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

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.

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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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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 ◽

10.7717/peerj.11410 ◽

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.

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Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis

Genes ◽

10.3390/genes10100730 ◽

2019 ◽

Vol 10 (10) ◽

pp. 730 ◽

Cited By ~ 4

Author(s):

Sun ◽

Wang ◽

Ma ◽

Li ◽

Liu

Keyword(s):

Somatic Embryogenesis ◽

Upland Cotton ◽

Expression Profiles ◽

Gene Families ◽

Early Response ◽

Auxin Signaling ◽

Evolutionary Divergence ◽

Genome Wide ◽

A Genome ◽

Early Response Genes

Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.

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

10.21203/rs.3.rs-17430/v1 ◽

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.

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Genome-Wide Identification and Expression Analysis of the Protease Inhibitor Gene Families in Tomato

Genes ◽

10.3390/genes11010001 ◽

2019 ◽

Vol 11 (1) ◽

pp. 1 ◽

Cited By ~ 3

Author(s):

Yuxuan Fan ◽

Wei Yang ◽

Qingxia Yan ◽

Chunrui Chen ◽

Jinhua Li

Keyword(s):

Expression Analysis ◽

Developmental Stages ◽

Expression Profiles ◽

In Silico Analysis ◽

Gene Families ◽

Crop Species ◽

Specific Expression ◽

Transcription Analysis ◽

Genome Wide ◽

Wilt Virus

The protease inhibitors (PIs) in plants are involved primarily in defense against pathogens and pests and in response to abiotic stresses. However, information about the PI gene families in tomato (Solanum lycopersicum), one of the most important model plant for crop species, is limited. In this study, in silico analysis identified 55 PI genes and their conserved domains, phylogenetic relationships, and chromosome locations were characterized. According to genetic structure and evolutionary relationships, the PI gene families were divided into seven families. Genome-wide microarray transcription analysis indicated that the expression of SlPI genes can be induced by abiotic (heat, drought, and salt) and biotic (Botrytis cinerea and tomato spotted wilt virus (TSWV)) stresses. In addition, expression analysis using RNA-seq in various tissues and developmental stages revealed that some SlPI genes were highly or preferentially expressed, showing tissue- and developmental stage-specific expression profiles. The expressions of four representative SlPI genes in response to abscisic acid (ABA), salicylic acid (SA), ethylene (Eth), gibberellic acid (GA). and methyl viologen (MV) were determined. Our findings indicated that PI genes may mediate the response of tomato plants to environmental stresses to balance hormone signals. The data obtained here will improve the understanding of the potential function of PI gene and lay a foundation for tomato breeding and transgenic resistance to stresses.

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The rust fungus Melampsora larici-populina expresses a conserved genetic program and distinct sets of secreted protein genes during infection of its two host plants, larch and poplar

10.1101/229971 ◽

2017 ◽

Author(s):

Cécile Lorrain ◽

Clémence Marchal ◽

Stéphane Hacquard ◽

Christine Delaruelle ◽

Jérémy Pétrowski ◽

...

Keyword(s):

Host Plants ◽

Expression Profiles ◽

Rust Fungus ◽

Gene Families ◽

Infection Process ◽

Rust Fungi ◽

Secreted Protein ◽

Alternate Host ◽

Specific Expression ◽

Clonal Multiplication

SummaryMechanims required for broad spectrum or specific host colonization of plant parasites are poorly understood. As a perfect illustration, heteroecious rust fungi require two alternate host plants to complete their life cycle. Melampsora larici-populina infects two taxonomically unrelated plants, larch on which sexual reproduction is achieved and poplar on which clonal multiplication occurs leading to severe epidemics in plantations. High-depth RNA sequencing was applied to three key developmental stages of M. larici-populina infection on larch: basidia, pycnia and aecia. Comparative transcriptomics of infection on poplar and larch hosts was performed using available expression data. Secreted protein was the only significantly over-represented category among differentially expressed M. larici-populina genes in basidia, pycnia and aecia compared together, highlighting their probable involvement in the infection process. Comparison of fungal transcriptomes in larch and poplar revealed a majority of rust genes commonly expressed on the two hosts and a fraction exhibiting a host-specific expression. More particularly, gene families encoding small secreted proteins presented striking expression profiles that highlight probable candidate effectors specialized on each host. Our results bring valuable new information about the biological cycle of rust fungi and identify genes that may contribute to host specificity.

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Genome-wide Identification, Evolutionary and Functional Analyses of Kfb Family Members in Potato

10.21203/rs.3.rs-1193858/v1 ◽

2022 ◽

Author(s):

Ruimin Tang ◽

Haitao Dong ◽

Liheng He ◽

Peng Li ◽

Yuanrui Shi ◽

...

Keyword(s):

Anthocyanin Biosynthesis ◽

Expression Profiles ◽

Expression Patterns ◽

Family Members ◽

Structure Evolution ◽

Duplicated Genes ◽

Physiological Processes ◽

Localization Analysis ◽

And Function ◽

Functional Mechanisms

Abstract Background: Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but this family members have not been systematically identified and analyzed in potato. Results: Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the KFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups according to their structural and phylogenetic features. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses. Transcriptomic and qRT-PCR analyses of StKFBs deciphered that multiple StKFB genes were differentially expressed in three colored potato tubers. Genes that were highly expressed in yellow fleshed tubers (Jin-16) and were lowly expressed in the red- (Red Rose-2) or purple-fleshed (Xisen-8) tubers, such as StKFB07, StKFB15, StKFB23, StKFB29 and StKFB44, may negatively regulate anthocyanin biosynthesis.Conclusions: This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings set the stage for further study of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.

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

BMC Plant Biology ◽

10.1186/s12870-020-02811-8 ◽

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.

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Intricate Regulation of Phosphoenolpyruvate Carboxykinase (PEPCK) Isoforms in Normal Physiology and Disease

Current Molecular Medicine ◽

10.2174/1566524019666190404155801 ◽

2019 ◽

Vol 19 (4) ◽

pp. 247-272 ◽

Cited By ~ 2

Author(s):

Venu Seenappa ◽

Manjunath B. Joshi ◽

Kapaettu Satyamoorthy

Keyword(s):

Translational Regulation ◽

Phosphoenolpyruvate Carboxykinase ◽

Current Knowledge ◽

Regulatory Elements ◽

Copy Number Variations ◽

Specific Expression ◽

Physiological Processes ◽

Clade B ◽

And Function ◽

Endogenous Modulators

Background:The phosphoenolpyruvate carboxykinase (PEPCK) isoforms are considered as rate-limiting enzymes for gluconeogenesis and glyceroneogenesis pathways. PEPCK exhibits several interesting features such as a) organelle-specific isoforms (cytosolic and a mitochondrial) in vertebrate clade, b) tissue-specific expression of isoforms and c) organism-specific requirement of ATP or GTP as a cofactor. In higher organisms, PEPCK isoforms are intricately regulated and activated through several physiological and pathological stimuli such as corticoids, hormones, nutrient starvation and hypoxia. Isoform-specific transcriptional/translational regulation and their interplay in maintaining glucose homeostasis remain to be fully understood. Mounting evidence indicates the significant involvement of PEPCK isoforms in physiological processes (development and longevity) and in the progression of a variety of diseases (metabolic disorders, cancer, Smith–Magenis syndrome).Objective:The present systematic review aimed to assimilate existing knowledge of transcriptional and translational regulation of PEPCK isoforms derived from cell, animal and clinical models.Conclusion:Based on current knowledge and extensive bioinformatics analysis, in this review we have provided a comparative (epi)genetic understanding of PCK1 and PCK2 genes encompassing regulatory elements, disease-associated polymorphisms, copy number variations, regulatory miRNAs and CpG densities. We have also discussed various exogenous and endogenous modulators of PEPCK isoforms and their signaling mechanisms. A comprehensive review of existing knowledge of PEPCK regulation and function may enable identification of the underlying gaps to design new pharmacological strategies and interventions for the diseases associated with gluconeogenesis.

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Primate-specific histone variants

Genome ◽

10.1139/gen-2020-0094 ◽

2020 ◽

pp. 1-10

Author(s):

Dongbo Ding ◽

Thi Thuy Nguyen ◽

Matthew Y.H. Pang ◽

Toyotaka Ishibashi

Keyword(s):

Dna Repair ◽

Genomic Dna ◽

Expression Profiles ◽

Histone Variants ◽

Amino Acid Sequences ◽

Specific Expression ◽

Linker Histones ◽

Cellular Processes ◽

Core Histones ◽

And Function

Canonical histones (H2A, H2B, H3, and H4) are present in all eukaryotes where they package genomic DNA and participate in numerous cellular processes, such as transcription regulation and DNA repair. In addition to the canonical histones, there are many histone variants, which have different amino acid sequences, possess tissue-specific expression profiles, and function distinctly from the canonical counterparts. A number of histone variants, including both core histones (H2A/H2B/H3/H4) and linker histones (H1/H5), have been identified to date. Htz1 (H2A.Z) and CENP-A (CenH3) are present from yeasts to mammals, and H3.3 is present from Tetrahymena to humans. In addition to the prevalent variants, others like H3.4 (H3t), H2A.Bbd, and TH2B, as well as several H1 variants, are found to be specific to mammals. Among them, H2BFWT, H3.5, H3.X, H3.Y, and H4G are unique to primates (or Hominidae). In this review, we focus on localization and function of primate- or hominidae-specific histone variants.

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