Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants

Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses

Oryza sativa L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups based on phylogenetic analysis and identifying four segmental duplication events. RNA-seq data analysis revealed high expression levels of OsALs in different tissues, growth stages, and their responsiveness to stresses. RT-qPCR data showed significant expression of OsALs in different abiotic stresses. Identification of potential cis-regulatory elements in promoter regions has also unveiled their involvement. Tertiary structures of the proteins were predicted. These findings would lay the groundwork for future research to reveal their molecular mechanism in stress tolerance and plant development.

Genome-Wide Identification and Characterization of the CCT Gene Family in Rapeseed (Brassica napus L.)

The CCT gene family is present in plants and is involved in biological processes such as flowering, circadian rhythm regulation, plant growth and development, and stress resistance. We identified 87, 62, 46, and 40 CCTs at the whole-genome level in B. napus, B. rapa, B. oleracea, and A. thaliana, respectively. The CCTs can be classified into five groups based on evolutionary relationships, and each of these groups can be further subdivided into three subfamilies (COL, CMF, and PRR) based on function. Our analysis of chromosome localization, gene structure, collinearity, cis-acting elements, and expression patterns in B. napus revealed that the distribution of the 87 BnaCCTs on the chromosomes of B. napus was uneven. Analysis of gene structure and conserved motifs revealed that, with the exception of a few genes that may have lost structural domains, the majority of genes within the same group exhibited similar structures and conserved domains. The gene collinearity analysis identified 72 orthologous genes, indicating gene duplication and expansion during the evolution of BnaCCTs. Analysis of cis-acting elements identified several elements related to abiotic and biotic stress, plant hormone response, and plant growth and development in the promoter regions of BnaCCTs. Expression pattern and protein interaction network analysis showed that BnaCCTs are differentially expressed in various tissues and under stress conditions. The PRR subfamily genes have the highest number of interacting proteins, indicating their significant role in the growth, development, and response to abiotic stress of B. napus.

Genome-wide identification, expression analysis, and abiotic stress response of the CBL and CIPK gene families in Artocarpus nanchuanensis

Artocarpus nanchuanensis, the northernmost species in the jackfruit genus, has great economic and horticultural value due to its nutritious fruit and beautiful tree shape. Calcineurin B-like proteins (CBLs) act as plant-specific Ca2+ sensors and participate in regulating plant responses to various abiotic stresses by interacting with CBL-interacting protein kinases (CIPKs). However, the characteristics and functions of the CBL and CIPK genes in A. nanchuanensis are still unclear. Here, we identified 14 CBL and 33 CIPK genes from the A. nanchuanensis genome, and based on phylogenetic analysis, they were divided into 4 and 7 clades, respectively. Gene structure and motif analysis indicated that the AnCBL and AnCIPK genes were relatively conserved. Colinear analysis showed that segmental duplication contributed to the expansion of the AnCBL and AnCIPK gene families. Expression analysis showed that AnCBL and AnCIPK genes were widely expressed in various tissues of A. nanchuanensis and exhibited tissue-specific expression. In addition, three genes (AnCBL6, AnCIPK7/8) may play important roles in response to salt, cold, and drought stresses. In summary, this study lays an important foundation for the improvement of stress resistance in A. nanchuanensis and provides new insight for the functional research on CBL and CIPK gene families.

Genome-wide identification and stress response analysis of BcaCPK gene family in amphidiploid Brassica carinata

BACKGROUND

Calcium-dependent protein kinases (CPKs) are crucial for recognizing and transmitting Ca2+ signals in plant cells, playing a vital role in growth, development, and stress response. This study aimed to identify and detect the potential roles of the CPK gene family in the amphidiploid Brassica carinata (BBCC, 2n = 34) using bioinformatics methods.

RESULTS

Based on the published genomic information of B. carinata, a total of 123 CPK genes were identified, comprising 70 CPK genes on the B subgenome and 53 on the C subgenome. To further investigate the homologous evolutionary relationship between B. carinata and other plants, the phylogenetic tree was constructed using CPKs in B. carinata and Arabidopsis thaliana. The phylogenetic analysis classified 123 family members into four subfamilies, where gene members within the same subfamily exhibited similar conserved motifs. Each BcaCPK member possesses a core protein kinase domain and four EF-hand domains. Most of the BcaCPK genes contain 5 to 8 introns, and these 123 BcaCPK genes are unevenly distributed across 17 chromosomes. Among these BcaCPK genes, 120 replicated gene pairs were found, whereas only 8 genes were tandem duplication, suggesting that dispersed duplication mainly drove the family amplification. The results of the Ka/Ks analysis indicated that the CPK gene family of B. carinata was primarily underwent purification selection in evolutionary selection. The promoter region of most BcaCPK genes contained various stress-related cis-acting elements. qRT-PCR analysis of 12 selected CPK genes conducted under cadmium and salt stress at various points revealed distinct expression patterns among different family members in response to different stresses. Specifically, the expression levels of BcaCPK2.B01a, BcaCPK16.B02b, and BcaCPK26.B02 were down-regulated under both stresses, whereas the expression levels of other members were significantly up-regulated under at least one stress.

CONCLUSION

This study systematically identified the BcaCPK gene family in B. carinata, which contributes to a better understanding the CPK genes in this species. The findings also serve as a reference for analyzing stress responses, particularly in relation to cadmium and salt stress in B. carinata.

Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants

The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.

Characterization of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Its Response to Abiotic Stress in Rice (Oryza sativa L.)

Fatty acyl-CoA reductase (FAR) is an important NADPH-dependent enzyme that can produce primary alcohol from fatty acyl-CoA or fatty acyl-carrier proteins as substrates. It plays a pivotal role in plant growth, development, and stress resistance. Herein, we performed genome-wide identification and expression analysis of FAR members in rice using bioinformatics methods. A total of eight OsFAR genes were identified, and the OsFARs were comprehensively analyzed in terms of phylogenetic relationships, duplication events, protein motifs, etc. The cis-elements of the OsFARs were predicted to respond to growth and development, light, hormones, and abiotic stresses. Gene ontology annotation analysis revealed that OsFAR proteins participate in biological processes as fatty acyl-CoA reductase during lipid metabolism. Numerous microRNA target sites were present in OsFARs mRNAs. The expression analysis showed that OsFARs were expressed at different levels during different developmental periods and in various tissues. Furthermore, the expression levels of OsFARs were altered under abiotic stresses, suggesting that FARs may be involved in abiotic stress tolerance in rice. The findings presented here serve as a solid basis for further exploring the functions of OsFARs.

Genome-wide identification of the N6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.)

BACKGROUND

N6-methyladenosine (m6A) is one of the common internal RNA modifications found in eukaryotes. The m6A modification can regulate various biological processes in organisms through the modulation of alternative splicing, alternative polyadenylation, folding, translation, localization, transport, and decay of multiple types of RNA, without altering the nucleotide sequence. The three components involved in m6A modification, namely writer, eraser, and reader, mediate the abundance of RNA m6A modification through complex collaborative actions. Currently, research on m6A regulatory genes in plants is still in its infancy.

RESULTS

In this study, we identified 52 candidate m6A regulatory genes in common tobacco (Nicotiana tabacum L.). Gene structure, conserved domains, and motif analysis showed structural and functional diversity among different subgroups of tobacco m6A regulatory genes. The amplification of m6A regulatory genes were mainly driven by polyploidization and dispersed duplication, and duplicated genes evolved through purified selection. Based on the potential regulatory network and expression pattern analysis of m6A regulatory genes, a significant number of m6A regulatory genes might play important roles in growth, development, and stress response processes. Furthermore, we have confirmed the critical role of NtFIP37B, an m6A writer gene in tobacco, in enhancing drought resistance.

CONCLUSIONS

This study provides useful information for better understanding the evolution of m6A regulatory genes and the role of m6A modification in tobacco stress response, and lays the foundation for further elucidating the function of m6A regulatory genes in tobacco.

Physiological Control and Genetic Basis of Leaf Curvature and Heading in Brassica rapa L

BACKGROUND

Heading is an important agronomic feature for Chinese cabbage, cabbage, and lettuce. The heading leaves function as nutrition storage organs, which contribute to the high quality and economic worth of leafy heads. Leaf development is crucial during the heading stage, most genes previously predicted to be involved in the heading process are based on Arabidopsis leaf development studies.

AIM OF REVIEW

Till date, there is no published review article that demonstrated a complete layout of all the identified regulators of leaf curvature and heading. In this review, we have summarized all the identified physiological and genetic regulators that are directly or indirectly involved in leaf curvature and heading in Brassica crops. By integrating all identified regulators that provide a coherent logic of leaf incurvature and heading, we proposed a molecular mechanism in Brassica crops with graphical illustrations. This review adds value to future breeding of distinct heading kinds of cabbage and Chinese cabbage by providing unique insights into leaf development.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Leaf curvature and heading are established by synergistic interactions among genes, transcription factors, microRNAs, phytohormones, and environmental stimuli that regulate primary and secondary morphogenesis. Various genes have been identified using transformation and genome editing that are responsible for the formation of leaf curvature and heading in Brassica crops. A range of leaf morphologies have been observed in Brassica, which are established because of the mutated determinants that are responsible for cell division and leaf polarity.

Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum

KEY MESSAGE

This paper sheds light on the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 maybe involved in the ABA-dependent pathway of drought response. The MADS gene family is a key regulatory factor family that controls growth, reproduction, and response to abiotic stress in plants. However, the molecular evolution of this family is rarely reported. Here, a total of 265 MADS genes were identified in Setaria italica (foxtail millet), Setaria viridis (green millet), and Panicum virgatum (switchgrass) and analyzed by bioinformatics, including physicochemical characteristics, subcellular localization, chromosomal position and duplicate, motif distribution, genetic structure, genetic evolvement, and expression patterns. Phylogenetic analysis was used to categorize these genes into M and MIKC types. The distribution of motifs and gene structure were similar for the corresponding types. According to a collinearity study, the MADS genes have been mostly conserved during evolution. The principal cause of their expansion is segmental duplication. However, the MADS gene family tends to shrink in foxtail millet, green millet, and switchgrass. The MADS genes were subjected to purifying selection, but several positive selection sites were also identified in three species. And most of the promoters of MADS genes contain cis-elements related to stress and hormonal response. RNA-seq and quantitative Real-time PCR (qRT-PCR) analysis also were examined. SiMADS genes expression levels are considerably changed in reaction to various treatments, following qRT-PCR analysis. This sheds fresh light on the evolution and expansion of the MADS family in foxtail millet, green millet, and switchgrass, and lays the foundation for further research on their functions.

Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages

BACKGROUND

In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages.

RESULTS

Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations.

CONCLUSIONS

This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.

Genome-wide identification and characterization of the bZIP gene family and their function in starch accumulation in Chinese chestnut (Castanea mollissima Blume)

The transcription factors of basic leucine zipper (bZIP) family genes play significant roles in stress response as well as growth and development in plants. However, little is known about the bZIP gene family in Chinese chestnut (Castanea mollissima Blume). To better understand the characteristics of bZIPs in chestnut and their function in starch accumulation, a series of analyses were performed including phylogenetic, synteny, co-expression and yeast one-hybrid analyses. Totally, we identified 59 bZIP genes that were unevenly distributed in the chestnut genome and named them CmbZIP01 to CmbZIP59. These CmbZIPs were clustered into 13 clades with clade-specific motifs and structures. A synteny analysis revealed that segmental duplication was the major driving force of expansion of the CmbZIP gene family. A total of 41 CmbZIP genes had syntenic relationships with four other species. The results from the co-expression analyses indicated that seven CmbZIPs in three key modules may be important in regulating starch accumulation in chestnut seeds. Yeast one-hybrid assays showed that transcription factors CmbZIP13 and CmbZIP35 might participate in starch accumulation in the chestnut seed by binding to the promoters of CmISA2 and CmSBE1_2, respectively. Our study provided basic information on CmbZIP genes, which can be utilized in future functional analysis and breeding studies.

Identification, characterization of Apyrase (APY) gene family in rice (Oryza sativa) and analysis of the expression pattern under various stress conditions

Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1)-cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress-responsive pathway in plants. This study was designed for the identification, characterization, and for analysis of APY gene expression in Oryza sativa. This investigation discovered nine APYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution of OsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for future in-vivo analysis, unveil the molecular mechanisms of APY genes in stress response, and contribute to the development of stress-tolerant rice varieties.

Genome-Wide Comprehensive Analysis of the Nitrogen Metabolism Toolbox Reveals Its Evolution and Abiotic Stress Responsiveness in Rice (Oryza sativa L.)

Nitrogen metabolism (NM) plays an essential role in response to abiotic stresses for plants. Enzyme activities have been extensively studied for nitrogen metabolism-associated pathways, but the knowledge of nitrogen metabolism-associated genes involved in stress response is still limited, especially for rice. In this study, we performed the genome-wide characterization of the genes putatively involved in nitrogen metabolism. A total of 1110 potential genes were obtained to be involved in nitrogen metabolism from eight species (Arabidopsis thaliana (L.) Heynh., Glycine max (L.) Merr., Brassica napus L., Triticum aestivum L., Sorghum bicolor L., Zea mays L., Oryza sativa L. and Amborella trichopoda Baill.), especially 104 genes in rice. The comparative phylogenetic analysis of the superfamily revealed the complicated divergence of different NM genes. The expression analysis among different tissues in rice indicates the NM genes showed diverse functions in the pathway of nitrogen absorption and assimilation. Distinct expression patterns of NM genes were observed in rice under drought stress, heat stress, and salt stress, indicating that the NM genes play a curial role in response to abiotic stress. Most NM genes showed a down-regulated pattern under heat stress, while complicated expression patterns were observed for different genes under salt stress and drought stress. The function of four representative NM genes (OsGS2, OsGLU, OsGDH2, and OsAMT1;1) was further validated by using qRT-PCR analysis to confirm their responses to these abiotic stresses. Based on the predicted transcription factor binding sites (TFBSs), we built a co-expression regulatory network containing transcription factors (TFs) and NM genes, of which the constructed ERF and Dof genes may act as the core genes to respond to abiotic stresses. This study provides novel sights to the interaction between nitrogen metabolism and the response to abiotic stresses.

Genome-Wide Identification, Characterization, and Expression Analysis of CHS Gene Family Members in Chrysanthemum nankingense

The chalcone synthase (CHS) gene family catalyzes the first committed step in the biosynthesis of flavonoids and plays key roles in various biological processes in plants. However, systematic studies of the CHS gene family in chrysanthemum remain unknown to date. In this study, 16 CnCHS genes were identified by searching the complete genome sequence of Chrysanthemum nankingense. Most contained two exons and one intron with Chal-sti-synt_N and Chal-sti-synt_C domains. A phylogenetic tree of CnCHSs indicated divergence into three major groups, including I, II, and III. Analyses of the genes and promoters of these genes indicated that there are many cis-acting elements that respond to light, phytohormones, stress, and developmental stages. The CnCHS genes have extensive patterns of expression in various tissues and stages of flower development. Tandemly repeated and segmental repeat genes were expressed at higher levels in different tissues than most of the CnCHS genes that have been identified. CnCHS10 is expressed at higher levels in various flower organs than in vegetative tissues, particularly in disc floret petals and pistils. Our study provides valuable information for the systematic analysis of the CnCHS gene family, which also contributes to further research on flavonoid synthesis and petal colors of chrysanthemum.

Genome-wide identification and characterization of AP2/ERF gene superfamily during flower development in Actinidia eriantha

BACKGROUND

As one of the largest transcription factor families in plants, AP2/ERF gene superfamily plays important roles in plant growth, development, fruit ripening and biotic and abiotic stress responses. Despite the great progress has been made in kiwifruit genomic studies, little research has been conducted on the AP2/ERF genes of kiwifruit. The increasing kiwifruit genome resources allowed us to reveal the tissue expression profiles of AP2/ERF genes in kiwifruit on a genome-wide basis.

RESULTS

In present study, a total of 158 AP2/ERF genes in A. eriantha were identified. All genes can be mapped on the 29 chromosomes. Phylogenetic analysis divided them into four main subfamilies based on the complete protein sequences. Additionally, our results revealed that the same subfamilies contained similar gene structures and conserved motifs. Ka/Ks calculation indicated that AP2/ERF gene family was undergoing a strong purifying selection and the evolutionary rates were slow. RNA-seq showed that the AP2/ERF genes were expressed differently in different flower development stages and 56 genes were considered as DEGs among three contrasts. Moreover, qRT-PCR suggested partial genes showed significant expressions as well, suggesting they could be key regulators in flower development in A. eriantha. In addition, two genes (AeAP2/ERF061, AeAP2/ERF067) had abundant transcription level based on transcriptomes, implying that they may play a crucial role in plant flower development regulation and flower tissue forming.

CONCLUSIONS

We identified AP2/ERF genes and demonstrated their gene structures, conserved motifs, and phylogeny relationships of AP2/ERF genes in two related species of kiwifruit, A. eriantha and A. chinensis, and their potential roles in flower development in A. eriantha. Such information would lay the foundation for further functional identification of AP2/ERF genes involved in kiwifruit flower development.

HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress

Heat shock proteins protect plants from abiotic stress, such as salt, drought, heat, and cold stress. HSP70 is one of the major members of the heat shock protein family. To explore the mechanism of HSP70 in Brassica rapa, we identified 28 putative HSP70 gene family members using state-of-the-art bioinformatics-based tools and methods. Based on chromosomal mapping, HSP70 genes were the most differentially distributed on chromosome A03 and the least distributed on chromosome A05. Ka/Ks analysis revealed that B. rapa evolution was subjected to intense purifying selection of the HSP70 gene family. RNA-sequencing data and expression profiling showed that heat and cold stress induced HSP70 genes. The qRT-PCR results verified that the HSP70 genes in Chinese cabbage (Brassica rapa ssp. pekinensis) are stress-inducible under both cold and heat stress. The upregulated expression pattern of these genes indicated the potential of HSP70 to mitigate environmental stress. These findings further explain the molecular mechanism underlying the responses of HSP70 to heat and cold stress.

Genome-Wide Study of Hsp90 Gene Family in Cabbage (Brassica oleracea var. capitata L.) and Their Imperative Roles in Response to Cold Stress

Heat shock protein 90 (Hsp90) plays an important role in plant developmental regulation and defensive reactions. Several plant species have been examined for the Hsp90 family gene. However, the Hsp90 gene family in cabbage has not been well investigated to date. In this study, we have been discovered 12 BoHsp90 genes in cabbage (Brassica oleracea var. capitata L.). These B. oleracea Hsp90 genes were classified into five groups based on phylogenetic analysis. Among the five groups, group one contains five Hsp90 genes, including BoHsp90-1, BoHsp90-2, BoHsp90-6, BoHsp90-10, and BoHsp90-12. Group two contains three Hsp90 genes, including BoHsp90-3, BoHsp90-4, and BoHsp90. Group three only includes one Hsp90 gene, including BoHsp90-9. Group four were consisting of three Hsp90 genes including BoHsp90-5, BoHsp90-7, and BoHsp90-8, and there is no Hsp90 gene from B. oleracea in the fifth group. Synteny analysis showed that a total of 12 BoHsp90 genes have a collinearity relationship with 5 Arabidopsis genes and 10 Brassica rapa genes. The promoter evaluation revealed that the promoters of B. oleracea Hsp90 genes included environmental stress-related and hormone-responsive cis-elements. RNA-seq data analysis indicates that tissue-specific expression of BoHsp90-9 and BoHsp90-5 were highly expressed in stems, leaves, silique, and flowers. Furthermore, the expression pattern of B. oleracea BoHsp90 exhibited that BoHsp90-2, BoHsp90-3, BoHsp90-7, BoHsp90-9, BoHsp90-10, and BoHsp90-11 were induced under cold stress, which indicates these Hsp90 genes perform a vital role in cold acclimation and supports in the continual of normal growth and development process. The cabbage Hsp90 gene family was found to be differentially expressed in response to cold stress, suggesting that these genes play an important role in cabbage growth and development under cold conditions.

Genome-wide identification of BAM (β-amylase) gene family in jujube (Ziziphus jujuba Mill.) and expression in response to abiotic stress

BACKGROUND

Elevated temperature and drought stress have substantial impacts on fruit quality, especially in terms of sugar metabolism and content. β-Amylase (BAM) plays a critical role in regulating jujube fruit sugar levels and abiotic stress response. Nevertheless, little is known about the regulatory functions of the BAM genes in jujube fruit.

RESULTS

Nine jujube BAM genes were identified, clustered into four groups, and characterized to elucidate their structure, function, and distribution. Multiple sequence alignment and gene structure analysis showed that all ZjBAM genes contain Glu-186 and Glu-380 residues and are highly conserved. Phylogenetic and synteny analysis further indicated that the ZjBAM gene family is evolutionarily conserved and formed collinear pairs with the BAM genes of peach, apple, poplar, Arabidopsis thaliana, and cucumber. A single tandem gene pair was found within the ZjBAM gene family and is indicative of putative gene duplication events. We also explored the physicochemical properties, conserved motifs, and chromosomal and subcellular localization of ZjBAM genes as well as the interaction networks and 3D structures of ZjBAM proteins. A promoter cis-acting element analysis suggested that ZjBAM promoters comprise elements related to growth, development, phytohormones, and stress response. Furthermore, a metabolic pathways annotation analysis showed that ZjBAMs are significantly upregulated in the starch and sucrose metabolism, thereby controlling starch-maltose interconversion and hydrolyzing starch to maltose. Transcriptome and qRT-PCR analyses revealed that ZjBAMs respond positively to elevated temperature and drought stress. Specifically, ZjBAM1, ZjBAM2, ZjBAM5, and ZjBAM6 are significantly upregulated in response to severe drought. Bimolecular fluorescence complementation analysis demonstrated ZjBAM1-ZjAMY3, ZjBAM8-ZjDPE1, and ZjBAM7-ZjDPE1 protein interactions that were mainly present in the plasma membrane and nucleus.

CONCLUSION

The jujube BAM gene family exhibits high evolutionary conservation. The various expression patterns of ZjBAM gene family members indicate that they play key roles in jujube growth, development, and abiotic stress response. Additionally, ZjBAMs interact with α-amylase and glucanotransferase. Collectively, the present study provides novel insights into the structure, evolution, and functions of the jujube BAM gene family, thus laying a foundation for further exploration of ZjBAM functional mechanisms in response to elevated temperature and drought stress, while opening up avenues for the development of economic forests in arid areas.

Genome-Wide Identification and Characterization of DnaJ Gene Family in Grape (Vitis vinifera L.)

Grape production in southern China suffers great loss due to various environmental stresses. To understand the mechanism of how the grape plants respond to these stresses is an active area of research in developing cultivation techniques. Plant stress resistance is known to rely on special proteins. Amongst them, DnaJ protein (HSP40) serves as co-chaperones of HSP70, playing crucial roles in various stress response. However, the DnaJ proteins encoded by the DnaJ gene family in Vitis vinifera L. have not been fully described yet. In this study, we identified 78 VvDnaJs in the grape genome that can be classified into three groups—namely, DJA, DJB, and DJC. To reveal the evolutionary and stress response mechanisms for the VvDnaJ gene family, their evolutionary and expression patterns were analyzed using the bioinformatic approach and qRT-PCR. We found that the members in the same group exhibited a similar gene structure and protein domain organization. Gene duplication analysis demonstrated that segmental and tandem duplication may not be the dominant pathway of gene expansion in the VvDnaJ gene family. Codon usage pattern analysis showed that the codon usage pattern of VvDnaJs differs obviously from the monocotyledon counterparts. Tissue-specific analysis revealed that 12 VvDnaJs present a distinct expression profile, implying their distinct roles in various tissues. Cis-acting element analysis showed that almost all VvDnaJs contained the elements responsive to either hormones or stresses. Therefore, the expression levels of VvDnaJs subjected to exogenous hormone applications and stress treatments were determined, and we found that VvDnaJs were sensitive to hormone treatments and shade, salt, and heat stresses, especially VIT_00s0324g00040. The findings of this study could provide comprehensive information for the further investigation on the genetics and protein functions of the DnaJ gene family in grape.

Genome-Wide Identification, Characterization and Expression Analysis of the CIPK Gene Family in Potato (Solanum tuberosum L.) and the Role of StCIPK10 in Response to Drought and Osmotic Stress

The potato (Solanum tuberosum L.), one of the most important food crops worldwide, is sensitive to environmental stresses. Sensor–responder complexes comprising calcineurin B-like (CBL) proteins and CBL-interacting protein kinases (CIPKs) not only modulate plant growth and development but also mediate numerous stress responses. Here, using a Hidden Markov Model and BLAST searches, 27 CIPK genes were identified in potato and divided into five groups by phylogenetic analysis and into two clades (intron-poor and intron-rich) by gene structure analysis. Quantitative reverse-transcription PCR (qRT-PCR) assays revealed that StCIPK genes play important roles in plant growth, development and abiotic stress tolerance. Up-regulated expression of StCIPK10 was significantly induced by drought, PEG6000 and ABA. StCIPK10 enhances both the ability of potato to scavenge reactive oxygen species and the content of corresponding osmoregulation substances, thereby strengthening tolerance to drought and osmotic stress. StCIPK10 is located at the intersection between the abscisic acid and abiotic stress signaling pathways, which control both root growth and stomatal closure in potato. In addition, StCIPK10 interacts with StCBL1, StCBL4, StCBL6, StCBL7, StCBL8, StCBL11 and StCBL12, and is specifically recruited to the plasma membrane by StCBL11.

Genome-Wide Characterization and Expression Analysis of bZIP Gene Family Under Abiotic Stress in Glycyrrhiza uralensis

bZIP gene family is one of the largest transcription factor families. It plays an important role in plant growth, metabolic, and environmental response. However, complete genome-wide investigation of bZIP gene family in Glycyrrhiza uralensis remains unexplained. In this study, 66 putative bZIP genes in the genome of G. uralensis were identified. And their evolutionary classification, physicochemical properties, conserved domain, functional differentiation, and the expression level under different stress conditions were further analyzed. All the members were clustered into 13 subfamilies (A–K, M, and S). A total of 10 conserved motifs were found in GubZIP proteins. Members from the same subfamily shared highly similar gene structures and conserved domains. Tandem duplication events acted as a major driving force for the evolution of bZIP gene family in G. uralensis. Cis-acting elements and protein–protein interaction networks showed that GubZIPs in one subfamily are involved in multiple functions, while some GubZIPs from different subfamilies may share the same functional category. The miRNA network targeting GubZIPs showed that the regulation at the transcriptional level may affect protein–protein interaction networks. We suspected that domain-mediated interactions may categorize a protein family into subfamilies in G. uralensis. Furthermore, the tissue-specific gene expression patterns of GubZIPs were analyzed using the public RNA-seq data. Moreover, gene expression level of 66 bZIP family members under abiotic stress treatments was quantified by using qRT-PCR. The results of this study may serve as potential candidates for functional characterization in the future.

Genome-Wide and Comprehensive Analysis of the Multiple Stress-Related CAF1 (CCR4-Associated Factor 1) Family and Its Expression in Poplar

Poplar is one of the most widely used tree in afforestation projects. However, it is susceptible to abiotic and biotic stress. CCR4-associated factor 1 (CAF1) is a major member of CCR4-NOT, and it is mainly involved in transcriptional regulation and mRNA degradation in eukaryotes. However, there are no studies on the molecular phylogeny and expression of the CAF1 gene in poplar. In this study, a total of 19 PtCAF1 genes were identified in the Populus trichocarpa genome. Phylogenetic analysis of the PtCAF1 gene family was performed with two closely related species (Arabidopsis thaliana and Oryza sativa) to investigate the evolution of the PtCAF1 gene. The tissue expression of the PtCAF1 gene showed that 19 PtCAF1 genes were present in different tissues of poplar. Additionally, the analysis of the expression of the PtCAF1 gene showed that the CAF1 family was up-regulated to various degrees under biotic and abiotic stresses and participated in the poplar stress response. The results of our study provide a deeper understanding of the structure and function of the PtCAF1 gene and may contribute to our understanding of the molecular basis of stress tolerance in poplar.

Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in apple (Malus domestica)

Auxin is a necessary phytohormone for fruit development, accompanying the whole process of fruit growth and development. The Aux/IAA gene family is one of the early auxin-responsive gene families. At present, there were few reports involved in Aux/IAA genes in the fruit, especially in apple. In our study, we identified 42 MdAux/IAAs, phylogenetic analysis showed that Aux/IAA proteins from apple, tomato, and strawberry were clustered into 5 groups, 42 MdAux/IAAs randomly distributed on 13 chromosomes. Additionally, a comprehensive analysis of Aux/IAA gene family was completed, including gene structures, conserved motifs, phylogenetic analysis, chromosome mapping, orthologous identification, selection pressure analyses, synteny analysis, and protein interaction. We also tested the expression of MdAux/IAAs in different tissues and fruit development stages using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), we found that the most members of Aux/IAA showed higher expression in seeds compared within stem and leaves, indicating they may play a role in regulating fruit development. We also declared that the expression of Aux/IAA gene was not consistent in the pericarp and seeds at the same developmental stage, 3 MdAux/IAAs of the pericarp were upregulated over 20-fold at 90 d and 5 MdAux/IAAs of the seeds were upregulated over 40-fold at 90 d. It was MdAux/IAA23 that showed extreme up-regulated expression in both pericarp and seeds. This study proved that the Aux/IAA gene families may perform a different function in apple fruit development and ripening, more importantly, it provided a foundation for further exploring the biological function of these MdAux/IAAs.

Genome-Wide Characterization, Evolution, and Expression Analysis of the Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Gene Family in Medicago truncatula

Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases (RLKs) in plants. They play roles in plant growth and developmental and physiological processes, but less is known about the functions of LRR-RLKs in Medicago truncatula. Our genome-wide analysis revealed 329 LRR-RLK genes in the M.truncatula genome. Phylogenetic and classification analysis suggested that these genes could be classified into 15 groups and 24 subgroups. A total of 321 genes were mapped onto all chromosomes, and 23 tandem duplications (TDs) involving 56 genes were distributed on each chromosome except 4. Twenty-seven M.truncatula LRR-RLK segmental duplication gene pairs were colinearly related. The exon/intron organization, motif composition and arrangements were relatively conserved among members of the same groups or subgroups. Using publicly available RNAseq data and quantitative real-time polymerase chain reaction (qRT-PCR), expression profiling suggested that LRR-RLKs were differentially expressed among different tissues, while some were expressed specifically in the roots and nodules. The expression of LRR-RLKs in A17 and 4 nodule mutants under rhizobial infection showed that 36 LRR-RKLs were highly upregulated in the sickle (skl) mutant [an ethylene (ET)-insensitive, Nod factor-hypersensitive mutant] after 12 h of rhizobium inoculation. Among these LRR-RLKs, six genes were also expressed specifically in the roots and nodules, which might be specific to the Nod factor and involved in autoregulation of the nodulation signal. Our results provide information on the LRR-RLK gene family in M. truncatula and serve as a guide for functional research of the LRR-RLKs.

Genome-wide analysis and transcript profiling of PSKR gene family members in Oryza sativa

Peptide signalling is an integral part of cell-to-cell communication which helps to relay the information responsible for coordinating cell proliferation and differentiation. Phytosulfokine Receptor (PSKR) is a transmembrane LRR-RLK family protein with a binding site for small signalling peptide, phytosulfokine (PSK). PSK signalling through PSKR promotes normal growth and development and also plays a role in defense responses. Like other RLKs, these PSKRs might have a role in signal transduction pathways related to abiotic stress responses. Genome-wide analysis of phytosulfokine receptor gene family has led to the identification of fifteen putative members in the Oryza sativa genome. The expression analysis of OsPSKR genes done using RNA-seq data, showed that these genes were differentially expressed in different tissues and responded specifically to heat, salt, drought and cold stress. Furthermore, the real-time quantitative PCR for fifteen OsPSKR genes revealed temporally and spatially regulated gene expression corresponding to salinity and drought stress. Our results provide useful information for a better understanding of OsPSKR genes and provide the foundation for additional functional exploration of the rice PSKR gene family in development and stress response.

Genome-wide analysis of the Saccharina japonica sulfotransferase genes and their transcriptional profiles during whole developmental periods and under abiotic stresses

BACKGROUND

As a unique sulfated polysaccharide, fucoidan is an important component of cell wall in brown seaweeds. Its biochemical properties are determined by the positions and quantity of sulfate groups. Sulfotransferases (STs) catalyze the sulfation process, which transfer the sulfuryl groups to carbohydrate backbones and are crucial for fucoidan biosynthesis. Nevertheless, the structures and functions of STs in brown seaweeds are rarely investigated.

RESULTS

There are a total of 44 ST genes identified from our genome and transcriptome analysis of Saccharina japonica, which were located in the 17 scaffolds and 11 contigs. The S. japonica ST genes have abundant introns and alternative splicing sites, and five tandem duplicated gene clusters were identified. Generally, the ST genes could be classified into five groups (Group I ~ V) based on phylogenetic analysis. Accordingly, the ST proteins, which were encoded by genes within the same group, contained similar conserved motifs. Members of the S. japonica ST gene family show various expression patterns in different tissues and developmental stages. Transcriptional profiles indicate that the transcriptional levels of more than half of the ST genes are higher in kelp basal blades than in distal blades. Except for ST5 and ST28, most ST genes are down-regulated with the kelp development stages. The expression levels of nine ST genes were detected by real-time quantitative PCR, which demonstrates that they responded to low salinity and drought stresses.

CONCLUSIONS

Various characteristics of the STs allow the feasibilities of S. japonica to synthesize fucoidans with different sulfate groups. This enables the kelp the potential to adapt to the costal environments and meet the needs of S. japonica growth.

Molecular functional analysis of auxin/indole-3-acetic acid proteins (Aux/IAAs) in plant disease resistance in cassava

Auxin/indole-3-acetic acid proteins (Aux/IAAs) play important roles in auxin signaling pathways, with extensive involvement in plant development and plant response to abiotic and biotic stresses. Manihot esculenta (Cassava) is one of the most important biomass energy crops in tropical regions; however, the information about Aux/IAA proteins remain limited in cassava. In this study, 37 MeAux/IAA gene family members were identified in cassava and a phylogenetic analysis was performed. The transcript levels of MeAux/IAAs were commonly regulated by the pathogen Xanthomonas axonopodis pv manihotis (Xam), and some of them were specifically localized to the nucleus. Moreover, the overexpression of MeAux/IAAs confers an improved disease resistance against Xam in Nicotiana benthamiana, while MeAux/IAAs-silenced plants show disease sensitivity against Xam in cassava, as evidenced by the leaf phenotype and leaf bacterial population. Consistent with the disease resistance, MeAux/IAAs regulated the transcript levels of PATHOGENESIS-RELATED GENES (MePRs), reactive oxygen species accumulation and callose development in the plants' defense response. Taken together, gene profile and functional analysis identified several MeAux/IAAs as novel members in plant disease resistance, providing important information for further utilization of MeAux/IAAs.

Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

Background

VQ proteins, the plant-specific transcription factors, are involved in plant development and multiple stresses; however, only few articles systematic reported the VQ genes in soybean.

Methods

In total, we identified 75 GmVQ genes, which were classified into 7 groups (I-VII). Conserved domain analysis indicated that VQ gene family members all contain the VQ domains. VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed that cis-elements related to stress responses, phytohormone responses and controlling physical as well as reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were showed expressing in nine tissues, suggesting their putative function in many aspects of plant growth and development as well as response to stress in Glycine max.

Results

This study aims to understand the roles of VQ genes in various development processes and their expression patterns in responses to stimuli. Our results provide basic information in identification and classification of GmVQ genes. Further experimental analysis will allows us to know the functions of GmVQs participation in plant growth and stress responses.

Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea

Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.

Systematic identification and expression pattern analysis of the Aux/IAA and ARF gene families in moso bamboo (Phyllostachys edulis)

Auxin plays a central role in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) and auxin response transcription factor (ARF) genes are key components of plant auxin signaling. However, little is known about the Aux/IAA and ARF gene families in moso bamboo (Phyllostachys edulis). In this paper, we first identified 35 putative PeIAAs and 24 PeARFs in the moso bamboo genome. These genes were clustered into two major groups (A and B) and four groups (I-IV), respectively, based on phylogenetic analysis. Next, analyses of evolutionary patterns and divergence demonstrated that both the PeIAAs and PeARFs experienced a large-scale duplication event around 15 million years ago (MYA). The divergence times of the two gene families were 31 MYA between moso bamboo and rice, and 46 MYA between moso bamboo and maize. Furthermore, the expression profiling of PeIAA and PeARF genes in various tissues and developmental stages revealed tissue-specific expression. qRT-PCR analysis confirmed the differential expression patterns of selected PeIAA and PeARF genes. And then a comprehensive expression analysis of these genes was also performed under exogenous hormone treatment by qRT-PCR. Many PeIAAs and PeARFs showed differential expression in response to IAA treatment. Subcellular localization results show that PeIAA8 is a nuclear localization protein. Most importantly, we demonstrate that single moso bamboo ARF can interact with multiple Aux/IAA proteins and vice versa. Collectively, the detailed analyses presented here will help in understanding the roles of the PeIAA and PeARF gene families and contribute to further research on their biological functions during development in moso bamboo.

Highly preserved roles of Brassica MIR172 in polyploid Brassicas: ectopic expression of variants of Brassica MIR172 accelerates floral transition

Functional characterization of regulatory genes governing flowering time is a research priority for breeding earliness in crop Brassicas. Highly polyploid genomes of Brassicas pose challenges in unraveling homeolog gene function. In Arabidopsis, five MIR172 paralogs control flowering time and floral organ identity by down-regulating AP2 and AP2-like genes. The impact of homeolog diversification on MIR172 loci, however, needs to be examined in morphologically diverse Brassicas. Herein, we analyze fractionation status and phylogeny of MIR172 and target AP2 from Brassicas and compare functionality of MIR172 variants representing distinct sub-genomes and progenitor genomes. Copy number analysis revealed higher retention of MIR172 loci relative to AP2 in diploid and amphi-diploid Brassica species. Dendrogram of 87 MIR172 sequences from Brassicaceae showed five major clusters corresponding to MIR172a-MIR172e which further separated into sub-genome and progenitor genome specific clades. Similar groupings were observed in the phylogeny of 11 Brassica AP2 and AP2-like genes. Over-expression of a pair of natural variants for each of MIR172b, MIR172d and MIR172e representing sub-genomes, progenitor genomes and species of Brassicas displayed floral acceleration in all transgenic lines indicating a strong selection pressure on MIR172. All gain-of-function lines, except 35S::MIR172e and 35S::MIR172e' displayed floral organ defects implying altered target spectrum of MIR172e relative to MIR172b and MIR172d. Expression of MIR172e caused marginal earliness in flowering time in B. juncea. In conclusion, this study demonstrates tightly preserved role of homeologs and natural variants of MIR172 family in mediating flowering in Brassicas and suggests their deployment for introgression of early flowering trait.

Evolution of the Aux/IAA Gene Family in Hexaploid Wheat

The Aux/IAA (IAA) gene family, involved in the auxin signalling pathway, acts as an important regulator in plant growth and development. In this study, we explored the evolutionary trajectory of the IAA family in common wheat. The results showed ten pairs of paralogs among 34 TaIAA family members. Seven of the pairs might have undergone segmental duplication, and the other three pairs appear to have experienced tandem duplication. Except for TaIAA15-16, these duplication events occurred in the ancestral genomes before the divergence of Triticeae. After that point, two polyploidization events shaped the current TaIAA family consisting of three subgenomic copies. The structure or expression pattern of the TaIAA family begins to differentiate in the hexaploid genome, where TaIAAs in the D genome lost more genes (eight) and protein secondary structures (α1, α3 and β5) than did the other two genomes. Expression analysis showed that six members of the TaIAA family were not expressed, and members such as TaIAA8, 15, 16, 28 and 33 exhibited tissue-specific expression patterns. In addition, three of the ten pairs of paralogs (TaIAA5-12, TaIAA15-16 and TaIAA29-30) showed similar expression patterns, and another five paralog pairs displayed differential expression patterns. Phylogenetic analysis showed that paralog pairs with high rates of evolution (ω > ω ₀), particularly TaIAA15-16 and TaIAA29-30, experienced greater motif loss, with only zero to two interacting IAA proteins. In contrast, most paralogous genes with low ω, such as TaIAA5-12, had more complete motifs and higher degrees of interaction with other family members.