scholarly journals Genome-Wide Identification, Characterization, and Expression Analysis of DDE_Tnp_4 Family Genes in Eriocheir sinensis

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1430
Author(s):  
Yuanfeng Xu ◽  
Jinbin Zheng ◽  
Yanan Yang ◽  
Zhaoxia Cui
Keyword(s):  
Phylogenetic Analysis ◽  
Environmental Stress ◽  
Tandem Duplication ◽  
High Salinity ◽  
Expression Profiles ◽  
Eriocheir Sinensis ◽  
Biological Processes ◽  
Synteny Analysis ◽  
Air Exposure ◽  
Genome Wide

DDE transposase 4 (DDE_Tnp_4) family is a large endonuclease family involved in a wide variety of biological processes. However, little information is available about this family in crustaceans. In this study, we used HMMER to identify 39 DDE_Tnp_4 family genes in Eriocheir sinensis genome, and the genes were classified into four subfamilies according to phylogenetic analysis. Gene expansions occurred among E. sinensis genome, and synteny analysis revealed that some DDE_Tnp_4 family genes were caused by tandem duplication. In addition, the expression profiles of DDE_Tnp_4 family genes in E. sinensis indicated that subfamily I and II genes were up-regulated in response to acute high salinity and air exposure stress. E. sinensis is a kind of economical crustacean with strong tolerance to environmental stress. We confirmed the expansion of DDE_Tnp_4 family genes in E. sinensis and speculated that this expansion is associated with strong tolerance of E. sinensis. This study sheds light on characterizations and expression profiles of DDE_Tnp_4 family genes in E. sinensis and provides an integrated framework for further investigation on environmental adaptive functions of DDE_Tnp_4 family in crustaceans.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-wide identification and expression analysis of the JAZ gene family in turnip

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kai Jia ◽  
Cunyao Yan ◽  
Jing Zhang ◽  
Yunxia Cheng ◽  
Wenwen Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Specific Protein ◽  
Gene Pairs ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structure And Expression

AbstractJAZ is a plant-specific protein family involved in the regulation of plant development, abiotic stresses, and responses to phytohormone treatments. In this study, we carried out a bioinformatics analysis of JAZ genes in turnip by determining the phylogenetic relationship, chromosomal location, gene structure and expression profiles analysis under stresses. The 36 JAZ genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The JAZ genes were located on 10 chromosomes. Two gene pairs were involved in tandem duplication events. We identified 44 collinear JAZ gene pairs in the turnip genome. Analysis of the Ka/Ks ratios indicated that the paralogs of the BrrJAZ family principally underwent purifying selection. Expression analysis suggested JAZ genes may be involved in the formation of turnip tuberous root, and they also participated in the response to ABA, SA, MeJA, salt stress and low-temperature stress. The results of this study provided valuable information for further exploration of the JAZ gene family in turnip.

scholarly journals Genome-Wide Identification and Functional Characterization of the Heat Shock Factor Family in Eggplant (Solanum melongena L.) under Abiotic Stress Conditions

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 915
Author(s):  
Jinglei Wang ◽  
Haijiao Hu ◽  
Wuhong Wang ◽  
Qingzhen Wei ◽  
Tianhua Hu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Heat Shock ◽  
Environmental Stress ◽  
Expression Pattern ◽  
Expression Profiles ◽  
Solanum Melongena ◽  
Environmental Stresses ◽  
Stress Conditions ◽  
Heat Shock Factors ◽  
Genome Wide

Plant heat shock factors (Hsfs) play crucial roles in various environmental stress responses. Eggplant (Solanum melongena L.) is an agronomically important and thermophilic vegetable grown worldwide. Although the functions of Hsfs under environmental stress conditions have been characterized in the model plant Arabidopsis thaliana and tomato, their roles in responding to various stresses remain unclear in eggplant. Therefore, we characterized the eggplant SmeHsf family and surveyed expression profiles mediated by the SmeHsfs under various stress conditions. Here, using reported Hsfs from other species as queries to search SmeHsfs in the eggplant genome and confirming the typical conserved domains, we identified 20 SmeHsf genes. The SmeHsfs were further classified into 14 subgroups on the basis of their structure. Additionally, quantitative real-time PCR revealed that SmeHsfs responded to four stresses—cold, heat, salinity and drought—which indicated that SmeHsfs play crucial roles in improving tolerance to various abiotic stresses. The expression pattern of SmeHsfA6b exhibited the most immediate response to the various environmental stresses, except drought. The genome-wide identification and abiotic stress-responsive expression pattern analysis provide clues for further analysis of the roles and regulatory mechanism of SmeHsfs under environmental stresses.

scholarly journals Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 397
Author(s):  
Rio Kashimoto ◽  
Kanako Hisata ◽  
Chuya Shinzato ◽  
Noriyuki Satoh ◽  
Eiichi Shoguchi
Keyword(s):  
Tandem Duplication ◽  
Common Ancestor ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Gene Clusters ◽  
Sea Surface ◽  
Last Common Ancestor ◽  
Synteny Analysis ◽  
Genome Wide ◽  
Genome Wide Survey

In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9–18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-wide Investigation and Expression Profiles of Heat Shock Transcription Factor (HSF) Gene Family in Maize (Zea mays L.) under Different Growth Stages and Abiotic Stress Conditions

2021 ◽  
Author(s):  
Saqlain Haider ◽  
Shazia Rehman ◽  
Yumna Ahmad ◽  
Ali Raza ◽  
Javaria Tabassum ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Zea Mays ◽  
Abiotic Stress ◽  
Heat Shock ◽  
Environmental Stress ◽  
Growth Stages ◽  
Maize Genome ◽  
Class A ◽  
Genome Wide

Heat shock transcription factors (HSFs) participate in regulating many environmental stress responses and biological processes in plants. Maize (Zea mays L.) is a major cash crop that is grown worldwide. However, the growth and yield of maize are affected by several adverse environmental inputs. Therefore, investigating the factors that regulate maize growth and development and resistance to abiotic stress is an essential task for developing stress-resilient maize varieties. Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs in the maize genome. The current study identified 25 ZmHSFs, randomly distributed throughout the maize genome. Phylogenetic analysis revealed that ZmHSFs are divided into three classes and 13 sub-classes. Gene structure and protein motif analysis supported the results obtained through the phylogenetic analysis. Domain analysis showed the DNA-binding domain to be the most conserved region of ZmHSFs. Segmental duplication is shown to be responsible for the expansion of ZmHSFs. Most of the ZmHSFs are localized inside the nucleus, and the ZmHSFs which belong to the same group show similar physio-chemical properties. The 3D structures revealed comparable conserved ZmHSFs protein structures. RNA-seq analysis revealed a major role of class A HSFs including, ZmHSFA-1a and ZmHSFA-2a in all the maize growth stages, i.e., seed, vegetative, and reproductive development. Furthermore, ZmHSFs displayed an obvious spatiotemporal expression. Under abiotic stress conditions (heat, drought, cold, UV, and salinity), members of class A and B ZmHSFs are induced. Gene ontology (GO) annotation analysis indicated a major role of ZmHSFs in resistance to environmental stress and regulation of primary metabolism. Further, the protein-protein interaction analysis showed that ZmHSFs interact with several molecular chaperons and major stress-responsive proteins. To summarize, this study provides novel insights for functional studies on the ZmHSFs in maize breeding programs.

scholarly journals Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ying Li ◽  
Qilu Song ◽  
Yamin Zhang ◽  
Zheng Li ◽  
Jialin Guo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
Related Development ◽  
Gene Structures

Abstract SQUAMOSA promoter-binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play roles in plant growth and development. The characteristics of SBP-box genes in rice (Oryza sativa) and Arabidopsis have been reported, but their potential roles in wheat (Triticum aestivum) are not fully understood. In this study, 48 SBP-box genes (TaSBPs) were identified; they were located in all wheat chromosomes except for 4B and 4D. Six TaSBPs were identified as tandem duplication genes that formed three tandem duplication pairs, while 22 were segmentally duplicated genes that formed 16 segmental duplication pairs. Subcellular localization prediction showed TaSBPs were located in nucleus. Among the 48 TaSBPs, 24 were predicted to be putative targets of TamiR156. Phylogenetic analysis showed that TaSBPs, AtSBPs, and OsSBPs that shared similar functions were clustered into the same subgroups. The phylogenetic relationships between the TaSBPs were supported by the identification of highly conserved motifs and gene structures. Four types of cis-elements––transcription-related, development-related, hormone-related, and abiotic stress-related elements––were found in the TaSBP promoters. Expression profiles indicated most TaSBPs participate in flower development and abiotic stress responses. This study establishes a foundation for further investigation of TaSBP genes and provides novel insights into their biological functions.

scholarly journals Comprehensive pathway analyses of schizophrenia risk loci point to dysfunctional postsynaptic signaling

2017 ◽  
Author(s):  
Dick Schijven ◽  
Daniel Kofink ◽  
Vinicius Tragante ◽  
Marloes Verkerke ◽  
Sara L. Pulit ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Association Studies ◽  
Enrichment Analysis ◽  
Large Contribution ◽  
Genome Wide Association Studies ◽  
Biological Processes ◽  
Gene Set ◽  
Genome Wide

AbstractLarge-scale genome-wide association studies (GWAS) have implicated many low-penetrance loci in schizophrenia. However, its pathological mechanisms are poorly understood, which in turn hampers the development of novel pharmacological treatments. Pathway and gene set analyses carry the potential to generate hypotheses about disease mechanisms and have provided biological context to genome-wide data of schizophrenia. We aimed to examine which biological processes are likely candidates to underlie schizophrenia by integrating novel and powerful pathway analysis tools using data from the largest Psychiatric Genomics Consortium schizophrenia GWAS (N = 79 845) and the most recent 2018 schizophrenia GWAS (N = 105 318). By applying a primary unbiased analysis (Multi-marker Analysis of GenoMic Annotation; MAGMA) to weigh the role of biological processes from the MSigDB database, we identified enrichment of common variants in synaptic plasticity and neuron differentiation gene sets. We supported these findings using MAGMA, Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA) and Interval Enrichment Analysis (INRICH) on detailed synaptic signaling pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and found enrichment in mainly the dopaminergic and cholinergic synapses. Moreover, shared genes involved in these neurotransmitter systems had a large contribution to the observed enrichment, protein products of top genes in these pathways showed more direct and indirect interactions than expected by chance, and expression profiles of these genes were largely similar among brain tissues. In conclusion, we provide strong and consistent genetics and protein-interaction informed evidence for the role of postsynaptic signaling processes in schizophrenia, opening avenues for future translational and psychopharmacological studies.

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