An RNA-Seq transcriptome analysis revealing novel insights into fluorine absorption and transportation in the tea plant

Botany ◽  
2020 ◽  
Vol 98 (5) ◽  
pp. 249-259
Author(s):  
Xin Huang ◽  
Pu Wang ◽  
Siyi Liu ◽  
Yaru Du ◽  
Dejiang Ni ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Fluorine Content ◽  
Tea Plant ◽  
Glutathione Metabolism ◽  
Rna Seq ◽  
High Concentration ◽  
Systematic Analysis ◽  
Shock Proteins

The tea plant [Camellia sinensis (L.) O. Kuntze] is a species with a high concentration of fluorine in its leaves, especially in the mature leaves. The physiological mechanisms for fluorine absorption and accumulation have been well studied, but the related molecular mechanisms are poorly understood in the tea plant. In this study, transcriptome analysis by RNA-Seq following exposure to 16 mg/L of fluorine for 0, 3, 6, and 24 h was performed to identify the candidate genes involved in the transmembrane transportation of fluorine. More than 1.23 billion high-quality reads were generated, and 259.84 million unigenes were assembled de novo, with 518 216 of them being annotated in the seven databases used. Meanwhile, a large number of transporters, transcription factors, and heat-shock proteins with differential expression in response to high levels of fluorine (P ≤ 0.05) were identified. Comparative transcriptome analysis showed that the uptake of fluorine is related to photosynthesis, plant hormone signal transduction, and glutathione metabolism. Further systematic analysis of nitrate and potassium transporter genes revealed that many of these genes regulate fluorine transportation in roots and leaves. Gene expression and fluorine content analysis in different cultivars revealed CsNRT1/PTR 3.1 and CsPT 8 as the key genes regulating the transmembrane transportation of fluorine in the tea plant.

De novo RNA-Seq based transcriptome analysis of Papiliotrema laurentii strain RY1 under nitrogen starvation

Gene ◽  
2018 ◽  
Vol 645 ◽  
pp. 146-156 ◽  
Author(s):  
Soumyadev Sarkar ◽  
Somnath Chakravorty ◽  
Avishek Mukherjee ◽  
Debanjana Bhattacharya ◽  
Semantee Bhattacharya ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Nitrogen Starvation ◽  
De Novo ◽  
Rna Seq

scholarly journals De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150273 ◽  
Author(s):  
Shivanjali Kotwal ◽  
Sanjana Kaul ◽  
Pooja Sharma ◽  
Mehak Gupta ◽  
Rama Shankar ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Rna Seq ◽  
Plantago Ovata ◽  
De Novo Transcriptome

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

scholarly journals Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Shan Lin ◽  
Zhicheng Zou ◽  
Cuibing Zhou ◽  
Hancheng Zhang ◽  
Zhiming Cai
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Purine Metabolism ◽  
Expression Data ◽  
Rna Seq ◽  
Metabolism Pathway ◽  
Caterpillar Fungus ◽  
Regulated Gene Expression ◽  
Late Stages

Caterpillar fungus is a well-known fungal Chinese medicine. To reveal molecular changes during early and late stages of adenosine biosynthesis, transcriptome analysis was performed with the anamorph strain of caterpillar fungus. A total of 2,764 differentially expressed genes (DEGs) were identified (p≤0.05, |log2 Ratio| ≥ 1), of which 1,737 were up-regulated and 1,027 were down-regulated. Gene expression profiling on 4–10 d revealed a distinct shift in expression of the purine metabolism pathway. Differential expression of 17 selected DEGs which involved in purine metabolism (map00230) were validated by qPCR, and the expression trends were consistent with the RNA-Seq results. Subsequently, the predicted adenosine biosynthesis pathway combined with qPCR and gene expression data of RNA-Seq indicated that the increased adenosine accumulation is a result of down-regulation of ndk, ADK, and APRT genes combined with up-regulation of AK gene. This study will be valuable for understanding the molecular mechanisms of the adenosine biosynthesis in caterpillar fungus.

scholarly journals Transcriptome Analysis of Banana (Musa acuminate L.) in Response to Low-Potassium Stress

Agronomy ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 169
Author(s):  
Min Xu ◽  
Can-Bin Zeng ◽  
Rui He ◽  
Zhen Yan ◽  
Zhao Qi ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Dry Weight ◽  
Phenotypic Traits ◽  
Rna Seq ◽  
Expression Of Genes ◽  
K Deficiency ◽  
Banana Leaves ◽  
Gene Functional Classification ◽  
Low K

Potassium (K+) is an abundant and important macronutrient for plants. It plays crucial roles in many growth and developmental processes, and growth is inhibited under low −K+ conditions. The molecular mechanisms operating under K+ starvation have been little reported in banana, which is a non-model plant. We conducted a transcriptome analysis of banana (Musa acuminata L. AAA group, cv. Cavendish) in response to low −K+ stress. The phenotypic traits and transcriptomic profiles of banana leaves and roots were compared between low −K+ (LK) and normal −K+ (NK) groups. The phenotypic parameters for the LK group, including fresh and dry weight, were lower than those for the NK group, which suggested that low −K+ stress may inhibit some important metabolic and biosynthetic processes. K+ content and biomass were both decreased in the LK group compared to the NK group. Following ribonucleic acid sequencing (RNA-Seq), a total of 26,796 expressed genes were detected in normal −K+ leaves (NKL), 27,014 were detected in low −K+ leaves (LKL), 29,158 were detected in normal −K+ roots (NKR), and 28,748 were detected in low −K+ roots (LKR). There were 797 up-regulated differentially expressed genes (DEGs) and 386 down-regulated DEGs in NKL versus LKL, while there were 1917 up-regulated DEGs and 2830 down-regulated DEGs in NKR versus LKR. This suggested that the roots were more sensitive to low −K+ stress than the leaves. DEGs related to K+ transport and uptake were analyzed in detail. Gene functional classification showed that the expression of genes regarding ABC transporters, protein kinases, transcription factors, and ion transporters were also detected, and may play important roles during K+ deficiency.

scholarly journals MiMIF-2 Effector of Meloidogyne incognita Exhibited Enzyme Activities and Potential Roles in Plant Salicylic Acid Synthesis

2020 ◽  
Vol 21 (10) ◽  
pp. 3507
Author(s):  
Jianlong Zhao ◽  
Zhenchuan Mao ◽  
Qinghua Sun ◽  
Qian Liu ◽  
Heng Jian ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Transcriptome Analysis ◽  
Meloidogyne Incognita ◽  
Plant Immunity ◽  
Acid Synthesis ◽  
Host Immunity ◽  
Parasitic Nematodes ◽  
Marker Genes ◽  
Rna Seq ◽  
Shock Proteins

Plant-parasitic nematodes secrete a series of effectors to promote parasitism by modulating host immunity, but the detailed molecular mechanism is ambiguous. Animal parasites secrete macrophage migration inhibitory factor (MIF)-like proteins for evasion of host immune systems, in which their biochemical activities play essential roles. Previous research demonstrated that MiMIF-2 effector was secreted by Meloidogyne incognita and modulated host immunity by interacting with annexins. In this study, we show that MiMIF-2 had tautomerase activity and protected nematodes against H2O2 damage. MiMIF-2 expression not only decreased the amount of H2O2 generation during nematode infection in Arabidopsis, but also suppressed Bax-induced cell death by inhibiting reactive oxygen species burst in Nicotiana benthamiana. Further, RNA-seq transcriptome analysis and RT-qPCR showed that the expression of some heat-shock proteins was down regulated in MiMIF-2 transgenic Arabidopsis. After treatment with flg22, RNA-seq transcriptome analysis indicated that the differentially expressed genes in MiMIF-2 expressing Arabidopsis were pointed to plant hormone signal transduction, compound metabolism and plant defense. RT-qPCR and metabolomic results confirmed that salicylic acid (SA) related marker genes and SA content were significantly decreased. Our results provide a comprehensive understanding of how MiMIF-2 modulates plant immunity and broaden knowledge of the intricate relationship between M. incognita and host plants.

De novo transcriptome analysis of mulberry (Morus L.) under drought stress using RNA-Seq technology

2014 ◽  
Vol 40 (4) ◽  
pp. 423-432 ◽  
Author(s):  
Heng Wang ◽  
Wei Tong ◽  
Li Feng ◽  
Qian Jiao ◽  
Li Long ◽  
...  
Keyword(s):  
Drought Stress ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Rna Seq ◽  
De Novo Transcriptome
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