The IQD gene family in soybean: structure, phylogeny, evolution and expression

Functional Analysis of the GhIQD1 Gene in Cotton Resistance to Verticillium Wilt

Cotton is a critical crop with massive economic implications worldwide. Verticillium wilt is a soil-borne ailment caused by Verticillium dahliae, which harms the growth and development of cotton. Therefore, investigating the genes associated with resistance to verticillium wilt is of particular significance. In this study, we identified the GhIQD1 gene through transcriptome analysis and experimentally characterized the role of the GhIQD1 gene in cotton against V. dahliae. The findings indicated that GhIQD1 acts as a calmodulin-binding protein. The expression of GhIQD1 was the highest in stems, and the expression level increased significantly following infection with V. dahliae. The expression in resistant cotton varieties was higher than in susceptible cotton varieties. Through overexpression of the GhIQD1 gene in tobacco, these transgenic plants exhibited improved resistance to V. dahliae. In contrast, by silencing the GhIQD1 gene in cotton through VIGS, the resistance to V. dahliae was reduced. Following inoculation, the leaves yellowed, and the disease index was higher. Transcriptome analysis of transgenic tobacco 72 h after inoculation indicated that overexpression of GhIQD1 increased the enrichment of the calmodulin pathway and stimulated the production of plant hormones alongside secondary metabolites. Consequently, we investigated the relationship between the GhIQD1 gene and plant disease-resistant hormones SA, JA, and ABA. In summary, this study uncovered the mechanism by which GhIQD1 conferred resistance to V. dahliae in cotton through positive regulation of JA and ABA, providing crucial information for further research on the adaptation of plants to pathogen invasion.

IQ domain-containing protein ZmIQD27 modulates water transport in maize

Plant metaxylem vessels provide physical support to promote upright growth and the transport of water and nutrients. A detailed characterization of the molecular network controlling metaxylem development is lacking. However, knowledge of the events that regulate metaxylem development could contribute to the development of germplasm with improved yield. In this paper, we screened an EMS-induced B73 mutant library, which covers 92% of maize (Zea mays) genes, to identify drought-sensitive phenotypes. Three mutants were identified, named iqd27-1, iqd27-2, and iqd27-3, and genetic crosses showed that they were allelic to each other. The causal gene in these 3 mutants encodes the IQ domain-containing protein ZmIQD27. Our study showed that defective metaxylem vessel development likely causes the drought sensitivity and abnormal water transport phenotypes in the iqd27 mutants. ZmIQD27 was expressed in the root meristematic zone where secondary cell wall deposition is initiated, and loss-of-function iqd27 mutants exhibited a microtubular arrangement disorder. We propose that association of functional ZmIQD27 with microtubules is essential for correct targeted deposition of the building blocks for secondary cell wall development in maize.

Genome-wide identification and analysis of the IQM gene family in soybean

IQM, a plant-specific calmodulin-binding protein, plays multiple roles in plant growth and development. Although a comprehensive analysis has been carried out on the IQM family genes in Arabidopsis and rice, the number and functions of IQM genes in other species have not been explored. In this study, we identified 15 members of the soybean (Glycine max) IQM gene family using BLASTP tools. These members were distributed on 12 soybean chromosomes and constitute six pairs caused by fragment duplication events. According to phylogeny, the 15 genes were divided into three subfamilies (I, II, and III), and members of the same subfamily had similar gene and protein structures. Yeast two-hybrid experiments revealed that the IQ motif is critical for the binding of GmIQM proteins to GmCaM, and its function is conserved in soybean, Arabidopsis, and rice. Based on real-time PCR, the soybean IQM genes were strongly induced by PEG and NaCl, suggesting their important biological functions in abiotic stress responses. Overall, this genome-wide analysis of the soybean IQM gene family lays a solid theoretical foundation for further research on the functions of GmIQM genes and could serve as a reference for the improvement and breeding of soybean stress resistance traits.

Genome-Wide Identification of the SUN Gene Family in Melon (Cucumis melo) and Functional Characterization of Two CmSUN Genes in Regulating Fruit Shape Variation

Melon (Cucumis melo) is an important economic crop cultivated worldwide. A unique SUN gene family plays a crucial role in regulating plant growth and fruit development, but many SUN family genes and their function have not been well-characterized in melon. In the present study, we performed genome-wide identification and bioinformatics analysis and identified 24 CmSUN family genes that contain integrated and conserved IQ67 domain in the melon genome. Transcriptome data analysis and qRT-PCR results showed that most CmSUNs are specifically enriched in melon reproductive organs, such as young flowers and ovaries. Through genetic transformation in melons, we found that overexpression of CmSUN23-24 and CmSUN25-26-27c led to an increased fruit shape index, suggesting that they act as essential regulators in melon fruit shape variation. Subcellular localization revealed that the CmSUN23-24 protein is located in the cytoplasmic membrane. A direct interaction between CmSUN23-24 and a Calmodulin protein CmCaM5 was found by yeast two-hybrid assay, which indicated their participation in the calcium signal transduction pathway in regulating plant growth. These findings revealed the molecular characteristics, expression profile, and functional pattern of the CmSUN genes, and may provide the theoretical basis for the genetic improvement of melon fruit breeding.

Genome-wide analysis of IQD proteins and ectopic expression of watermelon ClIQD24 in tomato suggests its important role in regulating fruit shape

The plant-specific IQ67 domain (IQD) is the largest class of calmodulin targets found in plants, and plays an important role in many biological processes, especially fruit development processes. However, the functional role of IQD proteins in the development of watermelon (Citrullus lanatus) shape remains unknown, as the IQD protein family in watermelon has not been systematically characterized. Herein, we elucidated the gene structures, chromosomal locations, evolutionary divergence, and functions of 35 IQD genes in the watermelon genome. The transcript profiles and quantitative real-time PCR analysis at different stages of fruit development showed that the ClIQD24 gene was highly expressed on 0 days after pollination. Furthermore, we found that the ectopic overexpression of ClIQD24 promoted tomato fruit elongation, thereby revealing the significance of ClIQD24 in the progression of watermelon shape. Our study will serve as a reference for further investigations on the molecular mechanisms underlying watermelon fruit shape formation.

IQD1 Involvement in Hormonal Signaling and General Defense Responses Against Botrytis cinerea

IQ Domain 1 (IQD1) is a novel Arabidopsis thaliana calmodulin-binding protein, which was found to be a positive regulator of glucosinolate (GS) accumulation and plant defense responses against insects. We demonstrate here that the IQD1 overexpressing line (IQD1 ^OXP ) was also more resistant also to the necrotrophic fungus Botrytis cinerea, whereas an IQD1 knockout line (iqd1-1) was much more sensitive. Furthermore, we showed that IQD1 is up-regulated by jasmonic acid (JA) and downregulated by salicylic acid (SA). A comparison of whole transcriptome expression between iqd1-1 and wild type plants revealed a substantial downregulation of genes involved in plant defense and hormone regulation. Further examination revealed a marked reduction of SA and increases in the levels of ethylene, JA and abscisic acid response genes in the iqd1-1 line. Moreover, quantification of SA, JA, and abscisic acids in IQD1 ^OXP and iqd1-1 lines relative to the wild type, showed a significant reduction in endogenous JA levels in the knockout line, simultaneously with increased SA levels. Relations between IQD1 ^OXP and mutants defective in plant-hormone response indicated that IQD1 cannot rescue the absence of NPR1 or impaired SA accumulation in the NahG line. IQD1 cannot rescue ein2 or eto1 mutations connected to the ethylene pathway involved in both defense responses against B. cinerea and in regulating GS accumulation. Furthermore, IQD1cannot rescue the aos, coi1 or jar1mutations, all involved in the defense response against B. cinerea and it depends on JAR1 to control indole glucosinolate accumulation. We also found that in the B. cinerea, which infected the iqd1-1 mutant, the most abundant upregulated group of proteins is involved in the degradation of complex carbohydrates, as correlated with the sensitivity of this mutant. In summary, our results suggest that IQD1 is an important A. thaliana defensive protein against B. cinerea that is integrated into several important pathways, such as those involved in plant defense and hormone responses.

Genome-wide identification, expression analysis and evolutionary relationships of the IQ67-domain gene family in common wheat (Triticum aestivum L.) and its progenitors

BACKGROUND

The plant-specific IQ67-domain (IQD) gene family plays an important role in plant development and stress responses. However, little is known about the IQD family in common wheat (Triticum aestivum L), an agriculturally important crop that provides more than 20% of the calories and protein consumed in the modern human diet.

RESULTS

We identified 125 IQDs in the wheat genome and divided them into four subgroups by phylogenetic analysis. The IQDs belonging to the same subgroup had similar exon-intron structure and conserved motif composition. Polyploidization contributed significantly to the expansion of IQD genes in wheat. Characterization of the expression profile of these genes revealed that a few T. aestivum (Ta)IQDs showed high tissue-specificity. The stress-induced expression pattern also revealed a potential role of TaIQDs in environmental adaptation, as TaIQD-2A-2, TaIQD-3A-9 and TaIQD-1A-7 were significantly induced by cold, drought and heat stresses, and could be candidates for future functional characterization. In addition, IQD genes in the A, B and D subgenomes displayed an asymmetric evolutionary pattern, as evidenced by their different gain or loss of member genes, expression levels and nucleotide diversity.

CONCLUSIONS

This study elucidated the potential biological functions and evolutionary relationships of the IQD gene family in wheat and revealed the divergent fates of IQD genes during polyploidization.

Genome-wide characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Class III peroxidases (PODs) are plant-specific glycoproteins, that play essential roles in various plant physiological processes and defence responses. To date, scarce information is available about the POD gene family in soybean. Hence, the present study is the first comprehensive report about the genome-wide characterization of GmPOD gene family in soybean (Glycine max L.). Here, we identified a total of 124 GmPOD genes in soybean, that are unevenly distributed across the genome. Phylogenetic analysis classified them into six distinct sub-groups (A-F), with one soybean specific subgroup. Exon-intron and motif analysis suggested the existence of structural and functional diversity among the sub-groups. Duplication analysis identified 58 paralogous gene pairs; segmental duplication and positive/Darwinian selection were observed as the major factors involved in the evolution of GmPODs. Furthermore, RNA-seq analysis revealed that 23 out of a total 124 GmPODs showed differential expression between drought-tolerant and drought-sensitive genotypes under stress conditions; however, two of them (GmPOD40 and GmPOD42) revealed the maximum deregulation in all contrasting genotypes. Overexpression (OE) lines of GsPOD40 showed considerably higher drought tolerance compared to wild type (WT) plants under stress treatment. Moreover, the OE lines showed enhanced photosynthesis and enzymatic antioxidant activities under drought stress, resulting in alleviation of ROS induced oxidative damage. Hence, the GsPOD40 enhanced drought tolerance in soybean by regulating the key physiological and biochemical pathways involved in the defence response. Lastly, the results of our study will greatly assist in further functional characterization of GsPODs in plant growth and stress tolerance in soybean.

Identification of Raf-Like Kinases B Subfamily Genes in Gossypium Species Revealed GhRAF42 Enhanced Salt Tolerance in Cotton

Salinity is a critical abiotic factor that significantly reduces agricultural production. Cotton is an important fiber crop and a pioneer on saline soil, hence genetic architecture that underpins salt tolerance should be thoroughly investigated. The Raf-like kinase B-subfamily (RAF) genes were discovered to regulate the salt stress response in cotton plants. However, understanding the RAFs in cotton, such as Enhanced Disease Resistance 1 and Constitutive Triple Response 1 kinase, remains a mystery. This study obtained 29, 28, 56, and 54 RAF genes from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively. The RAF gene family described allopolyploidy and hybridization events in allotetraploid cotton evolutionary connections. Ka/Ks analysis advocates that cotton evolution was subjected to an intense purifying selection of the RAF gene family. Interestingly, integrated analysis of synteny and gene collinearity suggested dispersed and segmental duplication events involved in the extension of RAFs in cotton. Transcriptome studies, functional validation, and virus-induced gene silencing on salt treatments revealed that GhRAF42 is engaged in salt tolerance in upland cotton. This research might lead to a better understanding of the role of RAFs in plants and the identification of suitable candidate salt-tolerant genes for cotton breeding.

Genome-Wide Identification and Characterization of the Potato IQD Family During Development and Stress

Calmodulin-binding proteins belong to the IQ67 domain (IQD) gene family and play essential roles in plant development and stress responses. However, the role of IQD gene family in potato (Solanum tuberosum L.) is yet to be known. In the present study, 23 StIQDs were identified in the potato genome and named StIQD1 to StIQD23. They were unevenly distributed on 10 of the 12 chromosomes. Phylogenetic analysis divided the IQDs into four subfamilies (IQD I–IV). StIQDs found in three of the four subfamilies. Synteny analysis confirmed that potato and tomato shared a close evolutionary relationship. Besides, RNA-Seq data analysis revealed that the expression of 19 of the 23 StIQDs was detected in at least one of the 12 tissues, and some of which showed a tissue-specific pattern. Quantitative reverse transcriptase–polymerase chain reaction results further confirmed that 14 StIQDs responded differently to various abiotic stresses, including drought, extreme temperature, and CaCl₂ treatment, suggesting their significance in stress response. This study presents a comprehensive overview of the potato IQD gene family and lays a foundation for further analysis of the StIQDs functions in plant development and stress response.

Identification of C2H2 subfamily ZAT genes in Gossypium species reveals GhZAT34 and GhZAT79 enhanced salt tolerance in Arabidopsis and cotton

Soil salinization is a vital factor that restricts the efficient and sustainable development of global agriculture. Studies enlightened that the C₂H₂ zinc finger proteins (C₂H₂-ZFP) were involved in regulating the stress response in plants. However, knowledge of the C₂H₂-ZFP subfamily C1 (ZAT; Zinc finger of Arabidopsis thaliana) in cotton is still a mystery. In this study, 47, 45, 94, and 88 ZAT genes were obtained from diploid A2, D5 and tetraploid AD1, AD2 cotton genomes, respectively. The function of hybridization and allopolyploidy in the evolutionary linkage of allotetraploid cotton was explained by the family of ZAT gene in 4 species. Duplication of gene activities indicates that the family of ZAT gene of cotton evolution was under strong purifying selection. The integration of previous transcriptome data related to NaCl stress, strongly suggests the GhZAT34 and GhZAT79 may interact with salt resistance in upland cotton. The expression level of certain ZAT genes, higher seed germination rate of transgenic Arabidopsis and gene- silenced cotton revealed that both genes were involved in the salt tolerance of upland cotton. This study may pave the substantial understandings into the role of ZATs genes in plants as well as suggest appropriate candidate genes for breeding of cotton varieties against salinity tolerance.

Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.)

Calmodulin (CaM) is considered as the most significant Ca²⁺ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.

New Insights Into Functions of IQ67-Domain Proteins

IQ67-domain (IQD) proteins, first identified in Arabidopsis and rice, are plant-specific calmodulin-binding proteins containing highly conserved motifs. They play a critical role in plant defenses, organ development and shape, and drought tolerance. Driven by comprehensive genome identification and analysis efforts, IQDs have now been characterized in several species and have been shown to act as microtubule-associated proteins, participating in microtubule-related signaling pathways. However, the precise molecular mechanisms underpinning their biological functions remain incompletely understood. Here we review current knowledge on how IQD family members are thought to regulate plant growth and development by affecting microtubule dynamics or participating in microtubule-related signaling pathways in different plant species and propose some new insights.

Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera)

The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public availability of grapevine genome enables us to perform identification, phylogeny, chromosomal orientation, and gene structure analysis of the IQD genes in grapevine. We identified 49 VvIQD genes (VvIQD1–VvIQD49) and further classified them into eight subgroups based on phylogenetic relationships. The 49 VvIQD genes were assigned to 19 different chromosomal positions. The collinear relationship between grapevine and Arabidopsis IQDs (VvIQD and AtIQD), and within grapevine VvIQDs, was highly conserved. In addition, most of duplicated gene pairs showed Ka/Ks ratio less than 1.00, indicating purifying selection within these gene pairs, implying functional discrepancy after duplication. Transcription profiling of VvIQD genes shed light on their specific role in grapevine tissue and organ development. The qRT-PCR validation of the 49 VvIQD genes in grape berry tissue from cultivars with distinct berry shape during developmental phases suggested candidate genes involved in the shape of grape berries. The subcellular prediction of VvIQD22, VvIQD23, VvIQD38, and VvIQD49 genes validated their localization in the nucleus and plasma membrane. The VvIQD49 protein interaction with VvCaM2 was also verified by bimolecular fluorescence complementation (BiFC) analysis in the plasma membrane. Our findings will be valuable for the functional genomic studies for desirable shape development of grape berries.

Enhancement of Glucosinolate Production in Watercress ( Nasturtium officinale) Hairy Roots by Overexpressing Cabbage Transcription Factors

Glucosinolates are secondary metabolites that play important roles in plant defense and human health, as their production in plants is enhanced by overexpressing transcription factors. Here, four cabbage transcription factors (IQD1-1, IQD1-2, MYB29-1, and MYB29-2) affecting genes in both aliphatic and indolic glucosinolates biosynthetic pathways and increasing glucosinolates accumulation were overexpressed in watercress. Five IQD1-1, six IQD1-2, five MYB29-1, six MYB29-2, and one GUS hairy root lines were created. The expression of all genes involved in glucosinolates biosynthesis was higher in transgenic lines than in the GUS hairy root line, in agreement with total glucosinolates contents, determined by high-performance liquid chromatography. In transgenic IQD1-1 (1), IQD1-2 (4), MYB29-1 (2), and MYB29-2 (1) hairy root lines, total glucosinolates were 3.39-, 3.04-, 2.58-, and 4.69-fold higher than those in the GUS hairy root lines, respectively. These results suggest a central regulatory function for IQD1-1, IQD1-2, MYB29-1, and MYB29-2 transcription factors in glucosinolates biosynthesis in watercress hairy roots.

Genome-wide analysis of the Chinese cabbage IQD gene family and the response of BrIQD5 in drought resistance

KEY MESSAGE

Thirty-five IQD genes were identified and analysed in Chinese cabbage and BrIQD5 transgenic plants enhanced the drought resistance of plants. The IQD (IQ67-domain) family plays an important role in various abiotic stress responses in plant species. However, the roles of IQD genes in the Chinese cabbage response to abiotic stress remain unclear. Here, 35 IQD genes, from BrIQD1 to BrIQD35, were identified in Chinese cabbage (Brassica rapa ssp. pekinensis). Based on the phylogenetic analysis, these genes were clustered into three subfamilies (I-III), and members within the same subfamilies shared conserved exon-intron distribution and motif composition. The 35 BrIQD genes were unevenly distributed on 9 of the 10 chromosomes with 4 segmental duplication events. Ka/Ks ratios showed that the duplicated BrIQDs had mainly experienced strong purifying selection. Quantitative real-time polymerase chain reaction of 35 BrIQDs under PEG6000 indicated that BrIQD5 was significantly induced by PEG6000. To verify BrIQD5 function, BrIQD5 was heterologously overexpressed in tobacco and was silenced in Chinese cabbage. BrIQD5-overexpressed plants showed more tolerance to drought stress than wild-type plants, while BrIQD5-silenced plants in Chinese cabbage showed decreased drought tolerance. Additionally, six BrIQD5 potential interactive proteins were isolated by the yeast two-hybrid assay, including BrCaMa, BrCaMb and four other stress-related proteins. Motif IQ1 of BrIQD5 is important for the interaction with BrCaMa and BrCaMb, and the isoleucine in motif IQ1 is an essential amino acid for calmodulin binding to BrIQD5. The identification and cloning of the new Chinese cabbage drought tolerance genes will promote the drought-resistant breeding of Chinese cabbage and help to better understand the mechanism of IQD involved in the drought tolerance of plants.

Calcium- and calmodulin-regulated microtubule-associated proteins as signal-integration hubs at the plasma membrane-cytoskeleton nexus

Plant growth and development are a genetically predetermined series of events but can change dramatically in response to environmental stimuli, involving perpetual pattern formation and reprogramming of development. The rate of growth is determined by cell division and subsequent cell expansion, which are restricted and controlled by the cell wall-plasma membrane-cytoskeleton continuum, and are coordinated by intricate networks that facilitate intra- and intercellular communication. An essential role in cellular signaling is played by calcium ions, which act as universal second messengers that transduce, integrate, and multiply incoming signals during numerous plant growth processes, in part by regulation of the microtubule cytoskeleton. In this review, we highlight recent advances in the understanding of calcium-mediated regulation of microtubule-associated proteins, their function at the microtubule cytoskeleton, and their potential role as hubs in crosstalk with other signaling pathways.

Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana

Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation, and cell morphology. Their organization and dynamics are co-ordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization, and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles for calcium in regulation of PC morphogenesis. Our work identifies IQD5 as a novel player in PC shape regulation and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.

Microtubule-associated protein IQ67 DOMAIN5 regulates morphogenesis of leaf pavement cells in Arabidopsis thaliana

Plant microtubules form a highly dynamic intracellular network with important roles for regulating cell division, cell proliferation, and cell morphology. Their organization and dynamics are co-ordinated by various microtubule-associated proteins (MAPs) that integrate environmental and developmental stimuli to fine-tune and adjust cytoskeletal arrays. IQ67 DOMAIN (IQD) proteins recently emerged as a class of plant-specific MAPs with largely unknown functions. Here, using a reverse genetics approach, we characterize Arabidopsis IQD5 in terms of its expression domains, subcellular localization, and biological functions. We show that IQD5 is expressed mostly in vegetative tissues, where it localizes to cortical microtubule arrays. Our phenotypic analysis of iqd5 loss-of-function lines reveals functions of IQD5 in pavement cell (PC) shape morphogenesis. Histochemical analysis of cell wall composition further suggests reduced rates of cellulose deposition in anticlinal cell walls, which correlate with reduced anisotropic expansion. Lastly, we demonstrate IQD5-dependent recruitment of calmodulin calcium sensors to cortical microtubule arrays and provide first evidence for important roles for calcium in regulation of PC morphogenesis. Our work identifies IQD5 as a novel player in PC shape regulation and, for the first time, links calcium signaling to developmental processes that regulate anisotropic growth in PCs.

The tomato IQD gene SUN24 regulates seed germination through ABA signaling pathway

Gene expression and functional analysis of the tomato IQD gene SUN24 revealed that it regulates seed germination through ABA signaling pathway. Ca²⁺ signaling plays crucial roles in diverse biological processes including ABA-mediated seed germination. The plant-specific IQ67-Domain (IQD) proteins are hypothesized to regulate Ca²⁺ signaling and plant development through interactions with calmodulins (CaMs). Despite a few IQD genes have been identified to regulate herbivore resistance and plant growth and development, the molecular functions of most members in this gene family are not known. In this study, we characterized the role of the tomato IQD gene SUN24 in seed germination. Using pSUN24::GUS reporter lines and by quantitative reverse transcription PCR analysis, we show that SUN24 is mainly expressed in the roots, flowers, young fruits, seeds, and other young developing tissues, and its expression is repressed by ABA treatments. Functional analysis shows that knockdown of SUN24 expression by RNA interference delays seed germination, whereas overexpression of this IQD gene promotes germination. Further gene expression analysis reveals that SUN24 negatively regulates expression of two key ABA signaling genes Solanum lycopersicum ABA-insensitive 3 (SlABI3) and SlABI5 in germinating seeds. Moreover, SUN24, targeting to microtubule and nuclear bodies, can interact with four tomato CaMs (SlCaM1, 2, 3, and 6) in yeast cells. Our results demonstrate that SUN24 regulates seed germination through ABA signaling pathway, expanding our understanding of the roles of the IQD protein family members in plant physiological processes.

The Microtubule-Associated Protein IQ67 DOMAIN5 Modulates Microtubule Dynamics and Pavement Cell Shape

The dynamic arrangement of cortical microtubules (MTs) plays a pivotal role in controlling cell growth and shape formation in plants, but the mechanisms by which cortical MTs are organized to regulate these processes are not well characterized. In particular, the dynamic behavior of cortical MTs is critical for their spatial organization, yet the molecular mechanisms controlling MT dynamics remain poorly understood. In this study, we used the puzzle piece-shaped pavement cells of Arabidopsis (Arabidopsis thaliana) leaves as a model system in which to study cortical MT organization. We isolated an ethyl methanesulfonate mutant with reduced interdigitation of pavement cells in cotyledons. This line carried a mutation in IQ67 DOMAIN5 (IQD5), which encodes a member of the plant-specific IQ motif protein family. Live-cell imaging and biochemical analyses demonstrated that IQD5 binds to MTs and promotes MT assembly. MT-depolymerizing drug treatment and in vivo MT dynamics assays suggested that IQD5 functions to stabilize MTs. Hence, our findings provide genetic, cell biological, and biochemical evidence that IQD5 regulates MT dynamics that affect MT organization and subsequent cell shape formation.

A comprehensive phylogeny of auxin homeostasis genes involved in adventitious root formation in carnation stem cuttings

Understanding the functional basis of auxin homeostasis requires knowledge about auxin biosynthesis, auxin transport and auxin catabolism genes, which is not always directly available despite the recent whole-genome sequencing of many plant species. Through sequence homology searches and phylogenetic analyses on a selection of 11 plant species with high-quality genome annotation, we identified the putative gene homologs involved in auxin biosynthesis, auxin catabolism and auxin transport pathways in carnation (Dianthus caryophyllus L.). To deepen our knowledge of the regulatory events underlying auxin-mediated adventitious root formation in carnation stem cuttings, we used RNA-sequencing data to confirm the expression profiles of some auxin homeostasis genes during the rooting of two carnation cultivars with different rooting behaviors. We also confirmed the presence of several auxin-related metabolites in the stem cutting tissues. Our findings offer a comprehensive overview of auxin homeostasis genes in carnation and provide a solid foundation for further experiments investigating the role of auxin homeostasis in the regulation of adventitious root formation in carnation.

Genome-wide identification, classification and expression analysis of the serine carboxypeptidase-like protein family in poplar

Previous studies have shown that the serine carboxypeptidase-like (SCPL) proteins in several plants play a key part in plant growth, development and stress responses. However, little is known about the functions of the SCPL genes in poplar. We identified 57 SCPL genes and divided into 3 subfamilies, which were unevenly distributed on 19 poplar chromosomes. Gene structure indicated that SCPL genes contain more introns, and motifs of each subfamily were relatively conserved. There were a total of 14 pairs of paralogs, with 6 pairs of these paralogs generated by segmental duplication and 1 generated by tandem duplication. In microsynteny analysis, large-scale duplication events played a key part in the expansion of Carboxypeptidase III genes. Expression of these genes was higher in mature leaf. Quantitative real-time PCR showed that majority of the SCPL genes were induced by methyl jasmonate (MeJA) treatment. PtSCPL27 and PtSCPL40 were located on the cytomembrane by conducting subcellular localization analysis. Our paper provides a theoretical basis for further functional research of PtSCPL genes and will benefit the molecular breeding for resistance to disease in poplar.

Genome-wide identification and evolution of the PIN-FORMED (PIN) gene family in Glycine max

Soybean (Glycine max) is one of the most important crop plants. Wild and cultivated soybean varieties have significant differences worth further investigation, such as plant morphology, seed size, and seed coat development; these characters may be related to auxin biology. The PIN gene family encodes essential transport proteins in cell-to-cell auxin transport, but little research on soybean PIN genes (GmPIN genes) has been done, especially with respect to the evolution and differences between wild and cultivated soybean. In this study, we retrieved 23 GmPIN genes from the latest updated G. max genome database; six GmPIN protein sequences were changed compared with the previous database. Based on the Plant Genome Duplication Database, 18 GmPIN genes have been involved in segment duplication. Three pairs of GmPIN genes arose after the second soybean genome duplication, and six occurred after the first genome duplication. The duplicated GmPIN genes retained similar expression patterns. All the duplicated GmPIN genes experienced purifying selection (Ka/Ks < 1) to prevent accumulation of non-synonymous mutations and thus remained more similar. In addition, we also focused on the artificial selection of the soybean PIN genes. Five artificially selected GmPIN genes were identified by comparing the genome sequence of 17 wild and 14 cultivated soybean varieties. Our research provides useful and comprehensive basic information for understanding GmPIN genes.

The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus

Calcium (Ca2+) signaling and dynamic reorganization of the cytoskeleton are essential processes for the coordination and control of plant cell shape and cell growth. Calmodulin (CaM) and closely related calmodulin-like (CML) polypeptides are principal sensors of Ca2+ signals. CaM/CMLs decode and relay information encrypted by the second messenger via differential interactions with a wide spectrum of targets to modulate their diverse biochemical activities. The plant-specific IQ67 DOMAIN (IQD) family emerged as possibly the largest class of CaM-interacting proteins with undefined molecular functions and biological roles. Here, we show that the 33 members of the IQD family in Arabidopsis (Arabidopsis thaliana) differentially localize, using green fluorescent protein (GFP)-tagged proteins, to multiple and distinct subcellular sites, including microtubule (MT) arrays, plasma membrane subdomains, and nuclear compartments. Intriguingly, the various IQD-specific localization patterns coincide with the subcellular patterns of IQD-dependent recruitment of CaM, suggesting that the diverse IQD members sequester Ca2+-CaM signaling modules to specific subcellular sites for precise regulation of Ca2+-dependent processes. Because MT localization is a hallmark of most IQD family members, we quantitatively analyzed GFP-labeled MT arrays in Nicotiana benthamiana cells transiently expressing GFP-IQD fusions and observed IQD-specific MT patterns, which point to a role of IQDs in MT organization and dynamics. Indeed, stable overexpression of select IQD proteins in Arabidopsis altered cellular MT orientation, cell shape, and organ morphology. Because IQDs share biochemical properties with scaffold proteins, we propose that IQD families provide an assortment of platform proteins for integrating CaM-dependent Ca2+ signaling at multiple cellular sites to regulate cell function, shape, and growth.

Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis)

Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20-35 MYA and 25-40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

Genome-wide analysis of the IQD gene family in maize

IQD gene family plays important roles in plant developmental processes and stress responses. To date, no systematic characterization of this gene family has been carried out in maize. In this study, 26 IQD genes, from ZmIQD1 to ZmIQD26, were identified using Blast search tools. The phylogenetic analysis showed these genes were divided into four subfamilies (IQD I-IV) and members within the same subfamily shared conserved exon/intron distribution and motif composition. The 26 ZmIQD genes are distributed unevenly on 8 of the 10 chromosomes, with 9 segmental duplication events, suggesting that the expansion of IQDs in maize was due to the segmental duplication. The analysis of Ka/Ks ratios showed that the duplicated ZmIQDs had primarily undergone strong purifying selection. In addition, the 26 ZmIQDs displayed different expression patterns at different developmental stages of maize based on transcriptome analysis. Further, quantitative real-time PCR analysis showed that all 26 ZmIQD genes were responsive to drought treatment, suggesting their crucial roles in drought stress response. Yeast two-hybrid assay proved that ZmIQD2 and ZmIQD15 can interact with ZmCaM2 and IQ or I in IQ motif is required for ZmIQD15 to combine with CaM2. Our results present a comprehensive overview of the maize IQD gene family and lay an important foundation for further analysis aimed at uncovering the biological functions of ZmIQDs in growth and development.

Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice

Background

WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots).

Results

In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns.

Conclusions

This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.

Reviewers

This article was reviewed by Prof Dandekar and Dr Andrade-Navarro.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0076-3) contains supplementary material, which is available to authorized users.

Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice

BACKGROUND

WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots).

RESULTS

In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns.

CONCLUSIONS

This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.

Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice

BACKGROUND

WRKY III genes have significant functions in regulating plant development and resistance. In plant, WRKY gene family has been studied in many species, however, there still lack a comprehensive analysis of WRKY III genes in the woody plant species poplar, three representative lineages of flowering plant species are incorporated in most analyses: Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots) and Oryza sativa (a model plant for monocots).

RESULTS

In this study, we identified 10, 6, 13 and 28 WRKY III genes in the genomes of Populus trichocarpa, grape (Vitis vinifera), Arabidopsis thaliana and rice (Oryza sativa), respectively. Phylogenetic analysis revealed that the WRKY III proteins could be divided into four clades. By microsynteny analysis, we found that the duplicated regions were more conserved between poplar and grape than Arabidopsis or rice. We dated their duplications by Ks analysis of Populus WRKY III genes and demonstrated that all the blocks were formed after the divergence of monocots and dicots. Strong purifying selection has played a key role in the maintenance of WRKY III genes in Populus. Tissue expression analysis of the WRKY III genes in Populus revealed that five were most highly expressed in the xylem. We also performed quantitative real-time reverse transcription PCR analysis of WRKY III genes in Populus treated with salicylic acid, abscisic acid and polyethylene glycol to explore their stress-related expression patterns.

CONCLUSIONS

This study highlighted the duplication and diversification of the WRKY III gene family in Populus and provided a comprehensive analysis of this gene family in the Populus genome. Our results indicated that the majority of WRKY III genes of Populus was expanded by large-scale gene duplication. The expression pattern of PtrWRKYIII gene identified that these genes play important roles in the xylem during poplar growth and development, and may play crucial role in defense to drought stress. Our results presented here may aid in the selection of appropriate candidate genes for further characterization of their biological functions in poplar.

The Lipoxygenase Gene Family in Poplar: Identification, Classification, and Expression in Response to MeJA Treatment

Background

Lipoxygenases (LOXs) are important dioxygenases in cellular organisms. LOXs contribute to plant developmental processes and environmental responses. However, a systematic and comprehensive analysis has not been focused on the LOX gene family in poplar. Therefore, in the present study, we performed a comprehensive analysis of the LOX gene family in poplar.

Results

Using bioinformatics methods, we identified a total of 20 LOX genes. These LOX genes were clustered into two subfamilies. The gene structure and motif composition of each subfamily were relatively conserved. These genes are distributed unevenly across nine chromosomes. The PtLOX gene family appears to have expanded due to high tandem and low segmental duplication events. Microarray analysis showed that a number of PtLOX genes have different expression pattern across disparate tissues and under various stress treatments. Quantitative real-time PCR (qRT-PCR) analysis was further performed to confirm the responses to MeJA treatment of the 20 poplar LOX genes. The results show that the PtLOX genes are regulated by MeJA (Methyl jasmonate) treatment.

Conclusions

This study provides a systematic analysis of LOX genes in poplar. The gene family analysis reported here will be useful for conducting future functional genomics studies to uncover the roles of LOX genes in poplar growth and development.