Identification of microRNAs responding to cold stress in Dongxiang common wild rice

Genome ◽  
2019 ◽  
Vol 62 (9) ◽  
pp. 635-642
Author(s):  
Wanxia Jiang ◽  
Wenkuan Shi ◽  
Xin Ma ◽  
Jie Zhao ◽  
Shanshan Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Wild Rice ◽  
Target Genes ◽  
Small Rna Sequencing ◽  
Growth Stages ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Common Wild Rice ◽  
Genome Wide ◽  
Different Growth Stages

Low temperature is a vital effector of rice at different growth stages. MicroRNAs (miRNAs) play important roles in responding to abiotic and biotic stresses. Here, we confirmed the cold tolerance of Dongxiang common wild rice and explored the miRNAs differentially expressed under cold stress using genome-wide small RNA sequencing. In total, 16 miRNAs, nine upregulated and seven downregulated by cold stress, were characterized in Dongxiang common wild rice, and their target genes were predicted. Additionally, an AgriGO analysis of the target genes revealed that they were enriched in several terms related to cold-stress tolerance, suggesting a complex response mechanism, involving miRNAs, to cold stress in Dongxiang common wild rice.

scholarly journals Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1867
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Jiatong Wei ◽  
Kewei Cai ◽  
Hongzhi Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Cold Stress ◽  
Gene Family ◽  
Gene Families ◽  
Regulatory Function ◽  
Wrky Gene ◽  
Wrky Transcription Factors ◽  
Biotic Stresses ◽  
Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

scholarly journals Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L.

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247170
Author(s):  
Md. Soyib Hasan ◽  
Vishal Singh ◽  
Shiful Islam ◽  
Md. Sifatul Islam ◽  
Raju Ahsan ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Drought Treatment ◽  
Specific Expression ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Genome Wide

Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1‐chloro‐2,4‐dinitrobenzene (CDNB) with the lowest binding energy of—5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.

scholarly journals Genome-Wide Expression Difference of MicroRNAs in Basal Cell Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Hai-Peng Wei ◽  
Song Zhan ◽  
Qing-An Zhu ◽  
Zhen-Juan Chen ◽  
Xian Feng ◽  
...  
Keyword(s):  
Basal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Basal Cell ◽  
Target Genes ◽  
Expression Profiles ◽  
Taqman Probe ◽  
Control Group ◽  
Small Rna Sequencing ◽  
Mirna Regulation ◽  
Genome Wide

Distinct expression of the miRNAs has rarely been explored in basal cell carcinoma (BCC) of skin, and the regulatory role of miRNAs in BCC development remains quite opaque. Here, we collected control tissues from adjacent noncancerous skin ( n = 15 ; control group) and tissues at tumor centers from patients with cheek BCC ( n = 15 ; BCC group) using punch biopsies. After six small RNA sequencing- (sRNA-seq-) based miRNA expression profiles were generated for both BCC and controls, including three biological replicates, we conducted comparative analysis on the sRNA-seq dataset, discovering 181 differentially expressed miRNAs (DEMs) out of the 1,873 miRNAs in BCCs. In order to validate the sRNA-seq data, expression of 15 randomly selected DEMs was measured using the TaqMan probe-based quantitative real-time PCR. Functional analysis of predicted target genes of DEMs in BCCs shows that these miRNAs are primarily involved in various types of cancers, immune response, epithelial growth, and morphogenesis, as well as energy production and metabolism, indicating that BCC development is caused, at least in part, by changes in miRNA regulation for biological and disease processes. In particular, the “basal cell carcinoma pathways” were found to be enriched by predicted DEM targets, and regulatory relationships between DEMs and their targeted genes in this pathway were further uncovered. These results revealed the association between BCCs and abundant miRNA molecules that regulate target genes, functional modules, and signaling pathways in carcinogenesis.

scholarly journals Genome-Wide Identification, Phylogenetic and Expression Pattern Analysis of GATA Family Genes in Cucumber (Cucumis sativus L.)

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1626
Author(s):  
Kaijing Zhang ◽  
Li Jia ◽  
Dekun Yang ◽  
Yuchao Hu ◽  
Martin Kagiki Njogu ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Constitutive Expression ◽  
Regulatory Elements ◽  
Homologous Gene ◽  
Abiotic And Biotic Stresses ◽  
Characteristic Type ◽  
Biotic Stresses ◽  
Gata Family

GATA transcription factors are a class of transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain, which play important roles in plant growth and development. The GATA gene family has been characterized in various plant species. However, GATA family genes have not been identified in cucumber. In this study, 26 GATA family genes were identified in cucumber genome, whose physicochemical characteristics, chromosomal distributions, phylogenetic tree, gene structures conserved motifs, cis-regulatory elements in promoters, homologous gene pairs, downstream target genes were analyzed. Tissue expression profiles of cucumber GATA family genes exhibited that 17 GATA genes showed constitutive expression, and some GATA genes showed tissue-specific expression patterns. RNA-seq analysis of green and virescent leaves revealed that seven GATA genes might be involved in the chloroplast development and chlorophyll biosynthesis. Importantly, expression patterns analysis of GATA genes in response to abiotic and biotic stresses indicated that some GATA genes respond to either abiotic stress or biotic stress, some GATA genes such as Csa2G162660, Csa3G017200, Csa3G165640, Csa4G646060, Csa5G622830 and Csa6G312540 were simultaneously functional in resistance to abiotic and biotic stresses. Overall, this study will provide useful information for further analysis of the biological functions of GATA factors in cucumber.

Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

2019 ◽  
Vol 17 (5) ◽  
pp. 448-451
Author(s):  
Fantao Zhang ◽  
Yuan Luo ◽  
Bin Ai ◽  
Yong Chen ◽  
Weidong Qi ◽  
...  
Keyword(s):  
Wild Rice ◽  
Oryza Rufipogon ◽  
Genomic Research ◽  
Cultivated Rice ◽  
Structural Variations ◽  
Rice Varieties ◽  
Common Wild Rice ◽  
Genome Wide ◽  
Rice Chromosomes ◽  
Molecular Marker Development

AbstractDongxiang common wild rice (Oryza rufipogon Griff., DXWR) is an important genetic resource for the improvement of cultivated rice. For the past three decades, great achievements have been made in the field of molecular marker development. Although structural variations (SVs) had been studied between DXWR and Nipponbare (Oryza sativa L. ssp. japonica), the development and application of SV markers in DXWR has not been reported. In this study, based on the genome-wide SV loci, we developed and synthesized a total of 195 SV markers that were evenly distributed across the 12 rice chromosomes. Then, these markers were tested for their stabilities and polymorphisms. Of these 195 markers, 147 (75.4%) were successfully amplified and displayed abundant polymorphisms between DXWR and Nipponbare. Meanwhile, through the genotyping of 20 rice varieties from 13 countries and areas, we concluded that these SV markers have a wide application prospect in the analysis of cultivated rice. Therefore, these molecular markers greatly enrich the number of markers available for DXWR, which will facilitate genomic research and molecular breeding for this important and endangered germplasm resource.

scholarly journals Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0180662 ◽  
Author(s):  
Wen Liu ◽  
Fozia Ghouri ◽  
Hang Yu ◽  
Xiang Li ◽  
Shuhong Yu ◽  
...  
Keyword(s):  
Wild Rice ◽  
Oryza Rufipogon ◽  
Common Wild Rice ◽  
Genome Wide ◽  
Oryza Rufipogon Griff

scholarly journals Dynamic changes of genomic methylation profiles at different growth stages in Chinese Tan sheep

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yufang Liu ◽  
Qiao Xu ◽  
Xiaolong Kang ◽  
Kejun Wang ◽  
Jve Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Economic Value ◽  
Growth Stages ◽  
Dynamic Changes ◽  
Genome Wide ◽  
Tan Sheep ◽  
Genomic Methylation ◽  
Different Growth Stages

Abstract Background Tan sheep, an important local sheep breed in China, is famous for their fur quality. One-month-old Tan sheep have white, curly hair with beautiful flower spikes, commonly known as “nine bends”, which has high economic value. However, the “nine bends” characteristic gradually disappears with age; consequently, the economic value of the Tan sheep decreases. Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression. Until now, no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages. In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing, and compared the DNA methylation levels at three different growth stages: 1, 24, and 48 months old (mon1, mon24, and mon48, respectively). Results In this study, 11 skin samples from three growth stages (four for mon1, four for mon24, and three for mon48) were used for DNA methylation analysis and gene expression profiling. There were 52, 288 and 236 differentially methylated genes (DMGs) identified between mon1 and mon24, mon1 and mon48, and mon24 and mon48, respectively. Of the differentially methylated regions, 1.11%, 7.61%, and 7.65% were in the promoter in mon1 vs. mon24, mon24 vs. mon48, and mon1 vs. mon48, respectively. DMGs were enriched in the MAPK and WNT signaling pathways, which are related to age growth and hair follicle morphogenesis processes. There were 51 DMGs associated with age growth and curly fleece formation. Four DMGs between mon1 and mon48 (KRT71, CD44, ROR2 and ZDHHC13) were further validated by bisulfite sequencing. Conclusions This study revealed dynamic changes in the genomic methylation profiles of mon1, mon24, and mon48 sheep, and the percentages of methylated cytosines were 3.38%, 2.85% and 4.17%, respectively. Of the DMGs, KRT71 and CD44 were highly methylated in mon1, and ROR2 and ZDHHC13 were highly methylated in mon48. These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.

scholarly journals Early-life stress induces genome-wide sex-dependent miRNA expression and correlation across limbic brain areas in rats

Epigenomics ◽  
2021 ◽  
Author(s):  
Lauren A McKibben ◽  
Yogesh Dwivedi
Keyword(s):  
Prefrontal Cortex ◽  
Mirna Expression ◽  
Life Stress ◽  
Early Life ◽  
Target Genes ◽  
Maternal Separation ◽  
Early Life Stress ◽  
Small Rna Sequencing ◽  
Dependent Manner ◽  
Genome Wide

Aims: The aim of this study was to assess regional- and sex-dependent changes in miRNA expression resulting from early-life stress (ELS). Materials and methods: Small RNA sequencing was used to determine sex-dependent changes in miRNAs after maternal separation, a rodent model of ELS, across the prefrontal cortex, amygdala and hippocampus. Results: Maternal separation induced anhedonia and altered miRNA expression in a sex-dependent manner, particularly in the prefrontal cortex and hippocampus. Gene ontology revealed that these miRNAs target genes with brain-specific biological functions. Conclusions: Using a network approach to explore miRNA signaling across the brain after ELS, regional differences were highlighted as key to studying the brain’s stress response, which indicates that sex is critical for understanding miRNA-mediated ELS-induced behavior.

scholarly journals Genome-wide identification and biochemical characterization of calcineurin B-like calcium sensor proteins in Chlamydomonas reinhardtii

2020 ◽  
Vol 477 (10) ◽  
pp. 1879-1892
Author(s):  
Manoj Kumar ◽  
Komal Sharma ◽  
Akhilesh K. Yadav ◽  
Kajal Kanchan ◽  
Madhu Baghel ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Biochemical Characterization ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Physiological Processes ◽  
Calcineurin B ◽  
Genome Wide ◽  
Dependent Protein ◽  
Sensor Proteins

Calcium (Ca2+) signaling is involved in the regulation of diverse biological functions through association with several proteins that enable them to respond to abiotic and biotic stresses. Though Ca2+-dependent signaling has been implicated in the regulation of several physiological processes in Chlamydomonas reinhardtii, Ca2+ sensor proteins are not characterized completely. C. reinhardtii has diverged from land plants lineage, but shares many common genes with animals, particularly those encoding proteins of the eukaryotic flagellum (or cilium) along with the basal body. Calcineurin, a Ca2+/calmodulin-dependent protein phosphatase, is an important effector of Ca2+ signaling in animals, while calcineurin B-like proteins (CBLs) play an important role in Ca2+ sensing and signaling in plants. The present study led to the identification of 13 novel CBL-like Ca2+ sensors in C. reinhardtii genome. One of the archetypical genes of the newly identified candidate, CrCBL-like1 was characterized. The ability of CrCBL-like1 protein to sense as well as bind Ca2+ were validated using two-step Ca2+-binding kinetics. The CrCBL-like1 protein localized around the plasma membrane, basal bodies and in flagella, and interacted with voltage-gated Ca2+ channel protein present abundantly in the flagella, indicating its involvement in the regulation of the Ca2+ concentration for flagellar movement. The CrCBL-like1 transcript and protein expression were also found to respond to abiotic stresses, suggesting its involvement in diverse physiological processes. Thus, the present study identifies novel Ca2+ sensors and sheds light on key players involved in Ca2+signaling in C. reinhardtii, which could further be extrapolated to understand the evolution of Ca2+ mediated signaling in other eukaryotes.

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