De novo assembly and transcriptome analysis of differentially expressed genes relevant to variegation in hawthorn flowers

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.

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

10.7287/peerj.preprints.2252v1 ◽

2016 ◽

Cited By ~ 1

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.

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Transcriptome de novo assembly and differentially expressed genes related to cytoplasmic male sterility in kenaf (Hibiscus cannabinus L.)

Molecular Breeding ◽

10.1007/s11032-014-0146-8 ◽

2014 ◽

Vol 34 (4) ◽

pp. 1879-1891 ◽

Cited By ~ 25

Author(s):

Peng Chen ◽

Shanmin Ran ◽

Ru Li ◽

Zhipeng Huang ◽

Jinghua Qian ◽

...

Keyword(s):

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Differentially Expressed Genes ◽

De Novo Assembly ◽

De Novo ◽

Hibiscus Cannabinus ◽

Differentially Expressed

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Differential Gene Expression Analysis of Wheat Breeding Lines Reveal Molecular Insights in Yellow Rust Resistance under Field Conditions

Agronomy ◽

10.3390/agronomy10121888 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1888

Author(s):

Sandeep Kumar Kushwaha ◽

Ramesh R. Vetukuri ◽

Firuz Odilbekov ◽

Nidhi Pareek ◽

Tina Henriksson ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

De Novo ◽

Puccinia Striiformis ◽

Specific Resistance ◽

Expression Profiles ◽

Yellow Rust ◽

Differentially Expressed ◽

Wheat Production ◽

Rust Infection

The evolution of pathogens in the changing climate raises new challenges for wheat production. Yellow rust is one of the major wheat diseases worldwide, leading to an increased use of fungicides to prevent significant yield losses. The enhancement of the resistance potential of wheat cultivars is a necessary and environmentally friendly solution for sustainable wheat production. In this study, we aimed to identify the differentially expressed genes induced upon yellow rust infection in the field. Reference and de novo based transcriptome analysis was performed among the resistant and susceptible lines of a bi-parental population to study the global transcriptome changes in contrasting wheat genotypes. Based on the analysis, the de novo transcriptome analysis approach was found to be more supportive for field studies. Expression profiles, gene ontology, KEGG pathway analysis and enrichment studies indicated the relation between differentially expressed genes of wheat and yellow rust infection. The h0igh expression of genes related to non-race specific resistance along with pathogen-specific resistance might be a reason for the better resistance ability of a resistant wheat genotype in the field. The targeted metagenomic analysis of wheat samples revealed that Puccinia striiformis tritici was the most dominant pathogen along with other pathogens on the collected leaf material and validating the disease scoring carried out in the field and transcriptomics analyses.

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