Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L

TALE gene family: identification, evolutionary and expression analysis under various exogenous hormones and waterlogging stress in Cucumis sativus L

BACKGROUND

Three Amino acid Loop Extension (TALE) belongs to the homeobox group of genes that are important constituents of plant systems. The TALE gene family is instrumental not only in growth and development but also plays an essential role in regulating plant response to environmental adversaries.

RESULTS

In the present study, we isolated 21 CsTALE genes from the cucumber (Cucumis sativus L.) genome database. Bioinformatics tools were put in place to understand the structural and functional components of the CsTALE gene family. The evolutionary analysis dissected them into seven subclades (KNOX-I, KNOX-II, and BELL-I to BELL-V). The cis-acting elements in the promoter region of CsTALE genes disclosed that they are key regulators of hormonal and stress-related processes. Additionally, the STRING database advocated the concerting role of CsTALE proteins with other key transcription factors potent in plant developmental biology. The CsmiR319 and CsmiR167a-3p targeting the CsTALE15 and CsTALE16, respectively, further assert the importance of the CsTALE gene family posttranscriptional-related processes. Tissue-specific gene expression unfolded the fundamental involvement of CsTALE genes as they were expressed throughout the developmental stages. Under waterlogging stress, the CsTALE17 expressed significantly higher values in WL, WL-NAA, and WL-ETH but not in WL-MeJA-treated samples.

CONCLUSIONS

The present study reveals the evolution and functions of the CsTALE gene family in cucumber. Our work will provide a platform that will help future researchers address the issue of waterlogging stress in the Yangtze River Delta.

Genome-wide characterisation of HD-Zip transcription factors and functional analysis of PbHB24 during stone cell formation in Chinese white pear (Pyrus bretschneideri)

BACKGROUND

The homodomain-leucine zipper (HD-Zip) is a conserved transcription factor family unique to plants that regulate multiple developmental processes including lignificaion. Stone cell content is a key determinant negatively affecting pear fruit quality, which causes a grainy texture of fruit flesh, because of the lignified cell walls.

RESULTS

In this study, a comprehensive bioinformatics analysis of HD-Zip genes in Chinese white pear (Pyrus bretschneideri) (PbHBs) was performed. Genome-wide identification of the PbHB gene family revealed 67 genes encoding PbHB proteins, which could be divided into four subgroups (I, II, III, and IV). For some members, similar intron/exon structural patterns support close evolutionary relationships within the same subgroup. The functions of each subgroup of the PbHB family were predicted through comparative analysis with the HB genes in Arabidopsis and other plants. Cis-element analysis indicated that PbHB genes might be involved in plant hormone signalling and external environmental responses, such as light, stress, and temperature. Furthermore, RNA-sequencing data and quantitative real-time PCR (RT-qPCR) verification revealed the regulatory roles of PbHB genes in pear stone cell formation. Further, co-expression network analysis revealed that the eight PbHB genes could be classified into different clusters of co-expression with lignin-related genes. Besides, the biological function of PbHB24 in promoting stone cell formation has been demonstrated by overexpression in fruitlets.

CONCLUSIONS

This study provided the comprehensive analysis of PbHBs and highlighted the importance of PbHB24 during stone cell development in pear fruits.

Functional Analysis of PbbZIP11 Transcription Factor in Response to Cold Stress in Arabidopsis and Pear

Cold stress is a prominent abiotic factor that adversely affects the growth and yield of pears, consequently restricting the cultivation range and resulting in substantial economic losses for the pear industry. Basic region-leucine zipper (bZIP) transcription factors are widely involved in multiple physiological and biochemical activities of plants, particularly in response to cold stress. In this study, the responsiveness of PbbZIP11 in pear to cold stress was investigated, and its role was explored by using pear callus and Arabidopsis thaliana. The findings revealed that overexpression of PbbZIP11 enhanced the tolerance of pear callus and Arabidopsis thaliana to cold stress. The antioxidant enzyme activities of transgenic plants were enhanced and the expression of C-repeat binding transcription factor (CBF) genes was increased as compared to wild-type plants. To better understand the biological function of PbbZIP11, mRNAs were isolated from overexpressed and wild-type Arabidopsis thaliana after cold stress for whole-genome sequencing. The results showed that the expression of some CBF downstream target genes changed after exposure to cold stress. The results suggested that the PbbZIP11 gene could participate in cold-stress signaling through the CBF-dependent pathway, which provides a theoretical basis for the PbbZIP11-mediated response to cold stress and for the genetic breeding of pear varieties with low-temperature tolerance.

Role of bZIP Transcription Factors in Response to NaCl Stress in Tamarix ramosissima under Exogenous Potassium (K+)

Salt stress is a significant environmental factor affecting plant growth and development, with NaCl stress being one of the most common types of salt stress. The halophyte, Tamarix ramosissima Ledeb (T. ramosissima), is frequently utilized for the afforestation of saline-alkali soils. Indeed, there has been limited research and reports by experts and scholars on the regulatory mechanisms of basic leucine zipper (bZIP) genes in T. ramosissima when treated with exogenous potassium (K+) to alleviate the effects of NaCl stress. This study focused on the bZIP genes in T. ramosissima roots under NaCl stress with additional KCl applied. We identified key candidate genes and metabolic pathways related to bZIP and validated them through quantitative real-time PCR (qRT-PCR). The results revealed that under NaCl stress with additional KCl applied treatments at 0 h, 48 h, and 168 h, based on Pfam protein domain prediction and physicochemical property analysis, we identified 20 related bZIP genes. Notably, four bZIP genes (bZIP_2, bZIP_6, bZIP_16, and bZIP_18) were labeled with the plant hormone signal transduction pathway, showing a predominant up-regulation in expression levels. The results suggest that these genes may mediate multiple physiological pathways under NaCl stress with additional KCl applied at 48 h and 168 h, enhancing signal transduction, reducing the accumulation of ROS, and decreasing oxidative damage, thereby enhancing the tolerance of T. ramosissima to NaCl stress. This study provides gene resources and a theoretical basis for further breeding of salt-tolerant Tamarix species and the involvement of bZIP transcription factors in mitigating NaCl toxicity.

Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures

BACKGROUND

Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR.

RESULTS

We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress.

CONCLUSIONS

The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.

Genome-Wide Identification and Expression Analysis of bZIP Family Genes in Stevia rebaudiana

The basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors widely distributed in eukaryotic organisms. In plants, they are not only involved in growth and development, defense and stress responses and regulation of physiological processes but also play a pivotal role in regulating secondary metabolism. To explore the function related to the bZIP gene family in Stevia rebaudiana Bertoni, we identified 105 SrbZIP genes at the genome-wide level and classified them into 12 subfamilies using bioinformation methods. Three main classes of cis-acting elements were found in the SrbZIP promoter regions, including development-related elements, defense and stress-responsive elements and phytohormone-responsive elements. Through protein-protein interaction network of 105 SrbZIP proteins, SrbZIP proteins were mainly classified into four major categories: ABF2/ABF4/ABI5 (SrbZIP51/SrbZIP38/SrbZIP7), involved in phytohormone signaling, GBF1/GBF3/GBF4 (SrbZIP29/SrbZIP63/SrbZIP60) involved in environmental signaling, AREB3 (SrbZIP88), PAN (SrbZIP12), TGA1 (SrbZIP69), TGA4 (SrbZIP82), TGA7 (SrbZIP31), TGA9 (SrbZIP95), TGA10 (SrbZIP79) and HY5 (SrbZIP96) involved in cryptochrome signaling, and FD (SrbZIP72) promoted flowering. The transcriptomic data showed that SrbZIP genes were differentially expressed in six S. rebaudiana cultivars ('023', '110', 'B1188', '11-14', 'GP' and 'GX'). Moreover, the expression levels of selected 15 SrbZIP genes in response to light, abiotic stress (low temperature, salt and drought), phytohormones (methyl jasmonate, gibberellic acid and salicylic acid) treatment and in different tissues were analyzed utilizing qRT-PCR. Some SrbZIP genes were further identified to be highly induced by factors affecting glycoside synthesis. Among them, three SrbZIP genes (SrbZIP54, SrbZIP63 and SrbZIP32) were predicted to be related to stress-responsive terpenoid synthesis in S. rebaudiana. The protein-protein interaction network expanded the potential functions of SrbZIP genes. This study firstly provided the comprehensive genome-wide report of the SrbZIP gene family, laying a foundation for further research on the evolution, function and regulatory role of the bZIP gene family in terpenoid synthesis in S. rebaudiana.

Genome-wide identification and comprehensive analysis of WRKY transcription factor family in safflower during drought stress

The WRKY family is an important family of transcription factors in plant development and stress response. Currently, there are few reports on the WRKY gene family in safflower (Carthamus tinctorius L.). In this study, a total of 82 CtWRKY genes were identified from the safflower genome and could be classified into 3 major groups and 5 subgroups based on their structural and phylogenetic characteristics. The results of gene structure, conserved domain and motif analyses indicated that CtWRKYs within the same subfamily maintained a consistent exon/intron organization and composition. Chromosomal localization and gene duplication analysis results showed that CtWRKYs were randomly localized on 12 chromosomes and that fragment duplication and purification selection may have played an important role in the evolution of the WRKY gene family in safflower. Promoter cis-acting element analysis revealed that the CtWRKYs contain many abiotic stress response elements and hormone response elements. Transcriptome data and qRT-PCR analyses revealed that the expression of CtWRKYs showed tissue specificity and a strong response to drought stress. Notably, the expression level of the CtWRKY55 gene rapidly increased more than eightfold under drought treatment and rehydration, indicating that it may be a key gene in response to drought stress. These results provide useful insights for investigating the regulatory function of the CtWRKY gene in safflower growth and development, as well as identifying key genes for future molecular breeding programmes.

Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis

Introduction

Agarwood, the dark-brown resin produced by Aquilaria trees, has been widely used as incense, spice, perfume or traditional medicine and 2-(2-phenethyl) chromones (PECs) are the key markers responsible for agarwood formation. But the biosynthesis and regulatory mechanism of PECs were still not illuminated. The transcription factor of basic leucine zipper (bZIP) presented the pivotal regulatory roles in various secondary metabolites biosynthesis in plants, which might also contribute to regulate PECs biosynthesis. However, molecular evolution and function of bZIP are rarely reported in Malvales plants, especially in Aquilaria trees.

Methods and results

Here, 1,150 bZIPs were comprehensively identified from twelve Malvales and model species genomes and the evolutionary process were subsequently analyzed. Duplication types and collinearity indicated that bZIP is an ancient or conserved TF family and recent whole genome duplication drove its evolution. Interesting is that fewer bZIPs in A. sinensis than that species also experienced two genome duplication events in Malvales. 62 AsbZIPs were divided into 13 subfamilies and gene structures, conservative domains, motifs, cis-elements, and nearby genes of AsbZIPs were further characterized. Seven AsbZIPs in subfamily D were significantly regulated by ethylene and agarwood inducer. As the typical representation of subfamily D, AsbZIP14 and AsbZIP41 were localized in nuclear and potentially regulated PECs biosynthesis by activating or suppressing type III polyketide synthases (PKSs) genes expression via interaction with the AsPKS promoters.

Discussion

Our results provide a basis for molecular evolution of bZIP gene family in Malvales and facilitate the understanding the potential functions of AsbZIP in regulating 2-(2-phenethyl) chromone biosynthesis and agarwood formation.

Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean

The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of nodulation-specific NIN proteins during nodulation and rhizobial infection under nitrogen starvation in soybean still remain unclear. Here, we investigated the genome-wide identification of RWP-RK transcription factors and their essential role in nitrate-inducible and stress-responsive gene expression in soybean. In total, 28 RWP-RK genes were identified from the soybean genome, which were unevenly distributed on 20 chromosomes from 5 distinct groups during phylogeny classification. The conserved topology of RWP-RK protein motifs, cis-acting elements, and functional annotation has led to their potential as key regulators during plant growth, development, and diverse stress responses. The RNA-seq data revealed that the up-regulation of GmRWP-RK genes in the nodules indicated that these genes might play crucial roles during root nodulation in soybean. Furthermore, qRT-PCR analysis revealed that most GmRWP-RK genes under Phytophthora sojae infection and diverse environmental conditions (such as heat, nitrogen, and salt) were significantly induced, thus opening a new window of possibilities into their regulatory roles in adaptation mechanisms that allow soybean to tolerate biotic and abiotic stress. In addition, the dual luciferase assay indicated that GmRWP-RK1 and GmRWP-RK2 efficiently bind to the promoters of GmYUC2, GmSPL9, and GmNIN, highlighting their possible involvement in nodule formation. Together, our findings provide novel insights into the functional role of the RWP-RK family during defense responses and root nodulation in soybean.

Genome-Wide Identification of MADS-Box Family Genes in Safflower (Carthamus tinctorius L.) and Functional Analysis of CtMADS24 during Flowering

Safflower is an important economic crop with a plethora of industrial and medicinal applications around the world. The bioactive components of safflower petals are known to have pharmacological activity that promotes blood circulation and reduces blood stasis. However, fine-tuning the genetic mechanism of flower development in safflower is still required. In this study, we report the genome-wide identification of MADS-box transcription factors in safflower and the functional characterization of a putative CtMADS24 during vegetative and reproductive growth. In total, 77 members of MADS-box-encoding genes were identified from the safflower genome. The phylogenetic analysis divided CtMADS genes into two types and 15 subfamilies. Similarly, bioinformatic analysis, such as of conserved protein motifs, gene structures, and cis-regulatory elements, also revealed structural conservation of MADS-box genes in safflower. Furthermore, the differential expression pattern of CtMADS genes by RNA-seq data indicated that type II genes might play important regulatory roles in floral development. Similarly, the qRT-PCR analysis also revealed the transcript abundance of 12 CtMADS genes exhibiting tissue-specific expression in different flower organs. The nucleus-localized CtMADS24 of the AP1 subfamily was validated by transient transformation in tobacco using GFP translational fusion. Moreover, CtMADS24-overexpressed transgenic Arabidopsis exhibited early flowering and an abnormal phenotype, suggesting that CtMADS24 mediated the expression of genes involved in floral organ development. Taken together, these findings provide valuable information on the regulatory role of CtMADS24 during flower development in safflower and for the selection of important genes for future molecular breeding programs.

Genomic characterization of bZIP transcription factors related to andrographolide biosynthesis in Andrographis paniculata

The basic leucine zipper (bZIP) transcription factor family plays an important role in various biological processes in plants. Andrographis paniculata (Burm.f) Nees, belonging to the family Acanthaceae, has been widely used as an important traditional herb with a wide range of pharmacological activities, such as antivenom, antiretroviral, anticancer and so on. However, there was no comprehensive analysis of bZIP gene family in the Andrographis paniculata been reported. In this study, we identified 62 bZIPs in Andrographis paniculata and grouped them into 12 subfamilies through the phylogenetic tree analysis. The bZIPs in the same groups have similar motif composition, exon-intron structure and domain distribution. In addition, the RNA-seq data gave a reference for selecting candidate bZIPs to make further function verification. Lastly, qRT-PCR analyses revealed seven ApbZIPs (ApbZIP4, ApbZIP19, ApbZIP30, ApbZIP42, ApbZIP50, ApbZIP52, ApbZIP62) were the most highly expressed in leaf and significantly up-regulated with MeJA and ABA treatment which may be involved in biosynthesis regulation of andrographolide. These data pave the way for further revealing the function of the bZIPs in Andrographis paniculata.

Genome-wide identification and analysis of bZIP gene family reveal their roles during development and drought stress in Wheel Wingnut (Cyclocarya paliurus)

Background

The bZIP gene family has important roles in various biological processes, including development and stress responses. However, little information about this gene family is available for Wheel Wingnut (Cyclocarya paliurus). 

Results

In this study, we identified 58 bZIP genes in the C. paliurus genome and analyzed phylogenetic relationships, chromosomal locations, gene structure, collinearity, and gene expression profiles. The 58 bZIP genes could be divided into 11 groups and were unevenly distributed among 16 C. paliurus chromosomes. An analysis of cis-regulatory elements indicated that bZIP promoters were associated with phytohormones and stress responses. The expression patterns of bZIP genes in leaves differed among developmental stages. In addition, several bZIP members were differentially expressed under drought stress. These expression patterns were verified by RT-qPCR.

Conclusions

Our results provide insights into the evolutionary history of the bZIP gene family in C. paliurus and the function of these genes during leaf development and in the response to drought stress. In addition to basic genomic information, our results provide a theoretical basis for further studies aimed at improving growth and stress resistance in C. paliurus, an important medicinal plant.

The bZIP Transcription Factor Family in Adzuki Bean (Vigna Angularis): Genome-Wide Identification, Evolution, and Expression Under Abiotic Stress During the Bud Stage

Adzuki bean (Vigna angularis) is an important dietary legume crop that was first cultivated and domesticated in Asia. Currently, little is known concerning the evolution and expression patterns of the basic leucine zipper (bZIP) family transcription factors in the adzuki bean. Through the PFAM search, 72 bZIP members of adzuki bean (VabZIP) were identified from the reference genome. Most of them were located on 11 chromosomes and seven on an unknown chromosome. A comprehensive analysis, including evolutionary, motifs, gene structure, cis-elements, and collinearity was performed to identify VabZIP members. The subcellular localization results showed VabZIPs might locate on the nuclear. Quantitative real-time PCR (qRT-PCR) analysis of the relative expression of VabZIPs in different tissues at the bud stage revealed that VabZIPs had a tissue-specific expression pattern, and its expression was influenced by abiotic stress. These characteristics of VabZIPs provide insights for future research aimed at developing interventions to improve abiotic stress resistance.

Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L

BACKGROUND

The basic leucine zipper (bZIP) transcription factor (TF) is one of the largest families of transcription factors (TFs). It is widely distributed and highly conserved in animals, plants, and microorganisms. Previous studies have shown that the bZIP TF family is involved in plant growth, development, and stress responses. The bZIP family has been studied in many plants; however, there is little research on the bZIP gene family in tobacco.

RESULTS

In this study, 77 bZIPs were identified in tobacco and named NtbZIP01 through to NtbZIP77. These 77 genes were then divided into eleven subfamilies according to their homology with Arabidopsis thaliana. NtbZIPs were unevenly distributed across twenty-two tobacco chromosomes, and we found sixteen pairs of segmental duplication. We further studied the collinearity between these genes and related genes of six other species. Quantitative real-time polymerase chain reaction analysis identified that expression patterns of bZIPs differed, including in different organs and under various abiotic stresses. NtbZIP49 might be important in the development of flowers and fruits; NtbZIP18 might be an important regulator in abiotic stress.

CONCLUSIONS

In this study, the structures and functions of the bZIP family in tobacco were systematically explored. Many bZIPs may play vital roles in the regulation of organ development, growth, and responses to abiotic stresses. This research has great significance for the functional characterisation of the tobacco bZIP family and our understanding of the bZIP family in higher plants.

Identification and functional characterization of safflower cysteine protease 1 as negative regulator in response to low-temperature stress in transgenic Arabidopsis

We performed genome-wide and heterologous expression analysis of the safflower cysteine protease family and found that inhibition of CtCP1 expression enhanced plant cold resistance. Cysteine protease (CP) is mainly involved in plant senescence and stress responses. However, the molecular mechanism of endogenous cysteine protease inhibition in plant stress tolerance is yet unknown. Here, we report the discovery and functional characterization of a candidate CP1 gene from safflower. The conserved structural topology of CtCPs revealed important insights into their possible roles in plant growth and stress responses. The qRT-PCR results implied that most of CtCP genes were highly expressed at fading stage suggesting that they are most likely involved in senescence process. The CtCP1 expression was significantly induced at different time points under cold, NaCl, H₂O₂ and PEG stress, respectively. The in-vitro activity of heterologously expressed CtCP1 protein showed highest protease activity for casein and azocasein substrates. The expression and phenotypic data together with antioxidant activity and physiological indicators revealed that transgenic plants inhibited by CtCP1-anti showed higher tolerance to low temperature than WT and CtCP1-OE plants. Our findings demonstrated the discovery of a new Cysteine protease 1 gene that exerted a detrimental effect on transgenic Arabidopsis under low-temperature stress.

Genome-wide identification and characterization of bZIP gene family and cloning of candidate genes for anthocyanin biosynthesis in pomegranate (Punica granatum)

BACKGROUND

The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved gene families in eukaryotes. In addition to participating in plant development and growth, bZIP transcription factors play crucial roles in various abiotic stress responses and anthocyanin accumulation. Up to now, analysis of bZIP gene family members in pomegranate (Punica granatum) has not been reported. Three published pomegranate genome sequences provide valuable resources for further gene function analysis.

RESULTS

Using bioinformatics analysis, 65 PgbZIPs were identified and analyzed from the 'Taishanhong' pomegranate genome. We divided them into 13 groups (A, B, C, D, E, F, G, H, I, J, K, M, and S) according to the phylogenetic relationship with those of Arabidopsis, each containing a different number of genes. The regularity of exon/intron number and distribution was consistent with the classification of groups in the evolutionary tree. Transcriptome analysis of different tissues showed that members of the PgbZIP gene family were differentially expressed in different developmental stages and tissues of pomegranate. Among them, we selected PgbZIP16 and PgbZIP34 as candidate genes which affect anthocyanin accumulation. The full-length CDS region of PgbZIP16 and PgbZIP34 were cloned from pomegranate petals by homologous cloning technique, encoding 170 and 174 amino acids, which were 510 bp and 522 bp, respectively. Subcellular localization assays suggested that both PgbZIP16 and PgbZIP34 were nucleus-localized. Real-time quantitative PCR (qPCR) was used to explore the expression of PgbZIP16 and PgbZIP34 in the petals of three kinds of ornamental pomegranates at the full flowering stage. The results demonstrated that the expression of PgbZIP16 in red petals was 5.83 times of that in white petals, while PgbZIP34 was 3.9 times. The results of transient expression in tobacco showed that consistent trends were observed in anthocyanin concentration and expression levels of related genes, which both increased and then decreased. Both PgbZIP16 and PgbZIP34 could promote anthocyanin accumulation in tobacco leaves. We obtained transgenic strains overexpressing PgbZIP16, and the histochemical staining for GUS activity showed that overexpressed PgbZIP16 seedlings were expressed in the stem. Transgenic experiments indicated that overexpression of PgbZIP16 significantly upregulated UF3GT, ANS and DFR genes in Arabidopsis and enhanced anthocyanin accumulation.

CONCLUSIONS

The whole genome identification, gene structure, phylogeny, gene cloning, subcellular location and functional verification of the pomegranate bZIP gene family provide a theoretical foundation for the functional study of the PgbZIP gene family and candidate genes for anthocyanin biosynthesis.

Genome-wide identification and expression analysis of bZIP transcription factors in oil palm (Elaeis guineensis Jacq.) under abiotic stress

The bZIP transcription factors are well-known transcription regulators and play a key role in regulating various developmental, biological processes, and stress responses in plants. However, information on bZIP transcription factors is not yet available in oil palm, an important oil yielding crop. The present study identified the 97 bZIP transcription factor family members in oil palm genome via a genome-wide approach. Phylogenetic analysis clustered all EgbZIPs into 12 clusters with Arabidopsis and rice bZIPs. EgbZIP gene structure analysis showed a distinct variation in the intron-exon organization among all EgbZIPs. Conserved motif analysis demonstrated the occurrence of ten additional conserved motifs besides having a common bZIP domain. All the identified 97 EgbZIPs were unevenly distributed on 16 chromosomes and exhibited tandem duplication in oil palm genome. Our results aslo demonstrated that tissue-specific expression patterns of EgbZIPs based on the available transcriptome data of six different tissue of oil palm. Stress-responsive expression analysis showed that 11EgbZIP transcription factors were highly expressed under cold, salinity, drought stress conditions. Taken together, our findings will provide insightful information on bZIP transcription factors as one of the stress-responsive regulators in oil palm.

The bZIP transcription factors in Liriodendron chinense: Genome-wide recognition, characteristics and cold stress response

The basic leucine zipper (bZIP) is a transcription factor family that plays critical roles in abiotic and biotic stress responses as well as plant development and growth. A comprehensive genome-wide study in Liriodendron chinense was conducted to identify 45 bZIP transcription factors (LchibZIPs), which were divided into 13 subgroups according the phylogenetic analysis. Proteins in the same subgroup shared similar gene structures and conserved domains, and a total of 20 conserved motifs were revealed in LchibZIP proteins. Gene localization analysis revealed that LchibZIP genes were unequally distributed across 16 chromosomes, and that 4 pairs of tandem and 9 segmental gene duplications existed. Concluding that segmental duplication events may be strongly associated with the amplification of the L. chinense bZIP gene family. We also assessed the collinearity of LchibZIPs between the Arabidopsis and Oryza and showed that the LchibZIP is evolutionarily closer to O. sativa as compared to the A. thaliana. The cis-regulatory element analysis showed that LchibZIPs clustered in one subfamily are involved in several functions. In addition, we gathered novel research suggestions for further exploration of the new roles of LchibZIPs from protein-protein interactions and gene ontology annotations of the LchibZIP proteins. Using the RNA-seq data and qRT-PCR we analyzed the gene expression patterns of LchibZIP genes, and showed that LchibZIP genes regulate cold stress, especially LchibZIP4 and LchibZIP7; and LchibZIP2 and LchibZIP28 which were up-regulated and down-regulated by cold stress, respectively. Studies of genetic engineering and gene function in L. chinense can benefit greatly from the thorough investigation and characterization of the L. chinense bZIP gene family.