Genome-Wide Identification of Seven Polyamine Oxidase Genes in Camellia sinensis (L.) and Their Expression Patterns Under Various Abiotic Stresses

Galactinol synthases (GolSs) are the key enzymes that participate in raffinose family oligosaccharides (RFO) biosynthesis, which perform a big role in modulating plant growth and response to biotic or abiotic stresses. To date, no systematic study of this gene family has been conducted in cassava (Manihot esculenta Crantz). Here, eight MeGolS genes are isolated from the cassava genome. Based on phylogenetic background, the MeGolSs are clustered into four groups. Through predicting the cis-elements in their promoters, it was discovered that all MeGolS members act as hormone-, stress-, and tissue-specific related elements to different degrees. MeGolS genes exhibit incongruous expression patterns in various tissues, indicating that different MeGolS proteins might have diverse functions. MeGolS1 and MeGolS3–6 are highly expressed in leaves and midveins. MeGolS3–6 are highly expressed in fibrous roots. Quantitative real-time Polymerase Chain Reaction (qRT-PCR) analysis indicates that several MeGolSs, including MeGolS1, 2, 5, 6, and 7, are induced by abiotic stresses. microRNA prediction analysis indicates that several abiotic stress-related miRNAs target the MeGolS genes, such as mes-miR156, 159, and 169, which also respond to abiotic stresses. The current study is the first systematic research of GolS genes in cassava, and the results of this study provide a basis for further exploration the functional mechanism of GolS genes in cassava.

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Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

Author(s):

Chenghao Zhang ◽

Wenqi Dong ◽

Zong-an Huang ◽

MyeongCheoul Cho ◽

Qingcang Yu ◽

...

Keyword(s):

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Environmental Stresses ◽

Transcriptional Level ◽

Specific Expression ◽

Capsicum Annuum L ◽

Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.)

PeerJ ◽

10.7717/peerj.4172 ◽

2017 ◽

Vol 5 ◽

pp. e4172 ◽

Cited By ~ 9

Author(s):

Bernard Kinuthia Karanja ◽

Liang Xu ◽

Yan Wang ◽

Everlyne M’mbone Muleke ◽

Bashir Mohammed Jabir ◽

...

Keyword(s):

Transcription Factor ◽

Abiotic Stresses ◽

Expression Patterns ◽

Hormone Signaling ◽

Preferential Expression ◽

Genome Wide ◽

Raphanus Sativus L ◽

Transcription Factor Genes ◽

Membrane Bound ◽

Polymerase Chain

NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.

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Genome-wide identification and expression analysis of NADPH oxidase genes in response to ABA and abiotic stresses, and in fibre formation in Gossypium

PeerJ ◽

10.7717/peerj.8404 ◽

2020 ◽

Vol 8 ◽

pp. e8404 ◽

Cited By ~ 4

Author(s):

Gaofeng Zhang ◽

Caimeng Yue ◽

Tingting Lu ◽

Lirong Sun ◽

Fushun Hao

Keyword(s):

Abiotic Stresses ◽

Growth And Development ◽

Expression Patterns ◽

Purifying Selection ◽

Fiber Formation ◽

Biotic And Abiotic Stresses ◽

Fibre Formation ◽

Genome Wide ◽

Regulation Mechanisms ◽

Respiratory Burst Oxidase

Plasma membrane NADPH oxidases, also named respiratory burst oxidase homologues (Rbohs), play pivotal roles in many aspects of growth and development, as well as in responses to hormone signalings and various biotic and abiotic stresses. Although Rbohs family members have been identified in several plants, little is known about Rbohs in Gossypium. In this report, we characterized 13, 13, 26 and 19 Rbohs in G. arboretum, G. raimondii, G. hirsutum and G. barbadense, respectively. These Rbohs were conservative in physical properties, structures of genes and motifs. The expansion and evolution of the Rbohs dominantly depended on segmental duplication, and were under the purifying selection. Transcription analyses showed that GhRbohs were expressed in various tissues, and most GhRbohs were highly expressed in flowers. Moreover, different GhRbohs had very diverse expression patterns in response to ABA, high salinity, osmotic stress and heat stress. Some GhRbohs were preferentially and specifically expressed during ovule growth and fiber formation. These results suggest that GhRbohs may serve highly differential roles in mediating ABA signaling, in acclimation to environmental stimuli, and in fiber growth and development. Our findings are valuable for further elucidating the functions and regulation mechanisms of the Rbohs in adaptation to diverse stresses, and in growth and development in Gossypium.

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Genome-wide identification and expression analysis of PUB genes in cotton

10.21203/rs.2.10518/v3 ◽

2020 ◽

Author(s):

Xuke Lu ◽

Na Shu ◽

Delong Wang ◽

Junjuan Wang ◽

Xiugui Chen ◽

...

Keyword(s):

Expression Analysis ◽

Abiotic Stresses ◽

Expression Patterns ◽

Structure Evolution ◽

Homologous Gene ◽

Segmental Duplications ◽

Gene Pairs ◽

Genome Wide ◽

Cotton Species ◽

Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those induced by salt, drought, hot and cold) to varying degrees.

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Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of JAZ Family Genes in Camellia Sinensis

International Journal of Molecular Sciences ◽

10.3390/ijms21072433 ◽

2020 ◽

Vol 21 (7) ◽

pp. 2433 ◽

Cited By ~ 1

Author(s):

Jiazhi Shen ◽

Zhongwei Zou ◽

Hongqing Xing ◽

Yu Duan ◽

Xujun Zhu ◽

...

Keyword(s):

Camellia Sinensis ◽

Abiotic Stresses ◽

Synergistic Effects ◽

Tea Plant ◽

Plant Genome ◽

Pcr Analysis ◽

Limited Information ◽

Genome Database ◽

Recombinant Cells ◽

Genome Wide

JAZ (Jasmonate ZIM-domain) proteins play pervasive roles in plant development and defense reaction. However, limited information is known about the JAZ family in Camellia sinensis. In this study, 12 non-redundant JAZ genes were identified from the tea plant genome database. Phylogenetic analysis showed that the 12 JAZ proteins belong to three groups. The cis-elements in promoters of CsJAZ genes and CsJAZ proteins interaction networks were also analyzed. Quantitative RT–PCR analysis showed that 7 CsJAZ genes were preferentially expressed in roots. Furthermore, the CsJAZ expressions were differentially induced by cold, heat, polyethylene glycol (PEG), methyl jasmonate (MeJA), and gibberellin (GA) stimuli. The Pearson correlations analysis based on expression levels showed that the CsJAZ gene pairs were differentially expressed under different stresses, indicating that CsJAZs might exhibit synergistic effects in response to various stresses. Subcellular localization assay demonstrated that CsJAZ3, CsJAZ10, and CsJAZ11 fused proteins were localized in the cell nucleus. Additionally, the overexpression of CsJAZ3, CsJAZ10, and CsJAZ11 in E. coli enhanced the growth of recombinant cells under abiotic stresses. In summary, this study will facilitate the understanding of the CsJAZ family in Camellia sinensis and provide new insights into the molecular mechanism of tea plant response to abiotic stresses and hormonal stimuli.

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Defining the function of SUMO system in pod development and abiotic stresses in Peanut

BMC Plant Biology ◽

10.1186/s12870-019-2136-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Yiyang Liu ◽

Jiao Zhu ◽

Sheng Sun ◽

Feng Cui ◽

Yan Han ◽

...

Keyword(s):

Abiotic Stresses ◽

Developmental Process ◽

Expression Patterns ◽

Rna Seq ◽

Specific Expression ◽

Genome Wide ◽

Pod Development ◽

Core Components ◽

Arachis Duranensis ◽

New Strategies

Abstract Background Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, little is known about SUMOylation in peanut (Arachis hypogaea L.), one of the world’s major food legume crops. In this study, we characterized the SUMOylation system from the diploid progenitor genomes of peanut, Arachis duranensis (AA) and Arachis ipaensis (BB). Results Genome-wide analysis revealed the presence of 40 SUMO system genes in A. duranensis and A. ipaensis. Our results showed that peanut also encodes a novel class II isotype of the SCE1, which was previously reported to be uniquely present in cereals. RNA-seq data showed that the core components of the SUMOylation cascade SUMO1/2 and SCE1 genes exhibited pod-specific expression patterns, implying coordinated regulation during pod development. Furthermore, both transcripts and conjugate profiles revealed that SUMOylation has significant roles during the pod development. Moreover, dynamic changes in the SUMO conjugates were observed in response to abiotic stresses. Conclusions The identification and organization of peanut SUMO system revealed SUMOylation has important roles during stress defense and pod development. The present study will serve as a resource for providing new strategies to enhance agronomic yield and reveal the mechanism of peanut pod development.

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In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Plants ◽

10.3390/plants9101393 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1393

Author(s):

Elham Mehri Eshkiki ◽

Zahra Hajiahmadi ◽

Amin Abedi ◽

Mojtaba Kordrostami ◽

Cédric Jacquard

Keyword(s):

Brassica Napus ◽

Abiotic Stresses ◽

Genetic Manipulation ◽

Expression Patterns ◽

Rna Seq ◽

Brassica Napus L ◽

Genome Wide ◽

A Genome ◽

Ssr Loci ◽

Post Transcriptional Regulation

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

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Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽

10.3390/agronomy10121855 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1855

Author(s):

Dan Luo ◽

Ziqi Jia ◽

Yong Cheng ◽

Xiling Zou ◽

Yan Lv

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Sequence Similarity ◽

Expression Profiles ◽

Expression Patterns ◽

Chromosomal Distribution ◽

Brassica Napus L ◽

Oil Crops ◽

Genome Wide ◽

Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

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Genome-wide identification and expression analysis of PUB genes in cotton

10.21203/rs.2.10518/v4 ◽

2020 ◽

Author(s):

Xuke Lu ◽

Na Shu ◽

Delong Wang ◽

Junjuan Wang ◽

Xiugui Chen ◽

...

Keyword(s):

Expression Analysis ◽

Abiotic Stresses ◽

Expression Patterns ◽

Structure Evolution ◽

Homologous Gene ◽

Segmental Duplications ◽

Gene Pairs ◽

Genome Wide ◽

Cotton Species ◽

Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those genes induced by salt, drought, hot and cold) to varying degrees.

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