scholarly journals Characterization of auxin transporter AUX, PIN and PILS gene families in pineapple and evaluation of expression profiles during reproductive development and under abiotic stresses

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11410
Author(s):  
Heming Zhao ◽  
Yan Maokai ◽  
Han Cheng ◽  
Mingliang Guo ◽  
Yanhui Liu ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Profiles ◽  
Lateral Roots ◽  
Expression Patterns ◽  
Gene Families ◽  
Transporter Gene ◽  
Specific Expression ◽  
Protein Motifs ◽  
A Genome ◽  
Auxin Transporter

Polar auxin transport in plant is mediated by influx and efflux transporters, which are encoded by AUX/LAX, PIN and PILS genes, respectively. The auxin transporter gene families have been characterized in several species from monocots and eudicots. However, a genome-wide overview of auxin transporter gene families in pineapple is not yet available. In this study, we identified a total of threeAcAUX genes, 12 AcPIN genes, and seven AcPILS genes in the pineapple genome, which were variably located on 15 chromosomes. The exon-intron structure of these genes and properties of deduced proteins were relatively conserved within the same family. Most protein motifs were widespread in the AUX, PIN or PILS proteins, whereas a few motifs were absent in only one or two proteins. Analysis of the expression profiles of these genes elucidated that several genes exhibited either preferential or tissue-specific expression patterns in vegetative and/or reproductive tissues. AcAUX2 was specifically expressed in the early developmental ovules, while AcPIN1b and AcPILS2 were strongly expressed in stamens and ovules. AcPIN9b, AcPILS1, AcPILS6a, 6b and 6c were abundantly expressed in stamens. Furthermore, qRT-PCR results showed that several genes in these families were responsive to various abiotic stresses. Comparative analysis indicated that the genes with close evolutionary relationships among pineapple, rice and Arabidopsis exhibited similar expression patterns. Overexpression of the AcAUX1 in Arabidopsis rescued the phenotype in aux1-T, and resulted in increased lateral roots in WT. These results will provide new insights into auxin transporter genes of pineapple and facilitate our understanding of their roles in pineapple growth and development.

scholarly journals Comprehensive Analysis and Expression Profiling of PIN, AUX/LAX, and ABCB Auxin Transporter Gene Families in Solanum tuberosum under Phytohormone Stimuli and Abiotic Stresses

2020 ◽  
Author(s):  
Chenghui Yang ◽  
Dongdong Wang ◽  
Chao Zhang ◽  
Minghui Ye ◽  
Nana Kong ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Biological Significance ◽  
Gene Families ◽  
Comprehensive Analysis ◽  
Pcr Analysis ◽  
Transporter Gene ◽  
A Genome ◽  
Auxin Transporter

Abstract Background:Auxin is the only plant hormone that exhibits transport polarity that is mediated by three classes of proteins, AUX/LAX influx carriers, the PIN and ABCB efflux carriers. Extensive studies have been conducted to examine the biological functions of auxin transporter genes using model plants systems and in several plant species. Despite this, information regarding the comprehensive analysis of auxin transporter genes in potato species and information regarding the expression patterns of these genes in response to external stresses remains scarce.Results: Here, we conducted a genome-wide annotation of the StLAX, StPIN, and StABCB auxin transporter gene families to examine genomic distributions, gene structures, phylogenic relationships and co-expression analysis. From these analyses, 5 StLAXs, 10 StPINs, and 22 StABCBs were identified in the potato genome and mapped to 12 chromosomes. Constructing co-expression networks revealed 18 gene modules and potato auxin transporter genes distributed in ten of them correlating to the development of various tissues. Tissue-specific expression analysis indicated that genes from the StLAX family were expressed at significantly higher levels compared to those of the other two gene families, suggesting that the StLAXs may be more important for these designated developmental stages in potato. Quantitative real-time PCR analysis indicated responsiveness of StLAXs, StPINs, and StABCBs to auxin and PATIs, implying their possible roles in mediating intercellular auxin homoeostasis and redistribution. Additionally, the differential expression levels of the StLAX, StPIN, and StABCB genes under ABA and abiotic stresses were indicative of their specific adaptive mechanisms regulating tolerance to various environmental stimuli. Promoter cis-regulatory element analyses were used to explore a large number of auxin-responsive and stress-related cis-elements within the promoters of the StLAX, StPIN, and StABCB genes that could account for their responsiveness to diverse stresses.Conclusions: In summary, we have provided comprehensive information on StLAX, StPIN, and StABCB auxin transporter gene families in potato. We are confident that our results provide a foundation for a better understanding of auxin transport in potato, as we have demonstrated the biological significance of these family genes in hormone signalling and adaption to environmental stresses.

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 ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
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.

scholarly journals Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

2020 ◽  
Vol 21 (19) ◽  
pp. 7180
Author(s):  
Hongfeng Wang ◽  
Hongjiao Jiang ◽  
Yiteng Xu ◽  
Yan Wang ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Feedback Regulation ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Model Legume ◽  
Genome Wide ◽  
A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

scholarly journals A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

2018 ◽  
Author(s):  
Yongkai Li ◽  
Xiaojie Cheng ◽  
Yaqin Fu ◽  
Qinqin Wu ◽  
Yuli Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Early Stage ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cellulose Synthase ◽  
Biotic And Abiotic Stresses ◽  
A Genome ◽  
Evolutionary Features ◽  
Different Tissues

Cell walls play an important role in the structure and morphology of plants as well as stress response, including various biotic and abiotic stresses. Although the comprehensive analysis of genes involved in cellulose synthase have been performed in model plants, such as Arabidopsis thaliana and rice, information regarding cellulose synthase-like (Csl) genes in maize is extremely limited. In this study, a total of 56 members of Csl gene family were identified in maize genome, which were classified into six subfamilies. Analysis of gene structure and conserved motif indicated functional similarities among the ZmCsl proteins within the same subfamily. Additionally, the 56 ZmCsl genes were dispersed on 10 chromosomes. The expression patterns of ZmCsl genes in different tissues using the transcriptome data revealed that most of ZmCsl genes had a relatively high expression in root and tassel tissues. Moreover, the expression profiles of ZmCsl genes under drought and re-watering indicated that the expression of ZmCsl genes were mainly responsive to early stage of drought stress. The protein-protein interaction network of ZmCsl genes proposed some potential interacted proteins. The data presented a comprehensive survey of Csl gene family in maize. The detailed description of maize Csl genes will be beneficial to understand their structural, functional, and evolutionary features. Importantly, we have described the differential expression profiles of these members across different tissues and under drought. This information will provide an important foundation for studying the roles of these ZmCsl genes in response to biotic and abiotic stresses.

scholarly journals Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

2020 ◽  
Author(s):  
Chong Yang ◽  
Juanjuan Li ◽  
Faisal Islam ◽  
Luyang Hu ◽  
Jiansu Wang ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Gene Families ◽  
Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes and will be beneficial to crop improvement.

scholarly journals Overexpression of MdIAA9 confers high tolerance to osmotic stress in transgenic tobacco

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7935 ◽  
Author(s):  
Dong Huang ◽  
Qian Wang ◽  
Dingyue Duan ◽  
Qinglong Dong ◽  
Shuang Zhao ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Profiles ◽  
Major Gene ◽  
Gene Families ◽  
Early Response ◽  
Specific Expression ◽  
Woody Perennial ◽  
Physiological Processes ◽  
And Function ◽  
Indole 3 Acetic Acid

Auxin is a plant hormone that takes part in a series of developmental and physiological processes. There are three major gene families that play a role in the early response of auxin and auxin/indole-3-acetic acid (Aux/IAA) is one of these. Although the genomic organization and function of Aux/IAA genes have been recognized in reference plants there have only been a few focused studies conducted with non-model crop plants, especially in the woody perennial species. We conducted a genomic census and expression analysis of Aux/IAA genes in the cultivated apple (Malus × domestica Borkh.). The Aux/IAA gene family of the apple genome was identified and analyzed in this study. Phylogenetic analysis showed that MdIAAs could be categorized into nine subfamilies and that these MdIAA proteins contained four whole or partially conserved domains of the MdIAA family. The spatio-specific expression profiles showed that most of the MdIAAs were preferentially expressed in specific tissues. Some of these genes were significantly induced by treatments with one or more abiotic stresses. The overexpression of MdIAA9 in tobacco (Nicotiana tabacum L.) plants significantly increased their tolerance to osmotic stresses. Our cumulative data supports the interactions between abiotic stresses and plant hormones and provides a theoretical basis for the mechanism of Aux/IAA and drought resistance in apples.

scholarly journals A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

2018 ◽  
Author(s):  
Yongkai Li ◽  
Xiaojie Cheng ◽  
Yaqin Fu ◽  
Qinqin Wu ◽  
Yuli Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Early Stage ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cellulose Synthase ◽  
Biotic And Abiotic Stresses ◽  
A Genome ◽  
Evolutionary Features ◽  
Different Tissues

Cell walls play an important role in the structure and morphology of plants as well as stress response, including various biotic and abiotic stresses. Although the comprehensive analysis of genes involved in cellulose synthase have been performed in model plants, such as Arabidopsis thaliana and rice, information regarding cellulose synthase-like (Csl) genes in maize is extremely limited. In this study, a total of 56 members of Csl gene family were identified in maize genome, which were classified into six subfamilies. Analysis of gene structure and conserved motif indicated functional similarities among the ZmCsl proteins within the same subfamily. Additionally, the 56 ZmCsl genes were dispersed on 10 chromosomes. The expression patterns of ZmCsl genes in different tissues using the transcriptome data revealed that most of ZmCsl genes had a relatively high expression in root and tassel tissues. Moreover, the expression profiles of ZmCsl genes under drought and re-watering indicated that the expression of ZmCsl genes were mainly responsive to early stage of drought stress. The protein-protein interaction network of ZmCsl genes proposed some potential interacted proteins. The data presented a comprehensive survey of Csl gene family in maize. The detailed description of maize Csl genes will be beneficial to understand their structural, functional, and evolutionary features. Importantly, we have described the differential expression profiles of these members across different tissues and under drought. This information will provide an important foundation for studying the roles of these ZmCsl genes in response to biotic and abiotic stresses.

scholarly journals Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhenming Yu ◽  
Guihua Zhang ◽  
Jaime A. Teixeira da Silva ◽  
Mingzhi Li ◽  
Conghui Zhao ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Dna Methyltransferase ◽  
Epigenetic Modification ◽  
Expression Profiles ◽  
Gene Families ◽  
Seedling Stage ◽  
Dendrobium Officinale ◽  
Integrated Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background DNA methylation is a conserved and important epigenetic modification involved in the regulation of numerous biological processes, including plant development, secondary metabolism, and response to stresses. However, no information is available regarding the identification of cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes in the orchid Dendrobium officinale. Results In this study, we performed a genome-wide analysis of DoC5-MTase and DodMTase gene families in D. officinale. Integrated analysis of conserved motifs, gene structures and phylogenetic analysis showed that eight DoC5-MTases were divided into four subfamilies (DoCMT, DoDNMT, DoDRM, DoMET) while three DodMTases were divided into two subfamilies (DoDML3, DoROS1). Multiple cis-acting elements, especially stress-responsive and hormone-responsive ones, were found in the promoter region of DoC5-MTase and DodMTase genes. Furthermore, we investigated the expression profiles of DoC5-MTase and DodMTase in 10 different tissues, as well as their transcript abundance under abiotic stresses (cold and drought) and at the seedling stage, in protocorm-like bodies, shoots, and plantlets. Interestingly, most DoC5-MTases were downregulated whereas DodMTases were upregulated by cold stress. At the seedling stage, DoC5-MTase expression decreased as growth proceeded, but DodMTase expression increased. Conclusions These results provide a basis for elucidating the role of DoC5-MTase and DodMTase in secondary metabolite production and responses to abiotic stresses in D. officinale.

scholarly journals Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Di Wu ◽  
Anqi Liu ◽  
Xiaoyu Qu ◽  
Jiayi Liang ◽  
Min Song
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Multigene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Specific Expression ◽  
Group I

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

scholarly journals The R2R3-MYB gene family in banana (Musa acuminata): genome-wide identification, classification and expression patterns

2020 ◽  
Author(s):  
Boas Pucker ◽  
Ashutosh Pandey ◽  
Bernd Weisshaar ◽  
Ralf Stracke
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Gene Families ◽  
Defense Responses ◽  
Musa Acuminata ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome ◽  
Myb Proteins ◽  
R2r3 Myb

AbstractThe R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-seq data. For 280 M. acuminata MYB genes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. The M. acuminata R2R3-MYB genes were functionally categorised, leading to the identification of seven clades containing only M. acuminata R2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded in Musa during genome evolution. This functional classification and expression analysis of the MYB gene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.

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