Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)

Abstract Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.

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Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus

Pathogens ◽

10.3390/pathogens8040183 ◽

2019 ◽

Vol 8 (4) ◽

pp. 183 ◽

Cited By ~ 4

Author(s):

Oh ◽

Lim ◽

Song ◽

Ahn ◽

Lee ◽

...

Keyword(s):

Varicella Zoster Virus ◽

Differentially Expressed Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Dermal Fibroblasts ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Human Dermal Fibroblasts ◽

Varicella Zoster ◽

Low Passage

Licensed live attenuated vaccines have been developed to prevent varicella zoster virus (VZV) infection, which causes chickenpox and shingles. The genomic sequences of both clinical- and vaccine-derived VZV strains have been analyzed previously. To further characterize the molecular signatures and complexity of wildtype (clinical) versus attenuated (vaccine-derived) VZV-mediated host cellular responses, we performed high-throughput next generation sequencing to quantify and compare the expression patterns of mRNAs and microRNAs (miRNAs) in primary human dermal fibroblasts (HDFs) infected with wildtype (YC01 low passage) and attenuated (YC01 high passage, SuduVax, and VarilRix) VZV strains. 3D-multidimensional scaling of the differentially expressed genes demonstrated the distinct grouping of wildtype and attenuated strains. In particular, we observed that HDFs infected with attenuated strains had more differentially expressed genes (DEGs) involved in the retinoic-acid inducible gene–I-like receptor and interferon-mediated signaling pathways compared with wildtype strains. Additionally, miRNA expression patterns were profiled following the infection of HDFs with VZV. Small RNA sequencing identified that several miRNAs were upregulated, including miR-146a-5p, which has been associated with other herpesvirus infections, whereas let-7a-3p was downregulated in both wildtype and attenuated VZV-infected cells. This study identified genes and miRNAs that may be essential in VZV pathogenesis.

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Comprehensive MicroRNA Expression Profile of the Mammary Gland in Lactating Dairy Cows With Extremely Different Milk Protein and Fat Percentages

Frontiers in Genetics ◽

10.3389/fgene.2020.548268 ◽

2020 ◽

Vol 11 ◽

Author(s):

Xiaogang Cui ◽

Shengli Zhang ◽

Qin Zhang ◽

Xiangyu Guo ◽

Changxin Wu ◽

...

Keyword(s):

Mammary Gland ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Small Rna ◽

Milk Protein ◽

Milk Composition ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Rna Seq

A total of 31 differentially expressed genes in the mammary glands were identified in our previous study using RNA sequencing (RNA-Seq), for lactating cows with extremely high and low milk protein and fat percentages. To determine the regulation of milk composition traits, we herein investigated the expression profiles of microRNA (miRNA) using small RNA sequencing based on the same samples as in the previous RNA-Seq experiment. A total of 497 known miRNAs (miRBase, release 22.1) and 49 novel miRNAs among the reads were identified. Among these miRNAs, 71 were found differentially expressed between the high and low groups (p < 0.05, q < 0.05). Furthermore, 21 of the differentially expressed genes reported in our previous RNA-Seq study were predicted as target genes for some of the 71 miRNAs. Gene ontology and KEGG pathway analyses showed that these targets were enriched for functions such as metabolism of protein and fat, and development of mammary gland, which indicating the critical role of these miRNAs in regulating the formation of milk protein and fat. With dual luciferase report assay, we further validated the regulatory role of 7 differentially expressed miRNAs through interaction with the specific sequences in 3′UTR of the targets. In conclusion, the current study investigated the complexity of the mammary gland transcriptome in dairy cattle using small RNA-seq. Comprehensive analysis of differential miRNAs expression and the data from previous study RNA-seq provided the opportunity to identify the key candidate genes for milk composition traits.

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Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings

BMC Plant Biology ◽

10.1186/s12870-019-2203-2 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 5

Author(s):

Houqing Zeng ◽

Xin Zhang ◽

Ming Ding ◽

Yiyong Zhu

Keyword(s):

Differentially Expressed Genes ◽

Transcriptome Sequencing ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Zn Deficiency ◽

Rice Seedlings ◽

Regulatory Pathways

Abstract Background Zinc (Zn) deficiency is one of the most widespread soil constraints affecting rice productivity, but the molecular mechanisms underlying the regulation of Zn deficiency response is still limited. Here, we aim to understand the molecular mechanisms of Zn deficiency response by integrating the analyses of the global miRNA and mRNA expression profiles under Zn deficiency and resupply in rice seedlings by integrating Illumina’s high-throughput small RNA sequencing and transcriptome sequencing. Results The transcriptome sequencing identified 360 genes that were differentially expressed in the shoots and roots of Zn-deficient rice seedlings, and 97 of them were recovered after Zn resupply. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply. The integrated analyses of miRNAome and transcriptome data showed that 12 differentially expressed genes are the potential target genes of 10 Zn-responsive miRNAs such as miR171g-5p, miR397b-5p, miR398a-5p and miR528-5p. Some miRNA genes and differentially expressed genes were selected for validation by quantitative RT-PCR, and their expressions were similar to that of the sequencing results. Conclusion These results provide insights into miRNA-mediated regulatory pathways in Zn deficiency response, and provide candidate genes for genetic improvement of Zn deficiency tolerance in rice.

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Small RNA and Transcriptome Sequencing Reveals miRNA Regulation of Floral Thermogenesis in Nelumbo nucifera

International Journal of Molecular Sciences ◽

10.3390/ijms21093324 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3324

Author(s):

Yu Zou ◽

Guanglong Chen ◽

Jing Jin ◽

Ying Wang ◽

Meiling Xu ◽

...

Keyword(s):

Small Rna ◽

Transcriptome Sequencing ◽

Developmental Stages ◽

Expression Patterns ◽

Nelumbo Nucifera ◽

Differentially Expressed ◽

Cellular Respiration ◽

Small Rna Sequencing ◽

Mirna Regulation ◽

Oxidoreductase Activity

The sacred lotus (Nelumbo nucifera Gaertn.) can produce heat autonomously and maintain a relatively stable floral chamber temperature for several days when blooming. Floral thermogenesis is critical for flower organ development and reproductive success. However, the regulatory role of microRNA (miRNA) underlying floral thermogenesis in N. nucifera remains unclear. To comprehensively understand the miRNA regulatory mechanism of thermogenesis, we performed small RNA sequencing and transcriptome sequencing on receptacles from five different developmental stages. In the present study, a total of 172 known miRNAs belonging to 39 miRNA families and 126 novel miRNAs were identified. Twenty-nine thermogenesis-related miRNAs and 3024 thermogenesis-related mRNAs were screened based on their expression patterns. Of those, seventeen differentially expressed miRNAs (DEMs) and 1765 differentially expressed genes (DEGs) had higher expression during thermogenic stages. The upregulated genes in the thermogenic stages were mainly associated with mitochondrial function, oxidoreductase activity, and the energy metabolism process. Further analysis showed that miR156_2, miR395a_5, miR481d, and miR319p may play an important role in heat-producing activity by regulating cellular respiration-related genes. This study provides comprehensive miRNA and mRNA expression profile of receptacle during thermogenesis in N. nucifera, which advances our understanding on the regulation of floral thermogenesis mediated by miRNA.

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Integrative analysis of transcriptome and proteome revealed nectary and nectar traits in the plant-pollinator interaction of Nitraria tangutorum Bobrov

BMC Plant Biology ◽

10.1186/s12870-021-03002-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Tingting Chen ◽

Yanwei Zhou ◽

Jingbo Zhang ◽

Ye Peng ◽

Xiuyan Yang ◽

...

Keyword(s):

Signal Transduction ◽

Differentially Expressed Genes ◽

Plant Pathogen ◽

Plant Hormone ◽

Flavonoid Biosynthesis ◽

Epidermal Cells ◽

Differentially Expressed ◽

Ascorbate Oxidase ◽

Nitraria Tangutorum ◽

Plant Pathogen Interaction

Abstract Background Nitraria tangutorum is an important desert shrub that shows resistance to drought, salt and wind erosion stresses. It is a central ecological species in its area. Here, we have studied how N. tangutorum has adapted to achieve a successful reproduction strategy. Results We found that N. tangutorum is mainly pollinated by insects of the Hymenoptera, Diptera and Coleoptera orders. Nitraria tangutorum has very small flowers, with the nectary composed of secretive epidermal cells from which nectar is secreted, located within the inner petals. In addition, analyzing the transcriptome of four successive flower developmental stages revealed that mainly differentially expressed genes associated with flower and nectary development, nectar biosynthesis and secretion, flavonoid biosynthesis, plant hormone signal transduction and plant-pathogen interaction show dynamic expression. From the nectar, we could identify seven important proteins, of which the L-ascorbate oxidase protein was first found in plant nectar. Based on the physiological functions of these proteins, we predict that floral nectar proteins of N. tangutorum play an important role in defending against microbial infestation and scavenging active oxygen. Conclusions This study revealed that N. tangutorum is an insect-pollinated plant and its nectary is composed of secretive epidermal cells that specialized into secretive trichomes. We identified a large number of differentially expressed genes controlling flower and nectary development, nectar biosynthesis and secretion, flavonoid biosynthesis, plant hormone signal transduction and plant-pathogen interaction. We suggest that proteins present in N. tangutorum nectar may have both an antibacterial and oxygen scavenging effect. These results provide a scientific basis for exploring how the reproductive system of N. tangutorum and other arid-desert plants functions.

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A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

10.21203/rs.2.16108/v1 ◽

2019 ◽

Author(s):

Shunkai Hu ◽

Yiqing Yang ◽

Mi Zhang ◽

Wei Xuan ◽

Zhongwei Zou ◽

...

Keyword(s):

Signal Transduction ◽

Transcription Factors ◽

Nitrogen Metabolism ◽

Differentially Expressed Genes ◽

Lateral Roots ◽

Nitrogen Concentration ◽

Tea Plant ◽

Differentially Expressed ◽

Auxin Signaling ◽

Low Nitrogen

Abstract Lateral roots (LRs) are the main organ for tea plant to absorb soil moisture and nutrients. Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. LRs formation and development are limited by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in LRs of tea plant treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of genes expression; thus, regulated lateral roots formation. Furthermore, metabolisms of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant LRs formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. This study provides new insights into the mechanisms associated with nitrogen-auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level

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Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa

Horticulture Research ◽

10.1038/s41438-021-00535-w ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Bo Chen ◽

Huimin Xu ◽

Yayu Guo ◽

Paul Grünhofer ◽

Lukas Schreiber ◽

...

Keyword(s):

Signal Transduction ◽

Plant Hormone ◽

Target Genes ◽

Populus Tomentosa ◽

Differentially Expressed ◽

Vascular Cambium ◽

Differentially Methylated Region ◽

Gene Body Methylation ◽

Transcription Analysis ◽

Global Methylation

AbstractTrees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium in Populus tomentosa during the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.

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Transcriptome-Based Analysis of Phosphite-Induced Resistance against Pathogens in Rice

Plants ◽

10.3390/plants9101334 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1334

Author(s):

Yuqing Huang ◽

Shengguan Cai ◽

Guoping Zhang ◽

Songlin Ruan

Keyword(s):

Signal Transduction ◽

Molecular Mechanism ◽

Differentially Expressed Genes ◽

Induced Resistance ◽

Plant Hormone ◽

Xanthomonas Oryzae ◽

Pyricularia Grisea ◽

Protection Effect ◽

Phenylpropanoid Biosynthesis ◽

Xanthomonas Oryzae Pv.Oryzae

Phosphite (PHI) has been used in the management of Phytophthora diseases since the 1970s.We assessed the effect of PHI on controlling the incidence of Xanthomonas oryzae pv.oryzae and Pyricularia grisea. As a result, PHI application significantly inhibited the incidence of the diseases. To clarify the molecular mechanism underlying this, a transcriptome study was employed. In total, 2064 differentially expressed genes (DEGs) were identified between control and PHI treatment. The key DEGs could be classified into phenylpropanoid biosynthesis (ko00940), starch and sucrose metabolism (ko00500), and plant hormone signal transduction (ko04075). The expressions of defense-related genes had a higher expression lever upon PHI treatment. This study provides new insights into the mechanism of protection effect of PHI against pathogens.

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HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽

10.3390/v13020244 ◽

2021 ◽

Vol 13 (2) ◽

pp. 244 ◽

Cited By ~ 1

Author(s):

Antonio Victor Campos Coelho ◽

Rossella Gratton ◽

João Paulo Britto de Melo ◽

José Leandro Andrade-Santos ◽

Rafael Lima Guimarães ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Differentially Expressed Genes ◽

Cd4 T Cells ◽

Expression Profiles ◽

Meta Analysis ◽

Differentially Expressed ◽

Rna Seq ◽

Infected Cells ◽

Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

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