities with MLL rearranged leukemias and flt-3 ITD AML cases, thus suggesting a partially common leukemogenic pathway.

scholarly journals De novo construction of a transcriptome for the stink bug crop pest Chinavia impicticornis during late development

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Bruno C. Genevcius ◽  
Tatiana T. Torres
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Average Length ◽  
Molecular Study ◽  
The Body ◽  
Cultivated Plants ◽  
Stink Bug ◽  
Rna Seq ◽  
Evolution And Development ◽  
Genetic Mechanisms

Chinavia impicticornis is a neotropical stink bug of economic importance for various crops. Little is known about the development of the species, or the genetic mechanisms that may favor the establishment of populations in cultivated plants. Here, we conduct the first large-scale molecular study of C. impicticornis. Using tissues derived from the genitalia and the rest of the body for two immature stages of both males and females, we generated RNA-seq data, then assembled and functionally annotated a transcriptome. The de novo-assembled transcriptome contained around 400,000 contigs, with an average length of 688 bp. After pruning duplicated sequences and conducting a functional annotation, the final annotated transcriptome comprised 39,478 transcripts, of which 12,665 were assigned to Gene Ontology (GO) terms. These novel datasets will be invaluable for the discovery of molecular processes related to morphogenesis and immature biology. We hope to contribute to the growing body of research on stink bug evolution and development, as well as to the development of biorational pest management solutions.

scholarly journals De Novo Foliar Transcriptome of Chenopodium amaranticolor and Analysis of Its Gene Expression During Virus-Induced Hypersensitive Response

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e45953 ◽  
Author(s):  
Yongqiang Zhang ◽  
Xinwu Pei ◽  
Chao Zhang ◽  
Zifeng Lu ◽  
Zhixing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hypersensitive Response ◽  
De Novo ◽  
Chenopodium Amaranticolor ◽  
Its Gene

scholarly journals De Novo Characterization of Japanese Scallop Mizuhopecten yessoensis Transcriptome and Analysis of Its Gene Expression following Cadmium Exposure

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e64485 ◽  
Author(s):  
Xiao-lin Meng ◽  
Mei Liu ◽  
Ke-yong Jiang ◽  
Bao-jie Wang ◽  
Xue Tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Cadmium Exposure ◽  
Japanese Scallop ◽  
Mizuhopecten Yessoensis ◽  
Its Gene

scholarly journals De novo construction of a transcriptome for the stink bug crop pest Chinavia impicticornis during late development

2020 ◽  
Author(s):  
Bruno C. Genevcius ◽  
Tatiana T. Torres
Keyword(s):  
Functional Annotation ◽  
Large Scale ◽  
De Novo ◽  
Average Length ◽  
Molecular Study ◽  
The Body ◽  
Cultivated Plants ◽  
Stink Bug ◽  
Rational Solutions ◽  
Males And Females

AbstractChinavia impicticornis is a Neotropical stink-bug (Hemiptera: Pentatomidae) with economic importance for different crops. Little is known about the development of the species, as well as the genetic mechanisms that may favor the establishment of populations in cultivated plants. Here we conduct the first large-scale molecular study with C. impicticornis. We generated RNA-seq data for males and females, at two immature stages, for the genitalia separately and for the rest of the body. We assembled the transcriptome and conduct a functional annotation. De novo assembled transcriptome based on whole bodies and genitalia of males and females contained around 400,000 contigs with an average length of 688 bp. After pruning duplicated sequences and conducting a functional annotation, the final annotated transcriptome comprised 39,478 transcripts of which 12,665 had GO terms assigned. These novel datasets will provide invaluable data for the discovery of molecular processes related to morphogenesis and immature biology. We hope to contribute to the growing research on stink bug evo-devo as well as the development of bio-rational solutions for pest management.

scholarly journals De novo characterization of Platycladus orientalis transcriptome and analysis of its gene expression during aging

2017 ◽  
Author(s):  
Ermei Chang ◽  
Xiamei Yao ◽  
Jin Zhang ◽  
Nan Deng ◽  
Zeping Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Potential Candidate ◽  
Platycladus Orientalis ◽  
Oxidation Reduction ◽  
Mda Content ◽  
As Stress

Platycladus orientalis in China has a lifespan of one to several thousands of years. The long lifespans of trees have attracted interest in aging at the molecular level. There is little information on how the global process is controlled. In this study, the MDA content, SOD and POD activities were higher in ancient P. orientalis than in 20-year-old Platycladus orientalis, and the content of protein showed the inverse trend. We obtained 48,044 unigenes having an average length of 896 bp from pooled samples of P. orientalis by transcriptome sequencing. Microarray analysis produced a high-resolution age-course profile of gene expression levels in different age of P. orientalis. In total, 418 differentially expressed genes were identified. The use of highly informative clustering revealed distinct time points at which oxidation reduction and photosynthesis pathways changed. Eight clusters with distinctive expression patterns were identified, the expression of metabolism, photosynthesis, oxidation reduction and transporters related genes were downregulated and protein synthesis, transcription, signal transduction and senescence related genes were upregulated with increasing age. Total chlorophyll, chlorophyll a, and chlorophyll b levels were decreased steadily with age. This study discovery of potential candidate genes affecting photosynthesis in different P. orientalis ages and at senescence, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses.

scholarly journals De novo characterization of a whitefly transcriptome and analysis of its gene expression during development

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 400 ◽  
Author(s):  
Xiao-Wei Wang ◽  
Jun-Bo Luan ◽  
Jun-Min Li ◽  
Yan-Yuan Bao ◽  
Chuan-Xi Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Its Gene

scholarly journals De novo characterization of Platycladus orientalis transcriptome and analysis of its gene expression during aging

2017 ◽  
Author(s):  
Ermei Chang ◽  
Xiamei Yao ◽  
Jin Zhang ◽  
Nan Deng ◽  
Zeping Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
De Novo ◽  
Average Length ◽  
Expression Patterns ◽  
Potential Candidate ◽  
Platycladus Orientalis ◽  
Oxidation Reduction ◽  
Mda Content ◽  
As Stress

Platycladus orientalis in China has a lifespan of one to several thousands of years. The long lifespans of trees have attracted interest in aging at the molecular level. There is little information on how the global process is controlled. In this study, the MDA content, SOD and POD activities were higher in ancient P. orientalis than in 20-year-old Platycladus orientalis, and the content of protein showed the inverse trend. We obtained 48,044 unigenes having an average length of 896 bp from pooled samples of P. orientalis by transcriptome sequencing. Microarray analysis produced a high-resolution age-course profile of gene expression levels in different age of P. orientalis. In total, 418 differentially expressed genes were identified. The use of highly informative clustering revealed distinct time points at which oxidation reduction and photosynthesis pathways changed. Eight clusters with distinctive expression patterns were identified, the expression of metabolism, photosynthesis, oxidation reduction and transporters related genes were downregulated and protein synthesis, transcription, signal transduction and senescence related genes were upregulated with increasing age. Total chlorophyll, chlorophyll a, and chlorophyll b levels were decreased steadily with age. This study discovery of potential candidate genes affecting photosynthesis in different P. orientalis ages and at senescence, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses.

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