Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici

Abstract Background As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. Results In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. Conclusions This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.

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Genome-wide identification and analysis of class III peroxidases in Betula pendula

BMC Genomics ◽

10.1186/s12864-021-07622-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Kewei Cai ◽

Huixin Liu ◽

Song Chen ◽

Yi Liu ◽

Xiyang Zhao ◽

...

Keyword(s):

Stress Responses ◽

Betula Pendula ◽

Expression Patterns ◽

Class Iii ◽

Physiological Processes ◽

Plant Life ◽

Genome Wide ◽

Plant Life Cycle ◽

Class Iii Peroxidases ◽

And Function

Abstract Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. Results We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

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Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

10.7287/peerj.preprints.27606v1 ◽

2019 ◽

Author(s):

Yongbin Wang ◽

Zhenfeng Jiang ◽

Zhenxiang Li ◽

Yuanling Zhao ◽

Weiwei Tan ◽

...

Keyword(s):

Glycine Max ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Pcr Analysis ◽

Rna Seq ◽

Biological Functions ◽

Conserved Domain ◽

Genome Wide ◽

Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

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Deficiency in the double-stranded RNA binding protein HYPONASTIC LEAVES1 increases sensitivity to the endoplasmic reticulum stress inducer tunicamycin in Arabidopsis

BMC Research Notes ◽

10.1186/s13104-019-4623-3 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Rikako Hirata ◽

Kei-ichiro Mishiba ◽

Nozomu Koizumi ◽

Yuji Iwata

Keyword(s):

Endoplasmic Reticulum ◽

Er Stress ◽

Stress Responses ◽

Rna Binding ◽

Transcriptional Response ◽

Mirna Biogenesis ◽

Loss Of Function ◽

Wild Type ◽

Protein Coding ◽

And Function

Abstract Objective microRNA (miRNA) is a small non-coding RNA that regulates gene expression by sequence-dependent binding to protein-coding mRNA in eukaryotic cells. In plants, miRNA plays important roles in a plethora of physiological processes, including abiotic and biotic stress responses. The present study was conducted to investigate whether miRNA-mediated regulation is important for the endoplasmic reticulum (ER) stress response in Arabidopsis. Results We found that hyl1 mutant plants are more sensitive to tunicamycin, an inhibitor of N-linked glycosylation that causes ER stress than wild-type plants. Other miRNA-related mutants, se and ago1, exhibited similar sensitivity to the wild-type, indicating that the hypersensitive phenotype is attributable to the loss-of-function of HYL1, rather than deficiency in general miRNA biogenesis and function. However, the transcriptional response of select ER stress-responsive genes in hyl1 mutant plants was indistinguishable from that of wild-type plants, suggesting that the loss-of-function of HYL1 does not affect the ER stress signaling pathways.

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Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens

International Journal of Molecular Sciences ◽

10.3390/ijms21030975 ◽

2020 ◽

Vol 21 (3) ◽

pp. 975 ◽

Cited By ~ 8

Author(s):

Xiaojun Pu ◽

Lixin Yang ◽

Lina Liu ◽

Xiumei Dong ◽

Silin Chen ◽

...

Keyword(s):

Stress Responses ◽

Physcomitrella Patens ◽

Myb Transcription Factor ◽

Rna Seq ◽

Genome Wide ◽

Terrestrial Environments ◽

Gene Structures ◽

Myb Genes ◽

Myb Proteins ◽

R2r3 Myb

MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments.

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Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

International Journal of Molecular Sciences ◽

10.3390/ijms21103711 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3711

Author(s):

Melina J. Sedano ◽

Alana L. Harrison ◽

Mina Zilaie ◽

Chandrima Das ◽

Ramesh Choudhari ◽

...

Keyword(s):

Rna Sequencing ◽

Expression Patterns ◽

Biological Significance ◽

Rna Seq ◽

Biological Functions ◽

Protein Coding ◽

Rna Molecules ◽

Non Coding Rna ◽

Genome Wide ◽

Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

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Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

10.21203/rs.2.20023/v1 ◽

2020 ◽

Author(s):

Duo Lv ◽

Gang Wang ◽

Yue Chen ◽

Liang-Rong Xiong ◽

Jing-Xian Sun ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Patterns ◽

Regulatory Elements ◽

Kinase Gene ◽

Cucumis Sativus L ◽

Lectin Receptor ◽

Genome Wide ◽

Cucumber Genome ◽

And Function

Abstract Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.).Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (Cs LecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.

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Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽

10.7717/peerj.7950 ◽

2019 ◽

Vol 7 ◽

pp. e7950 ◽

Cited By ~ 2

Author(s):

Yongbin Wang ◽

Lei Ling ◽

Zhenfeng Jiang ◽

Weiwei Tan ◽

Zhaojun Liu ◽

...

Keyword(s):

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth And Development ◽

Genomic Data ◽

Evolutionary Analysis ◽

Rna Seq ◽

Plant Growth And Development ◽

Genome Wide ◽

Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

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Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Scientific Reports ◽

10.1038/srep45981 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 38

Author(s):

Shuxia Li ◽

Xiang Yu ◽

Ning Lei ◽

Zhihao Cheng ◽

Pingjuan Zhao ◽

...

Keyword(s):

Drought Stress ◽

Experimental Studies ◽

Growth And Yield ◽

Rna Seq ◽

Functional Prediction ◽

Systematic Screening ◽

Cellular Processes ◽

Genome Wide ◽

Young Leaves ◽

And Control

Abstract Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

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Network analysis links genome-wide phenotypic and transcriptional stress responses in a bacterial pathogen with a large pan-genome

10.1101/071704 ◽

2016 ◽

Cited By ~ 1

Author(s):

Paul A. Jensen ◽

Zeyu Zhu ◽

Tim van Opijnen

Keyword(s):

Gene Expression ◽

Stress Responses ◽

Meta Analysis ◽

Bacterial Pathogen ◽

Metabolic Model ◽

Genetic Network ◽

Rna Seq ◽

Genome Wide ◽

A Genome ◽

Response To Stress

ABSTRACTBackgroundBacteria modulate subcellular processes to handle stressful environments. Genome-wide profiling of gene expression (RNA-Seq) and fitness (Tn-Seq) allows two views of the same genetic network underlying these responses. However, it remains unclear how they combine, enabling a bacterium to overcome a perturbation.ResultsHere we generate RNA-Seq and Tn-Seq profiles in three strains of S. pneumoniae in response to stress defined by different levels of nutrient depletion. These profiles show that genes that change their expression and/or become phenotypically important come from a diverse set of functional categories, and genes that are phenotypically important tend to be highly expressed. Surprisingly, we find that expression and fitness changes rarely occur on the same gene, which we confirmed by over 140 validation experiments. To rationalize these unexpected results we built the first genome-scale metabolic model of S. pneumoniae showing that differential expression and phenotypic importance actually correlate between nearest neighbors, although they are distinctly partitioned into small subnetworks. Moreover, a meta-analysis of 234 S. pneumoniae gene expression studies reveals that essential genes and phenotypically important subnetworks rarely change expression, indicating that they are shielded from transcriptional fluctuations and that a clear distinction exists between transcriptional and phenotypic response networks.ConclusionsWe present a genome-wide computational/experimental approach that contextualizes changes that occur on transcriptomic and phenomic levels in response to stress. Importantly, this highlights the need to connect disparate response networks, for instance in antibiotic target identification, where preferred targets are phenotypically important genes that would be overlooked by transcriptomic analyses alone.

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Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

BMC Genomics ◽

10.1186/s12864-021-08134-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zihan Cheng ◽

Xuemei Zhang ◽

Wenjing Yao ◽

Yuan Gao ◽

Kai Zhao ◽

...

Keyword(s):

Salt Stress ◽

Stress Responses ◽

Tissue Specificity ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Rna Seq ◽

Salt Stress Response ◽

Populus Simonii ◽

Cis Acting ◽

Genome Wide

Abstract Background Xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in cell wall reconstruction and stress resistance in plants. However, the detailed characteristics of XTH family genes and their expression pattern under salt stress have not been reported in poplar. Results In this study, a total of 43 PtrXTH genes were identified from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoters of the PtrXTH genes contain mutiple cis-acting elements related to growth and development and stress responses. Collinearity analysis revealed that the XTH genes from poplar has an evolutionary relationship with other six species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Based on RNA-Seq analysis, the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, there are11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress. In addition, the accuracy of RNA-Seq results was verified by RT-qPCR. Conclusion All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study will lay a theoretical foundation for further study on molecular function of XTH genes in poplar.

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