Genome-wide identification, characterization and expression analysis of the expansin gene family under drought stress in tea (Camellia sinensis L.)

During several developmental processes, expansins contribute to cell enlargement by promoting cell wall loosening. To explore the biological roles of expansins during drought stress response and to characterize different expansins in tea, we performed a detailed analysis of the expansin gene family covering phylogeny, gene structure, profiling of gene expression and co-expression network analysis. We identified a total of 40 expansin genes in the tea genome belonging to 3 subfamilies, out of which 29 tea expansins belong to EXPA, 9 to EXLA and 2 to EXPB subfamilies. A minimum of 3 and a maximum of 13 exons are present in the gene structure of expansins. Presence of drought stress responsive cis-acting elements in the upstream of promoter regions of 40% of the identified expansins shows that the putative expansins may have been involved in tea plant’s response to drought stress. At least 15 out of the 40 expansin genes are found to be differentially expressed in response to drought in each of the drought stress related public datasets analysed in-silico. TEA022767 belonging to EXPA subfamily is seen to be upregulated during drought stress, as revealed from the analysis of all three publicly available bio-projects. Co-expression network analysis shows that TEA022767 and TEA032954 form a connecting link between two expression correlation groups that further signifies their role in drought stress response in tea. This study helps to interpret and to understand the biological roles of diverse expansin genes in tea plants under drought stress conditions.

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Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

International Journal of Molecular Sciences ◽

10.3390/ijms23020614 ◽

2022 ◽

Vol 23 (2) ◽

pp. 614

Author(s):

Weiqi Sun ◽

Mengdi Li ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Gene Structure ◽

Stress Responses ◽

Stress Protein ◽

Purifying Selection ◽

Cis Acting ◽

Genome Wide ◽

Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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In silico characterization and comparison of the fruit ripening related beta‐ amylase (BAM) gene family in banana genome A and B

Indonesian Journal of Biotechnology ◽

10.22146/ijbiotech.65142 ◽

2021 ◽

Vol 26 (4) ◽

pp. 175

Author(s):

Erdianty Setiabudi ◽

Karlia Meitha ◽

Fenny Martha Dwivany

Keyword(s):

Gene Family ◽

Functional Characterization ◽

Genomic Analysis ◽

Starch Metabolism ◽

Promoter Regions ◽

Element Analysis ◽

Cis Acting ◽

Global Food Security ◽

Metabolism Regulation ◽

Functional Genomic Analysis

Banana is one of the most important commodities for maintaining global food security. Primary metabolic processes during the ripening of banana greatly affect post‐harvest quality, particularly in starch metabolism. The beta‐ amylase (BAM) gene family is known as a group of genes that plays an important role in starch metabolism regulation. In this study, we focused on the characterization and comparative analysis of the BAM gene family in DH Pahang and Pisang Klutuk Wulung (PKW) varieties, these being the AA and BB genomes, respectively. The sequences of BAM gene family were retrieved from the database of Musa acuminata ’DH Pahang’ and Musa balbisiana ’PKW’ genome, then structural and functional characterization was performed, followed by identification of cis‐acting elements in the BAM promoter regions. The results showed that the BAM gene family structure was relatively conserved in both genomes, and a putative BAM11 gene was found, the function of which has not been studied in other plants. Cis‐acting element analysis showed that they were distinct in the copy number and types of elements that were responsive to various phytohormones. This study suggested that the BAM genes involved in ripening are spatiotemporally regulated. However, further functional genomic analysis is required to describe the specific role and regulation of BAM genes during ripening in banana.

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Stress Resistance Heat Shock Protein 70 (HSP70) Analysis in Sorghum (Sorghum bicolor L.) at Genome-Wide Level

10.1101/2021.11.22.469496 ◽

2021 ◽

Author(s):

Kasahun Amare ◽

Mulugeta Kebede

Keyword(s):

Heat Shock ◽

Subcellular Localization ◽

Physicochemical Properties ◽

Sorghum Bicolor ◽

Gene Family ◽

Gene Structure ◽

Promoter Region ◽

Hsp70 Gene ◽

Cis Acting ◽

Region Analysis

Heat shock proteins (HSP70) play an important role in many biological processes. However, as typical in Sorghum bicolor, the systematic identification of the HSP70 gene is very limited, and the role of the Hsp70 gene in the evolution of Sorghum bicolor has not been described systematically a lot. To overcome the gap, Insilco analysis of HSP70 gene family was conducted.The investigation was utilizing the bioinformatics method to analyze the HSP70 gene family and it has been identified that 30 HSP70 genes from the genome sequence of Sorghum bicolor. A comprehensive analysis of these 30 identified genes undertaking the analysis of gene structure, phylogeny, and physicochemical properties, subcellular localization, and promoter region analysis. The gene structure visualization analyses revealed that 22 genes contains both 5’ and 3’ UTRS and one 5’ and one 3’ gene and 6 genes without UTR. The highest number of introns was recorded as 12 and those genes have shown that without in any intron. In the promoter region analysis, ten protein motifs are identified and characterized and 2219 cis-acting elements are identified. Among those, the promoter enhancer elements share the highest number (1411) and light-responsive elements share the next value (335). The physicochemical properties analysis revealed that 23 families have an acidic nature while four families are basic and the rests are neutral. In general, the different analyses performed disclosed their structural organization, subcellular localization, physicochemical properties, cis-acting elements, phylogenetic, and understress conditions. This study provides further information for the functional characterization of HSP70 and helps to understand the mechanisms of abiotic stress tolerance under diverse stress conditions in Sorghum bicolor.

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Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice (Oryza sativa)

International Journal of Molecular Sciences ◽

10.3390/ijms222112088 ◽

2021 ◽

Vol 22 (21) ◽

pp. 12088

Author(s):

Me-Sun Kim ◽

Kwon-Kyoo Kang ◽

Yong-Gu Cho

Keyword(s):

Functional Analysis ◽

Drought Stress ◽

Gene Family ◽

Ubiquitin Ligase ◽

Expression Patterns ◽

E3 Ubiquitin Ligase ◽

Sequencing Analysis ◽

Abiotic And Biotic Stresses ◽

Cis Acting ◽

Biotic Stresses

Proteins encoded by U-box type ubiquitin ligase (PUB) genes in rice are known to play an important role in plant responses to abiotic and biotic stresses. Functional analysis has revealed a detailed molecular mechanism involving PUB proteins in relation to abiotic and biotic stresses. In this study, characteristics of 77 OsPUB genes in rice were identified. Systematic and comprehensive analyses of the OsPUB gene family were then performed, including analysis of conserved domains, phylogenetic relationships, gene structure, chromosome location, cis-acting elements, and expression patterns. Through transcriptome analysis, we confirmed that 16 OsPUB genes show similar expression patterns in drought stress and blast infection response pathways. Numerous cis-acting elements were found in promoter sequences of 16 OsPUB genes, indicating that the OsPUB genes might be involved in complex regulatory networks to control hormones, stress responses, and cellular development. We performed qRT-PCR on 16 OsPUB genes under drought stress and blast infection to further identify the reliability of transcriptome and cis-element analysis data. It was confirmed that the expression pattern was similar to RNA-sequencing analysis results. The transcription of OsPUB under various stress conditions indicates that the PUB gene might have various functions in the responses of rice to abiotic and biotic stresses. Taken together, these results indicate that the genome-wide analysis of OsPUB genes can provide a solid basis for the functional analysis of U-box E3 ubiquitin ligase genes. The molecular information of the U-box E3 ubiquitin ligase gene family in rice, including gene expression patterns and cis-acting regulatory elements, could be useful for future crop breeding programs by genome editing.

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Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean

10.21203/rs.3.rs-388275/v1 ◽

2021 ◽

Author(s):

Min Wang ◽

Bowei Chen ◽

Wei Zhou ◽

Linan Xie ◽

Lishan Wang ◽

...

Keyword(s):

Stress Response ◽

Gene Family ◽

Soybean Genome ◽

Signal Pathways ◽

Type I ◽

Transcription Analysis ◽

Cis Acting ◽

Network Analyses ◽

Genome Wide ◽

Submergence Stress

Abstract Background: Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing a crucial role in plant growth and development. To date, however, the AHL gene family has not been studied in soybean. Results: To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I,II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean.Conclusion: 63 AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHL biological functions in soybean.

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Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

PeerJ ◽

10.7717/peerj.11938 ◽

2021 ◽

Vol 9 ◽

pp. e11938

Author(s):

Shilin Sun ◽

Bo Wang ◽

Qi Jiang ◽

Zhuoran Li ◽

Site Jia ◽

...

Keyword(s):

Drought Stress ◽

Gene Family ◽

Expression Patterns ◽

Structure Evolution ◽

Gene Gain ◽

Betula Platyphylla ◽

Ros Scavenging ◽

Promoter Regions ◽

Chromosomal Distribution ◽

Qrt Pcr

Background DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear. Methods The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results. Results A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17 were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

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Genome-Wide Analysis of the MADS-Box Gene Family in Foxtail Millet (Setaria Italica L.) and Expression Analyses to Reveal Their Role During Drought Stress

10.21203/rs.3.rs-1036026/v1 ◽

2021 ◽

Author(s):

Xinlei Ma ◽

Ningwei XU ◽

Pengpeng Gu ◽

Liqiang Du ◽

Zhenqing Guo ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Gene Family ◽

Expression Patterns ◽

Foxtail Millet ◽

Setaria Italica ◽

Pcr Analysis ◽

Induced Response ◽

Mads Box ◽

Element Analysis

Abstract MADS-box gene family is a key regulatory factor family, which controls vegetative growth, reproductive development and can be used to mediate abiotic stresses in many plants. However, Knowledge of this gene family is still limited in Setaria italica. In the present study, a total of 70 SitMADS genes were identified and renamed on the basis of the chromosomal distribution of the SitMADS genes. According to gene structure, conserved motif and phylogenetic feature, the 70 SitMADSs were classified into type-Ⅰ (Mα, Mβ, Mγ) and type-Ⅱ (MIKCC and MIKC*). All of the SitMADS genes were randomly distributed on nine chromosomes, and five tandem duplicated genes and 12 pairs of duplicated gene segments were detected in the SitMADS genes family. Synteny analysis provided a high homology between SitMADS genes and OsMADS genes. A cis-element analysis inferred that SitMADS genes, except for SitMADS23, possessed at least one drought stress response and ABA(Abscisic Acid)-induced response cis-element. Real-time quantitative PCR analysis was used to detect the expression patterns of SitMADS genes in various tissues and demonstrated that the genes responded drought stress and ABA treatments. SitMADS23, SitMADS42, SitMADS51, SitMADS52, SitMADS58 and SitMADS64 were highly expressed in PEG(Polyethylene glycol) and drought stress, which suggested its important role in drought stress response. SitMADS51, SitMADS63 and SitMADS64 seemed to be responsive to ABA hormone signaling, suggesting that they were involved in the ABA signaling pathways. This paper provided a deep insight into the evolutionary characteristics of SitMADS genes. The results provide comprehensive information for further analyses of the molecular functions of the MADS-box gene family in Setaria italica.

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Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean

BMC Genomics ◽

10.1186/s12864-021-07687-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Min Wang ◽

Bowei Chen ◽

Wei Zhou ◽

Linan Xie ◽

Lishan Wang ◽

...

Keyword(s):

Stress Response ◽

Gene Family ◽

Soybean Genome ◽

Signal Pathways ◽

Type I ◽

Transcription Analysis ◽

Cis Acting ◽

Network Analyses ◽

Genome Wide ◽

Submergence Stress

Abstract Background Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean. Results To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean. Conclusion Sixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.

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Characterization of the Liriodendron Chinense MYB Gene Family and Its Role in Abiotic Stress Response

Frontiers in Plant Science ◽

10.3389/fpls.2021.641280 ◽

2021 ◽

Vol 12 ◽

Author(s):

Weihuang Wu ◽

Sheng Zhu ◽

Liming Zhu ◽

Dandan Wang ◽

Yang Liu ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Abiotic Stress ◽

Drought Stress ◽

Stress Response ◽

Gene Family ◽

Growth And Development ◽

Regulatory Function ◽

Abiotic Stress Response ◽

A Genome ◽

Liriodendron Chinense

Liriodendron chinense (Lchi) is a Magnoliaceae plant, which is a basic angiosperm left behind by the Pleistocene and mainly distributed in the south of the Yangtze River. Liriodendron hybrids has good wood properties and is widely used in furniture and in other fields. It is not clear if they can adapt to different environmental conditions, such as drought and high and low temperatures, and the molecular mechanisms for this adaptation are unknown. Among plant transcription factors (TFs), the MYB gene family is one of the largest and is often involved in stress or adversity response signaling, growth, and development. Therefore, studying the role of MYBTFs in regulating abiotic stress signaling, growth, and development in Lchi is helpful to promote afforestation in different environments. In our research, a genome-wide analysis of the LchiMYB gene family was performed, including the phylogenetic relationship tree, gene exon-intron structure, collinearity, and chromosomal position. According to the evolutionary tree, 190 LchiMYBs were divided into three main branches. LchiMYBs were evenly distributed across 19 chromosomes, with their collinearity, suggesting that segment duplication events may have contributed to LchiMYB gene expansion. Transcriptomes from eight tissues, 11 stages of somatic embryogenesis, and leaves after cold, heat, and drought stress were used to analyze the function of the MYB gene family. The results of tissue expression analysis showed that most LchiMYB genes regulated bark, leaf, bud, sepal, stigma, and stamen development, as well as the four important stages (ES3, ES4, ES9, and PL) of somatic embryogenesis. More than 60 LchiMYBs responded to heat, cold, and drought stress; some of which underwent gene duplication during evolution. LchiMYB3 was highly expressed under all three forms of stress, while LchiMYB121 was strongly induced by both cold and heat stress. Eight genes with different expression patterns were selected and verified by quantitative real-time PCR (qRT-PCR) experiments. The results suggested that these LchiMYBs may regulate Lchi growth development and resistance to abiotic stress. This study shows the cross-regulatory function of LchiMYBs in the growth and development, asexual reproduction, and abiotic resistance of Lchi. This information will prove pivotal to directing further studies on the biological function of Lchi MYBTFs in genetic improvement and abiotic stress response.

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