scholarly journals De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome from Next-Generation mRNA Sequencing

2016 ◽  
Author(s):  
Zhongxian Xu ◽  
Hang Jie ◽  
Binlong Chen ◽  
Uma Gaur ◽  
Mingyao Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
De Novo Assembly ◽  
De Novo ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Musk Deer ◽  
Next Generation ◽  
Steroid Biosynthesis ◽  
Mrna Sequencing ◽  
Genetic Mechanisms

Musk secretion in male musk deer is regarded as a propitious mode of sexual election to attract a greater number of females. However, the genetic mechanisms of musk secretion are still poorly understood and unresolved making it necessary to elucidate the possible genetic mechanisms of musk formation. In the present study, we used heart and musk gland tissues from a male musk deer for next-generation mRNA sequencing, integrated with de novo assembly, unigenes annotation and differentially expressed genes analysis. A total of 239,383 transcripts and 208,730 unigenes were obtained from 2 pooled RNA samples. Annotated analysis indicated steroid compound metabolism (steroid biosynthesis, steroid hormone biosynthesis, aldosterone-regulated sodium reabsorption, terpenoid backbone biosynthesis) related to musk formation were annotated to many pathways; relevant genes were identified as well. In addition, 8,986 differentially expressed genes (6,068 up- and 2,198 down-regulated) between heart and musk gland were identified, among them, steroid component metabolism were abundant. Further exploration of functional enrichment analysis showed that pathways involved in musk secretion were up-regulated in musk gland compared with heart, especially steroid biosynthesis and terpenoid backbone biosynthesis whose metabolic productions were key components of musk. We identified several candidate genes such as DHCR7, DHCR24, NSDHL, CYP3A5, FDFT1, FDPS and HMGCL which were closely involved in metabolism of steroid, terpenoid and ketone bodies. Our data are expected to represent the most comprehensive sequence resource available for the forest musk deer so far, and provide a basis for further research on molecular genetics and functional genomics of musk secretion.

scholarly journals De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome from Next-Generation mRNA Sequencing

2016 ◽  
Author(s):  
Zhongxian Xu ◽  
Hang Jie ◽  
Binlong Chen ◽  
Uma Gaur ◽  
Mingyao Yang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
De Novo Assembly ◽  
De Novo ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Musk Deer ◽  
Next Generation ◽  
Steroid Biosynthesis ◽  
Mrna Sequencing ◽  
Genetic Mechanisms

Musk secretion in male musk deer is regarded as a propitious mode of sexual election to attract a greater number of females. However, the genetic mechanisms of musk secretion are still poorly understood and unresolved making it necessary to elucidate the possible genetic mechanisms of musk formation. In the present study, we used heart and musk gland tissues from a male musk deer for next-generation mRNA sequencing, integrated with de novo assembly, unigenes annotation and differentially expressed genes analysis. A total of 239,383 transcripts and 208,730 unigenes were obtained from 2 pooled RNA samples. Annotated analysis indicated steroid compound metabolism (steroid biosynthesis, steroid hormone biosynthesis, aldosterone-regulated sodium reabsorption, terpenoid backbone biosynthesis) related to musk formation were annotated to many pathways; relevant genes were identified as well. In addition, 8,986 differentially expressed genes (6,068 up- and 2,198 down-regulated) between heart and musk gland were identified, among them, steroid component metabolism were abundant. Further exploration of functional enrichment analysis showed that pathways involved in musk secretion were up-regulated in musk gland compared with heart, especially steroid biosynthesis and terpenoid backbone biosynthesis whose metabolic productions were key components of musk. We identified several candidate genes such as DHCR7, DHCR24, NSDHL, CYP3A5, FDFT1, FDPS and HMGCL which were closely involved in metabolism of steroid, terpenoid and ketone bodies. Our data are expected to represent the most comprehensive sequence resource available for the forest musk deer so far, and provide a basis for further research on molecular genetics and functional genomics of musk secretion.

Differentially Expressed Genes in Hypericin-Containing Hypericum perforatum Leaf Tissues as Revealed by De Novo Assembly of RNA-Seq

2016 ◽  
Vol 34 (5) ◽  
pp. 1027-1041 ◽  
Author(s):  
Miroslav Soták ◽  
Odeta Czeranková ◽  
Daniel Klein ◽  
Katarína Nigutová ◽  
Lothar Altschmied ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
De Novo Assembly ◽  
Hypericum Perforatum ◽  
De Novo ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Leaf Tissues

scholarly journals Transcriptome Sequencing Analysis Provides Insights Into the Response to Fusarium oxysporum in Lilium pumilum

2019 ◽  
Vol 15 ◽  
pp. 117693431983881
Author(s):  
Xiangfeng He ◽  
Wanyue Li ◽  
Wenzhu Zhang ◽  
Xiaotong Jin ◽  
Awraris Getachew Shenkute ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Differentially Expressed Genes ◽  
De Novo ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Basal Rot ◽  
Phenylpropanoid Biosynthesis

Lily basal rot, caused by Fusarium oxysporum f. sp. lilii, is one of the most serious diseases of lily. Although the lily germplasm which is resistant to F. oxysporum has been used in disease-resistant breeding, few studies on its molecular mechanism of disease resistance have been reported. To comprehensively study the mechanism of resistance to F. oxysporum, transcriptome sequencings of root tissues from Lilium pumilum inoculated with F. oxysporum or sterile water for 6, 12, or 24 h were performed. A total of 50 GB of data were obtained from the transcriptome sequencings of the 6 L. pumilum samples, and 217 098 Unigenes were obtained after the de novo assembly, of which 38.36% Unigenes were annotated. The sequencing results showed that the numbers of differentially expressed genes at 6, 12, and 24 h after inoculation compared with the control were 111, 254, and 2500, respectively. The functional enrichment analysis of the differentially expressed genes showed that several pathways were involved in responses of L. pumilum, mainly including starch and sucrose metabolism, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, vitamin B6 (VB6) biosynthesis, acid biosynthesis, proteasome, and ribosome. Transcription factor analysis revealed that the WRKY and ERF families played important roles in responses of L. pumilum to F. oxysporum. The results of this study elucidate the molecular responses to F. oxysporum in lily and lay a theoretical foundation for improving lily breeding and strategies for lily basal rot resistance.

scholarly journals Differential gene expression analysis of ankylosing spondylitis shows deregulation of the HLA-DRB, HLA-DQB, ITM2A, and CTLA4 genes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rowan AlEjielat ◽  
Anas Khaleel ◽  
Amneh H. Tarkhan
Keyword(s):  
Gene Expression ◽  
Ankylosing Spondylitis ◽  
Differentially Expressed Genes ◽  
Gene Network ◽  
Disease Diagnosis ◽  
Receptor Activation ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Inflammatory Disorder ◽  
Data Set

Abstract Background Ankylosing spondylitis (AS) is a rare inflammatory disorder affecting the spinal joints. Although we know some of the genetic factors that are associated with the disease, the molecular basis of this illness has not yet been fully elucidated, and the genes involved in AS pathogenesis have not been entirely identified. The current study aimed at constructing a gene network that may serve as an AS gene signature and biomarker, both of which will help in disease diagnosis and the identification of therapeutic targets. Previously published gene expression profiles of 16 AS patients and 16 gender- and age-matched controls that were profiled on the Illumina HumanHT-12 V3.0 Expression BeadChip platform were mined. Patients were Portuguese, 21 to 64 years old, were diagnosed based on the modified New York criteria, and had Bath Ankylosing Spondylitis Disease Activity Index scores > 4 and Bath Ankylosing Spondylitis Functional Index scores > 4. All patients were receiving only NSAIDs and/or sulphasalazine. Functional enrichment and pathway analysis were performed to create an interaction network of differentially expressed genes. Results ITM2A, ICOS, VSIG10L, CD59, TRAC, and CTLA-4 were among the significantly differentially expressed genes in AS, but the most significantly downregulated genes were the HLA-DRB6, HLA-DRB5, HLA-DRB4, HLA-DRB3, HLA-DRB1, HLA-DQB1, ITM2A, and CTLA-4 genes. The genes in this study were mostly associated with the regulation of the immune system processes, parts of cell membrane, and signaling related to T cell receptor and antigen receptor, in addition to some overlaps related to the IL2 STAT signaling, as well as the androgen response. The most significantly over-represented pathways in the data set were associated with the “RUNX1 and FOXP3 which control the development of regulatory T lymphocytes (Tregs)” and the “GABA receptor activation” pathways. Conclusions Comprehensive gene analysis of differentially expressed genes in AS reveals a significant gene network that is involved in a multitude of important immune and inflammatory pathways. These pathways and networks might serve as biomarkers for AS and can potentially help in diagnosing the disease and identifying future targets for treatment.

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