De novo transcriptome analysis reveals tissue-specific differences in gene expression in Salix arbutifolia

Trees ◽  
2016 ◽  
Vol 30 (5) ◽  
pp. 1647-1655 ◽  
Author(s):  
Guodong Rao ◽  
Yanfei Zeng ◽  
Jinkai Sui ◽  
Jianguo Zhang
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
De Novo ◽  
De Novo Transcriptome ◽  
Tissue Specific

scholarly journals De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nisha Dhiman ◽  
Anil Kumar ◽  
Dinesh Kumar ◽  
Amita Bhattacharya
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Analysis ◽  
Vegetative Growth ◽  
De Novo ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Tissue Specific ◽  
Nardostachys Jatamansi ◽  
Secondary Metabolite Biosynthesis

Abstract The study is the first report on de novo transcriptome analysis of Nardostachys jatamansi, a critically endangered medicinal plant of alpine Himalayas. Illumina GAIIx sequencing of plants collected during end of vegetative growth (August) yielded 48,411 unigenes. 74.45% of these were annotated using UNIPROT. GO enrichment analysis, KEGG pathways and PPI network indicated simultaneous utilization of leaf photosynthates for flowering, rhizome fortification, stress response and tissue-specific secondary metabolites biosynthesis. Among the secondary metabolite biosynthesis genes, terpenoids were predominant. UPLC-PDA analysis of in vitro plants revealed temperature-dependent, tissue-specific differential distribution of various phenolics. Thus, as compared to 25 °C, the phenolic contents of both leaves (gallic acid and rutin) and roots (p-coumaric acid and cinnamic acid) were higher at 15 °C. These phenolics accounted for the therapeutic properties reported in the plant. In qRT-PCR of in vitro plants, secondary metabolite biosynthesis pathway genes showed higher expression at 15 °C and 14 h/10 h photoperiod (conditions representing end of vegetative growth period). This provided cues for in vitro modulation of identified secondary metabolites. Such modulation of secondary metabolites in in vitro systems can eliminate the need for uprooting N. jatamansi from wild. Hence, the study is a step towards effective conservation of the plant.

scholarly journals Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]

2019 ◽  
Author(s):  
JUAN SALAZAR ◽  
Cristian Vergara ◽  
Claudia Jorquera ◽  
Patricio Zapata ◽  
Pedro Martínez Gómez ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Actinidia Deliciosa ◽  
De Novo Transcriptome ◽  
Tissue Specific

Abstract The authors have withdrawn this preprint from Research Square

scholarly journals RNA-Sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars

2020 ◽  
Author(s):  
Amandeep Mittal ◽  
Inderjit Singh Yadav ◽  
Naresh Kumar Arora ◽  
Rajbir Singh Boora ◽  
Meenakshi Mittal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Rna Sequencing ◽  
Fruit Development ◽  
De Novo ◽  
Transcriptome Assembly ◽  
White Pulp ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Tissue Specific

Abstract Background Guava ( Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has potential to set the stage for the functional genomics for traits of commerce. Results Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with N50 of 3,603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues and 68 genes among colored tissue comparisons. Mapping the differentially expressed transcripts over molecular pathways indicate significant hormonal changes during fruit development. Comparisons of red vs green peel in guava cv. Apple Colour, white pulp vs red pulp in Punjab pink and fruit maturation vs ripening in non-coloured Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways. Conclusions Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting colour genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.

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