scholarly journals Identification and characterization of MYB genes in Dimocarpus longan Lour.

2020 ◽  
Vol 49 (1) ◽  
pp. 97-104
Author(s):  
Wei Zheng ◽  
Xueming Dong ◽  
Qiuying Zhang ◽  
Xuefei Yu ◽  
Wenlan Li ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Leaf Tissue ◽  
Pcr Analysis ◽  
Phylogenetic Tree Analysis ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Dimocarpus Longan ◽  
Group B

The MYB gene family is one of the most widespread plant transcription factor (TF) families, and MYB TFs play key roles in plant development, hormone signal transduction, disease resistance, abiotic stress tolerance and secondary metabolism. Recently, many MYBs have been characterized in various plants. However, little is known about the MYBs involved in secondary metabolite biosynthesis in Dimocarpus longan Lour. (D. longan). Based on transcriptome data profiling (Accession number: SRP155595), 35 MYBs from D. longan (DlMYBs) were identified. On the basis of their physicochemical properties, phylogenetic relationships, conserved motifs, and tissue-specific expression profiles these Dimocarpus longan MYBs (DlMYBs) were analyzed. Fifteen motifs in DlMYBs using MEME were found and a phylogenetic tree analysis showed that the DlMYBs identified here were divided into three groups. Group A contained the greatest number (25) of DlMYBs, followed by group B (6) and group C (4). Quantitative real time PCR (qRT-PCR) analysis demonstrated that, of the 35 MYBs studied DlMYB-12 and DlMYB-22 showed large differences in tissue-specific expression, with both MYBs showing very high expression in leaf tissue. These results lay the foundation for further studies of the biosynthesis of secondary metabolites in D. longan and further highlight the importance of MYB TFs in plants.

scholarly journals Characterization and Tissue-specific Expression of bHLH Genes in Dimocarpus longan

2019 ◽  
Vol 47 (3) ◽  
Author(s):  
Wei ZHENG ◽  
Xueming DONG ◽  
Xuefei YU ◽  
Qiuying ZHANG ◽  
Ning CHEN
Keyword(s):  
Expression Patterns ◽  
Digital Object Identifier ◽  
Bhlh Transcription Factor ◽  
Rna Seq ◽  
Phylogenetic Tree Analysis ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Bhlh Genes ◽  
Dimocarpus Longan

In plants, the basic helix-loop-helix (bHLH) transcription factors (TFs) play pivotal roles in many biological processes including growth, stress response, and secondary metabolite synthesis. To date, many bHLH genes have been identified and characterized in diverse plant species. However, little is known regarding the bHLH genes in Dimocarpus longan Lour. (D. longan). Based on RNA-seq data, we identified 42 putative bHLH genes from D. longan and determined their putative functions using the NCBI Conserved Domain Search Tool and Pfam databases. The physicochemical properties, phylogenetic relationships, conserved motifs, gene ontology (GO) annotations, protein-protein interactions, and tissue-specific expression patterns of these bHLH genes were systematically explored. In total, ten motifs were found in DlbHLH proteins using MEME, among which two were highly conserved. Phylogenetic tree analysis found that DlbHLH proteins can be divided into nine groups, with group 2 being the largest. GO annotation results showed that the DlHLH genes were involved in various molecular functions. RNA-seq and qRT-PCR results revealed important differences in the expression patterns of 17 of the DlbHLH genes. In particular, DlbHLH-9, DlbHLH-19, DlbHLH-25, DlbHLH-26, and DlbHLH-35 were found to show significantly different expression patterns in root and leaf tissues. The results of this study will further enrich our knowledge regarding bHLH transcription factor genes and lay a foundation for enhancing the production of active secondary metabolites by genetic engineering in D. longan.   ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 3, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********

scholarly journals Genome-wide identification, structural analysis and expression profiles of SRS gene family in quinoa

2021 ◽  
Author(s):  
xiaolin zhu ◽  
baoqiang wang ◽  
xian wang ◽  
xiaohong wei
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Protein Interaction ◽  
Expression Profiles ◽  
Random Coil ◽  
Specific Expression ◽  
Tissue Specific ◽  
Response Elements ◽  
Tissue Specific Expression ◽  
Qrt Pcr

Abstract Based on the whole genome data information of quinoa, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (200 mmol/L), SA (200 umol/L) and low temperature (4℃) were detected by qRT-PCR. The results showed that a total of 10 SRS genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were 4 pairs of duplicated genes. The number of amino acids encoded ranged from 143 to 370, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil(Cc). Most of the CqSRS genes were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS gene was divided into three evolutionary groups, and the gene structure showed that the number of exons of CqSRS was between 2–5. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to SA, NaCl and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS family genes.

scholarly journals Molecular Characterization of A New IgZ3 Subclass from Common Carp (Cyprinus Carpio) and Comparative Expression Analysis of IgH Transcripts During Ontogeny of Larvae

2020 ◽  
Author(s):  
Fumiao Zhang ◽  
Mojin Li ◽  
Cui Lv ◽  
Guangcai Wei ◽  
Chang Wang ◽  
...  
Keyword(s):  
Common Carp ◽  
Aeromonas Hydrophila ◽  
Mrna Level ◽  
Development Stage ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Qrt Pcr ◽  
Immune Tissues

Abstract Background Immunoglobulins distributing among systemic immune tissues and mucosal immune tissues play an important role in teleost to protect them from infections in a pathogen-rich aquatic environment. Teleost IgZ/IgT subclasses with different tissue expression patterns may have varied immune functions.Results In the present study, a novel secreted IgZ heavy chain gene was cloned and characterized in common carp (Cyprinus carpio) which was different from the reported IgZ1 and IgZ2 in tissue-specific expression profile. The obtained IgZ-like subclass was designated as CcIgZ3 which complete open reading frame contained 1650 bp encoding a protein of 549 amino acid residues. The phylogenetic analysis revealed that CcIgZ3 was grouped with carp IgZ2 and was in the same branch as other teleosts IgZ/IgT. Basal expression detection of IgH in healthy adult common carp showed that CcIgZ3 transcripts were widely expressed in systemic immune tissues and Mucosal-associated lymphoid tissues. It was expressed at a higher level in the head kidney, gill, and gonad, followed by spleen, hindgut, oral epithelium, liver, brain, muscle, foregut, and blood, but at a very low level in the skin. The transcript level of CcIgZ3 mRNA in isolated leukocytes from peripheral blood cells was significantly higher than that of isolated leukocytes from the spleen. Different groups of common carp were infected with Aeromonas hydrophila via intraperitoneal injection and immersion respectively. The qRT-PCR analysis demonstrated that a significant difference in CcIgZ3 mRNA level between immersion and injection groups existed in all the detected tissues including head kidney, spleen, liver, and hindgut, especially in hindgut CcIgZ3 mRNA level was higher in immersion than in the injection group. Different routes for Aeromonas hydrophila challenge to common carp had comparatively less effect on IgM response. Further study on the relative expression of the IgH gene during the ontogeny of common carp presented that the tissue-specific expression profile of CcIgZ3 was very different from the others. In the early larval development stage of common carp from 1 dpf to 31 dpf, the qRT-PCR analysis demonstrated that the CcIgZ3 mRNA level increased gradually with a similar dynamic tendency of IgZ1 and IgZ2 and IgM was the dominant Ig with obviously higher abundance. The results of tissue-specific expression of IgH at 65 dpf of common carp showed that CcIgZ3 was expressed at mucosal sites including both hindgut and gill but IgZ1 was preferentially expressed in hindgut and IgZ2 in gill. Except for qRT-PCR analysis, the detection of the CcIgZ3-expressing cells and IgM-expressing cells by in situ hybridization was performed. The results showed that CcIgZ3 and IgM transcripts could be detected in the spleen, gill, and hindgut of the common carp at 65dpf. Conclusions These results revealed that CcIgZ3 gene transcript occurred in the early development stage of common carp not only in systemic tissues but also in mucosal tissues. CcIgZ3 could be induced with significantly different expression profiles at immune tissues after the challenge by Aeromonas hydrophila immersion and intraperitoneal injection, which indicated that CcIgZ3 might play a more important role in mucosal immunity than in systemic immunity.

Differential expression of the closely linked KISS1, REN, and FLJ10761 genes in transgenic mice

2004 ◽  
Vol 17 (1) ◽  
pp. 4-10 ◽  
Author(s):  
Ravi Nistala ◽  
Xiaoji Zhang ◽  
Curt D. Sigmund
Keyword(s):  
Transgenic Mice ◽  
Human Chromosome ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Artificial Chromosome ◽  
Chromosome 1 ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Human Chromosome 1

We previously reported the development and characterization of transgenic mice containing a large 160-kb P1 artificial chromosome (PAC) encompassing the renin (REN) locus from human chromosome 1. Here we demonstrate that PAC160 not only encodes REN, but also complete copies of the next upstream (KISS1) and downstream ( FLJ10761 ) gene along human chromosome 1. Incomplete copies of the second upstream (PEPP3) and downstream (SOX13) genes are also present. The gene order PEPP3-KISS1-REN-FLJ10761-SOX13 is conserved in mice containing either one or two copies of the REN locus. Despite the close localization of KISS1, REN, and FLJ10761 , they each exhibit distinct, yet overlapping tissue-specific expression profiles in humans. The tissue-specific expression patterns of REN and FLJ10761 were retained in transgenic mice containing PAC160. Expression of REN and FLJ10761 were also proportional to copy number. Expression of KISS1 in PAC160 mice showed both similarities and differences to humans. These data suggest that expression of gene blocks encoded on large genomic clones are retained when the clones are used to generate transgenic mice. Genomic elements which act to insulate genes from their neighbors are also apparently retained.

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