Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum

Abstract Background The coronatine insensitive 1 (COI1) gene is the core member of jasmonate signaling pathway, which is closely related to plant biotic and abiotic resistance. However, there have been no reports on COI1 in sugarcane (Sacharum spp.). Hence, systematically investigating the characteristics of the COI1 multigene family in sugarcane can provide a means to study and manipulate the jasmonic acid signaling pathway. Results A total of 156 COI1 proteins were obtained from the genomes of 19 land plants, while none were obtained from five algae species. A phylogenetic tree demonstrated that these COI1 proteins were classified into four groups, while 31 proteins of SsCOI1 from Saccharum spontaneum, SbCOI1 from Sorghum bicolor, and ShCOI1 from Saccharum spp. hybrid cultivar R570 clustered into three groups. Synteny analysis and duplication patterns revealed that COI1 genes expanded through various genome replication events and could have experienced strong purifying selective pressure during evolution in S. spontaneum, S. bicolor, and R570. An investigation of cis-acting elements suggests that COI1 genes may be involved in plant growth and development and response to various stresses. Expression analysis implied that 21 SsCOI1 genes were constitutively expressed, and had positive responses to drought, cold, and Sporisorium scitamineum stresses with different expression patterns. Among them, seven SsCOI1 haplotype genes may play different roles in response to methyl jasmonate. Furthermore, the ShCOI1–4, ShCOI1–5, and ShCOI1–6 genes were cloned from Saccharum spp. hybrid cultivar ROC22. Real-time quantitative PCR (RT-qPCR) analysis demonstrated that these three ShCOI1 genes had divergent expression profiles in response to salicylic acid, abscisic acid, polyethylene glycol, cold, and S. scitamineum. Conclusions These results suggest that COI1 genes may act in sugarcane growth, development, and response to various stresses via different regulatory mechanisms, which laying a foundation for the functional identification of the sugarcane COI1 gene.

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Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400875 ◽

2019 ◽

Vol 10 (2) ◽

pp. 443-454

Author(s):

Chang Liu ◽

Cornelius Tlotliso Sello ◽

Yujian Sui ◽

Jingtao Hu ◽

Shaokang Chen ◽

...

Keyword(s):

Signaling Pathway ◽

Developmental Stages ◽

De Novo ◽

Transcriptome Assembly ◽

Expression Profiles ◽

Expression Patterns ◽

Mitogen Activated Protein Kinase ◽

Receptor Interaction ◽

Keratinocyte Proliferation ◽

Skin Development

In order to enrich the Anser cygnoides genome and identify the gene expression profiles of primary and secondary feather follicles development, de novo transcriptome assembly of skin tissues was established by analyzing three developmental stages at embryonic day 14, 18, and 28 (E14, E18, E28). Sequencing output generated 436,730,608 clean reads from nine libraries and de novo assembled into 56,301 unigenes. There were 2,298, 9,423 and 12,559 unigenes showing differential expression in three stages respectively. Furthermore, differentially expressed genes (DEGs) were functionally classified according to genes ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and series-cluster analysis. Relevant specific GO terms such as epithelium development, regulation of keratinocyte proliferation, morphogenesis of an epithelium were identified. In all, 15,144 DEGs were clustered into eight profiles with distinct expression patterns and 2,424 DEGs were assigned to 198 KEGG pathways. Skin development related pathways (mitogen-activated protein kinase signaling pathway, extra-cellular matrix -receptor interaction, Wingless-type signaling pathway) and genes (delta like canonical Notch ligand 1, fibroblast growth factor 2, Snail family transcriptional repressor 2, bone morphogenetic protein 6, polo like kinase 1) were identified, and eight DEGs were selected to verify the reliability of transcriptome results by real-time quantitative PCR. The findings of this study will provide the key insights into the complicated molecular mechanism and breeding techniques underlying the developmental characteristics of skin and feather follicles in Anser cygnoides.

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A Preliminary Study on the Characteristics of microRNAs in Ovarian Stroma and Follicles of Chuanzhong Black Goat during Estrus

Genes ◽

10.3390/genes11090970 ◽

2020 ◽

Vol 11 (9) ◽

pp. 970

Author(s):

Tingting Lu ◽

Xian Zou ◽

Guangbin Liu ◽

Ming Deng ◽

Baoli Sun ◽

...

Keyword(s):

Signaling Pathway ◽

Mirna Expression ◽

Expression Profiles ◽

Expression Patterns ◽

Hormone Secretion ◽

Mapk Signaling ◽

Functional Enrichment ◽

Small Rna Sequencing ◽

Follicular Maturation ◽

Ovarian Stroma

microRNAs (miRNAs) play a significant role in ovarian follicular maturity, but miRNA expression patterns in ovarian stroma (OS), large follicles (LF), and small follicles (SF) have been rarely explored. We herein aimed to identify miRNAs, their target genes and signaling pathways, as well as their interaction networks in OS, LF, and SF of Chuanzhong black goats at the estrus phase using small RNA-sequencing. We found that the miRNA expression profiles of LF and SF were more similar than those of OS—32, 16, and 29 differentially expressed miRNAs were identified in OS vs. LF, OS vs. SF, and LF vs. SF, respectively. Analyses of functional enrichment and the miRNA-targeted gene interaction network suggested that miR-182 (SMC3), miR-122 (SGO1), and miR-206 (AURKA) were involved in ovarian organogenesis and hormone secretion by oocyte meiosis. Furthermore, miR-202-5p (EREG) and miR-485-3p (FLT3) were involved in follicular maturation through the MAPK signaling pathway, and miR-2404 (BMP7 and CDKN1C) played a key role in follicular development through the TGF-β signaling pathway and cell cycle; nevertheless, further research is warranted. To our knowledge, this is the first study to investigate miRNA expression patterns in OS, LF, and SF of Chuanzhong black goats during estrus. Our findings provide a theoretical basis to elucidate the role of miRNAs in follicular maturation. These key miRNAs might provide candidate biomarkers for the diagnosis of follicular maturation and will assist in developing new therapeutic targets for female goat infertility.

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Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress

International Journal of Molecular Sciences ◽

10.3390/ijms20225676 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5676 ◽

Cited By ~ 1

Author(s):

Haifeng Yan ◽

Mingzhi Li ◽

Yuping Xiong ◽

Jianming Wu ◽

Jaime A. Teixeira da Silva ◽

...

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Protein Sequences ◽

Santalum Album ◽

Biotic And Abiotic Stress ◽

Functional Identification ◽

Wrky Protein

WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.

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Selection and validation of reference genes for normalization of qRT-PCR data to study secondary metabolite related genes in industrial hemp

10.21203/rs.3.rs-394417/v1 ◽

2021 ◽

Author(s):

Michihito Deguchi ◽

Shobha Potlakayala ◽

Zachary Spuhler ◽

Hannah George ◽

Vijay Sheri ◽

...

Keyword(s):

Gene Expression ◽

Heavy Metal ◽

Expression Analysis ◽

Reference Genes ◽

Cannabis Sativa ◽

Expression Profiles ◽

Expression Patterns ◽

Qrt Pcr ◽

Differential Gene ◽

Industrial Hemp

Abstract Industrial hemp (Cannabis sativa L.) is a dioecious crop widely known for its production of phytocannabinoids, flavonoids, and terpenes. In the past two years since its legalization, there has been significant interest in researching this important crop for pharmaceutical applications. Although many scientific reports have demonstrated gene expression analysis of hemp through OMICs approaches, accurate validation of omics data cannot be performed because of lack of reliable reference genes for normalization of qRT-PCR data. The differential gene expression patterns of 13 candidate reference genes under osmotic, heavy metal, hormonal, and UV stress were evaluated through four software packages: geNorm, NormFinder, BestKeeper, and RefFinder. The EF-1a ranked as the most stable reference gene across all stresses, TUB was the most stable under osmotic stress, and TATA was the most stable under both heavy metal and hormonal stress. The expression profiles of two cannabinoid pathway genes, AAE1 and THCAS, using the two most stable and single least stable reference genes confirmed that two most stables genes were apt for normalization of gene expression data. This work will contribute to the future studies on the expression analysis of hemp genes regulating the synthesis, transport and accumulation of secondary metabolites.

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Comparative Gene Expression Analysis Reveals Similarities and Differences of Chronic Myeloid Leukemia Phases

Cancers ◽

10.3390/cancers14010256 ◽

2022 ◽

Vol 14 (1) ◽

pp. 256

Author(s):

Annemarie Schwarz ◽

Ingo Roeder ◽

Michael Seifert

Keyword(s):

Gene Expression ◽

Chronic Myeloid Leukemia ◽

Signaling Pathway ◽

Myeloid Leukemia ◽

Expression Profiles ◽

Expression Patterns ◽

Chronic Phase ◽

Receptor Interaction ◽

Similarities And Differences

Chronic myeloid leukemia (CML) is a slowly progressing blood cancer that primarily affects elderly people. Without successful treatment, CML progressively develops from the chronic phase through the accelerated phase to the blast crisis, and ultimately to death. Nowadays, the availability of targeted tyrosine kinase inhibitor (TKI) therapies has led to long-term disease control for the vast majority of patients. Nevertheless, there are still patients that do not respond well enough to TKI therapies and available targeted therapies are also less efficient for patients in accelerated phase or blast crises. Thus, a more detailed characterization of molecular alterations that distinguish the different CML phases is still very important. We performed an in-depth bioinformatics analysis of publicly available gene expression profiles of the three CML phases. Pairwise comparisons revealed many differentially expressed genes that formed a characteristic gene expression signature, which clearly distinguished the three CML phases. Signaling pathway expression patterns were very similar between the three phases but differed strongly in the number of affected genes, which increased with the phase. Still, significant alterations of MAPK, VEGF, PI3K-Akt, adherens junction and cytokine receptor interaction signaling distinguished specific phases. Our study also suggests that one can consider the phase-wise CML development as a three rather than a two-step process. This is in accordance with the phase-specific expression behavior of 24 potential major regulators that we predicted by a network-based approach. Several of these genes are known to be involved in the accumulation of additional mutations, alterations of immune responses, deregulation of signaling pathways or may have an impact on treatment response and survival. Importantly, some of these genes have already been reported in relation to CML (e.g., AURKB, AZU1, HLA-B, HLA-DMB, PF4) and others have been found to play important roles in different leukemias (e.g., CDCA3, RPL18A, PRG3, TLX3). In addition, increased expression of BCL2 in the accelerated and blast phase indicates that venetoclax could be a potential treatment option. Moreover, a characteristic signaling pathway signature with increased expression of cytokine and ECM receptor interaction pathway genes distinguished imatinib-resistant patients from each individual CML phase. Overall, our comparative analysis contributes to an in-depth molecular characterization of similarities and differences of the CML phases and provides hints for the identification of patients that may not profit from an imatinib therapy, which could support the development of additional treatment strategies.

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Identification of Molecular Subgroups in Liver Cirrhosis by Gene Expression Profiles

10.21203/rs.3.rs-484882/v1 ◽

2021 ◽

Author(s):

Ying-xue Zhang ◽

Feng-xia Sun ◽

Xiao-ling Li ◽

Qing-hua Liu ◽

Zi-meng Chen ◽

...

Keyword(s):

Gene Expression ◽

Liver Cirrhosis ◽

Expression Analysis ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Receptor Interaction ◽

Molecular Characteristics ◽

Specific Gene ◽

Subgroup Ii

Abstract Background: Cirrhosis is a common clinical chronic progressive liver disease and has become one of the main causes of death worldwide. The condition of liver cirrhosis is complex and there is also clinical heterogeneity. Identifying liver cirrhosis based on molecular characteristics has become a challenge.Methods: To reveal the potential molecular characteristics of different types of cirrhosis, we divided 79 patients with cirrhosis into 4 subgroups based on gene expression profiles. These gene expression profiles were retrieved from the mprehensive gene expression database. In addition, these subgroups showed different expression patterns. To reveal the differences between subgroups, we used weighted gene co-expression analysis and identified six subgroup-specific gene co-expression analysis modules.Results: The characteristics ofWCGNAmodules indicate that TGF - β signaling pathway,viral protein interaction with cytokines and cytokine receptors, including a variety of chemokines and inflammatory factors, are upregulated in subgroup I, indicating that subjects in subgroup I may show inflammatory characteristics; fatty acid metabolism, biosynthesis of cofactors, carbon metabolism and protein processing pathway in endoplasmic reticulum were significantly enriched in subgroup II, which indicated that the subjects in subgroup II might have the characteristics of active metabolism; arrhythmogenic right ventricular cardiomyopathy and Neuroactive ligand−receptor interaction are significantly enriched in subgroup IV; we did not find a significant upregulation pathway in the third subgroup.Conclusion: The subgroups classification of liver cirrhosis cases shows that patients from different subgroups may have unique gene expression patterns, which indicates that patients in each subgroup should receive more personalized treatment.

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63Identification of insulin signaling pathway-related circulating circRNAs as biomarkers of type 2 diabetes

International Journal of Epidemiology ◽

10.1093/ije/dyab168.731 ◽

2021 ◽

Vol 50 (Supplement_1) ◽

Author(s):

Yu-xiang Yan ◽

Jia-Jiang-Hui Li ◽

Huan-Bo Xiao ◽

Jing Dong ◽

Xi Chu

Keyword(s):

Type 2 Diabetes ◽

Signaling Pathway ◽

Insulin Signaling ◽

Expression Profiles ◽

Insulin Signaling Pathway ◽

Circular Rnas ◽

Circulating Biomarkers ◽

Real Time Quantitative Pcr ◽

Novel Biomarkers

Abstract Background The underlying molecular mechanism of type 2 diabetes (T2D) is that abnormalities occur in the insulin signaling pathway. Circular RNAs (circRNAs) are involved in the development of diseases by regulating gene expression and become promising novel biomarkers for diseases. This study systematically screened and validated the insulin signaling pathway-related circulating circRNAs in T2D. Methods circRNA expression profiles were screened by microarray between five T2D patients and five healthy controls. The candidate circRNAs were then selected from those differently expressed circRNAs whose potential target miRNAs are involved in regulating key genes in the isulin signaling pathway. The expression of candidate circRNAs were validated in a second sample with 20 T2D cases and 20 controls by real-time quantitative PCR. Eventually, the association between circRNAs and T2D and their clinical significance were further confirmed in a large independent sample, including 103 T2D cases, 93 controls and 80 individuals with impaired fasting glucose (IFG) as prediabetes cases. Results Four circRNAs including hsa_circ_0063425, hsa_circ_0056891, hsa_circ_0078166 and hsa_circ_0071336 were validated by RT-qPCR. Low expressed circ_0063425, hsa_circ_0056891 and hsa_circ_0071336 were independent predictor of T2D, IFG and insulin resistance. The three-circRNA panel had a high accuracy for diagnosing T2D and IFG, especially when BMI was integrated. Bioinformatics Gene Ontology and pathway analysis confirmed that these circRNAs involve in the regulation of insulin signaling pathway. Conclusion circ_0063425, hsa_circ_0056891 and hsa_circ_0071336 are valuable circulating biomarkers for T2D, and may involve in regulating insulin signaling pathway. Key messages Insulin signaling pathway-related circulating circRNAs were identification as biomarkers of T2D.

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Identification and Functional Characterization of Apple MdCKX5.2 in Root Development and Abiotic Stress Tolerance

Horticulturae ◽

10.3390/horticulturae8010062 ◽

2022 ◽

Vol 8 (1) ◽

pp. 62

Author(s):

Yang Liu ◽

Xun Wang ◽

Xiaofei Wang ◽

Wensheng Gao ◽

Chunxiang You

Keyword(s):

Expression Analysis ◽

Root Development ◽

Expression Profiles ◽

Abiotic Stress Tolerance ◽

Expression Patterns ◽

Functional Characterization ◽

Primary Root ◽

Cytokinin Oxidase ◽

Lateral Root Development ◽

Exogenous Cytokinin

Cytokinin oxidase/dehydrogenases (CKXs) are the key enzymes in cytokinin degradation and have been widely studied in model plants. Little is known about apple’s (Malus×domestica) CKX genes. Here, using genome-wide analysis, we identified 10 MdCKX genes in apple. The phylogenetics, chromosome locations, and genome structures were then tested. Expression analysis showed that MdCKX genes had different expression profiles in apple, pointing to the different roles. Meanwhile, relative expression analysis showed that these genes have different expression patterns in response to several exogenous cytokinin factors, including trans-zeatin (ZT), thidiazuron (TDZ), and N6-furfuryladenine (KT). Finally, we introduced the MdCKX5.2 gene into Arabidopsis to evaluate its functions, and the results suggested the transgenic Arabidopsis displayed phenotypes related to promoting primary root and lateral root development, response to exogenous ZT, and conferring to drought and salt tolerant. Taken together, our results provide insights on the possible application of the MdCKX5.2 gene for molecular breeding in apples.

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20 Profiling circRNA and lncRNA Expression in Key Bovine Metabolic Tissues

Journal of Animal Science ◽

10.1093/jas/skab235.016 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 9-9

Author(s):

Jian Wang ◽

Hui-Zeng Sun ◽

Eóin O’Hara ◽

Hong Chen ◽

Leluo Guan

Keyword(s):

Signaling Pathway ◽

Balance Control ◽

Expression Profiles ◽

Expression Patterns ◽

Adipose Tissues ◽

Mitofusin 2 ◽

Tissue Specific ◽

Lncrna Expression ◽

Non Coding Rnas ◽

Subcutaneous Adipose

Abstract CircRNAs and lncRNAs are non-coding RNAs that regulate many biological processes at the cellular level. However, knowledge of their function and expression patterns in cattle remains scarce. We investigated circRNA and lncRNA expression profiles in four key metabolic tissues of beef cattle (rumen, liver, muscle, and subcutaneous adipose) using RNA-Seq. Bioinformatic analysis of 189 samples collected from 48 cattle identified 19,766 circRNAs and 10,615 lncRNAs across all four tissues. PCA revealed the expression profiles of both circ- and lncRNA were clearly separated by tissue, suggesting their expression patterns are tissue dependent. Moreover, both datasets contained large numbers of transcripts that were unique to each tissue, underlining the divergence in function across metabolic sites. Further functional analysis of tissue specific circRNAs using the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that lysine degradation, peroxisome, insulin resistance, and ubiquitin-mediated proteolysis unique to the rumen, liver, muscle, and adipose tissues, respectively. The same analysis of the lncRNAs revealed that purine metabolism, fatty acid degradation, cAMP signaling pathway, and AGE-RAGE signaling pathway in diabetic complications were uniquely enriched in the rumen, liver, muscle, and subcutaneous adipose tissues, respectively. Together, these results revealed tissue specific metabolic pathways that may be regulated by the multiple non-coding RNAs. More specifically, circDLG1 and lncMSTRG.12092.8 were predicted to regulate the expression of Lymphocyte Antigen 6 Family Member G5B (LY6G5B) and pyruvate kinase M1/2 (PKM), Adenylate Kinase 1 (AK1), and Mitofusin 2 (MFN2), respectively, indicating regulatory roles in host immune response, glycolysis, energy balance control, and mitochondrial fusion, all of which may contribute to regulation of energy metabolism. Our findings show that expression profiles of circRNAs and lncRNAs differ among metabolic tissues, and these transcripts may play crucial roles in regulating metabolism in cattle.

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Identification and Characterization of the Grape WRKY Family

BioMed Research International ◽

10.1155/2014/787680 ◽

2014 ◽

Vol 2014 ◽

pp. 1-14 ◽

Cited By ~ 8

Author(s):

Ying Zhang ◽

Jian can Feng

Keyword(s):

Transcription Factors ◽

Pathogenic Bacteria ◽

Expression Profiles ◽

Expression Patterns ◽

Structural Features ◽

Functional Identification ◽

Wrky Transcription Factors ◽

Genes Expression ◽

Wrky Proteins

WRKY transcription factors have functions in plant growth and development and in response to biotic and abiotic stresses. Many studies have focused on functional identification of WRKY transcription factors, but little is known about the molecular phylogeny or global expression patterns of the complete WRKY family. In this study, we identified 80 WRKY proteins encoded in the grape genome. Based on the structural features of these proteins, the grapeWRKYgenes were classified into three groups (groups 1–3). Analysis ofWRKYgenes expression profiles indicated that 28WRKYgenes were differentially expressed in response to biotic stress caused by grape whiterot and/or salicylic acid (SA). In that 16WRKYgenes upregulated both by whiterot pathogenic bacteria and SA. The results indicated that 16 WRKY proteins participated in SA-dependent defense signal pathway. This study provides a basis for cloning genes with specific functions from grape.

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