PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Investigation of the potential regulation of the UDP-glycosyltransferase genes on rice grain size and abiotic stress response

Uridine diphosphate (UDP) glycosyltransferases (UGTs) are widely involved in various metabolic processes. In the present study, we performed a genome-wide survey and identified 199 Oryza sativa UGT genes (OsUGTs), which were classified into 17 groups. We showed that tandem duplication played a major role in the expansion of the OsUGT family, which experienced purifying selection during the evolution process. 163 OsUGTs were expressed in at least one of the six tested tissues, and were clustered into three groups according to their tissue expression profiles. By using the RFGB database, we identified different haplotypes of seven OsUGTs that were highly expressed in seeds, and showed significant differences in grain size among different haplotypes. Moreover, our results also uncovered differential responses of OsUGTs expression to abiotic stresses and hormone treatments, including drought, salt, cold, heat, ABA, JA and AUXIN. By using quantitative real-time PCR, we further confirmed the differential expression of nine selected OsUGTs under ABA, JA, salt, drought and cold treatments, among which OsUGT5 and OsUGT182 were induced by all these five treatments. Our results provide insight into the role of several UGT genes for physiological responses, which will facilitate to investigate their function in regulating rice development and abiotic stress responses.

In-silico analysis and transformation of OsMYB48 transcription factor driven by CaMV35S promoter in model plant - Nicotiana tabacum L. conferring abiotic stress tolerance

Global crop yield has been affected by a number of abiotic stresses. Heat, salinity, and drought stress are at the top of the list as serious environmental growth-limiting factors. To enhance crop productivity, molecular approaches have been used to determine the key regulators affecting stress-related phenomena. MYB transcription factors (TF) have been reported as one of the promising defensive proteins against the unfavorable conditions that plants must face. Different roles of MYB TFs have been suggested such as regulation of cellular growth and differentiation, hormonal signaling, mediating abiotic stress responses, etc. To gain significant insights, a comprehensive in-silico analysis of OsMYB TF was carried out in comparison with 21 dicot MYB TFs and 10 monocot MYB TFs. Their chromosomal location, gene structure, protein domain, and motifs were analyzed. The phylogenetic relationship was also studied, which resulted in the classification of proteins into four basic groups: groups A, B, C, and D. The protein motif analysis identified several conserved sequences responsible for cellular activities. The gene structure analysis suggested that proteins that were present in the same class, showed similar intron-exon structures. Promoter analysis revealed major cis-acting elements that were found to be responsible for hormonal signaling and initiating a response to abiotic stress and light-induced mechanisms. The transformation of OsMYB TF into tobacco was carried out using the Agrobacterium-mediated transformation method, to further analyze the expression level of a gene in different plant parts, under stress conditions. To summarize, the current studies shed light on the evolution and role of OsMYB TF in plants. Future investigations should focus on elucidating the functional roles of MYB transcription factors in abiotic stress tolerance through targeted genetic modification and CRISPR/Cas9-mediated genome editing. The application of omics approaches and systems biology will be indispensable in delineating the regulatory networks orchestrated by MYB TFs, facilitating the development of crop genotypes with enhanced resilience to environmental stressors. Rigorous field validation of these genetically engineered or edited crops is imperative to ascertain their utility in promoting sustainable agricultural practices.

Unveiling kiwifruit TCP genes: evolution, functions, and expression insights

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLEFERATING-CELL-FACTORS (TCP) gene family is a plant-specific transcriptional factor family involved in leaf morphogenesis and senescence, lateral branching, hormone crosstalk, and stress responses. To date, a systematic study on the identification and characterization of the TCP gene family in kiwifruit has not been reported. Additionally, the function of kiwifruit TCPs in regulating kiwifruit responses to the ethylene treatment and bacterial canker disease pathogen (Pseudomonas syringae pv. actinidiae, Psa) has not been investigated. Here, we identified 40 and 26 TCP genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes, respectively. The synteny analysis of AcTCPs illustrated that whole-genome duplication accounted for the expansion of the TCP family in Ac. Phylogenetic, conserved domain, and selection pressure analysis indicated that TCP family genes in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in TCP gene number and distribution. Our results also suggested that protein structure and cis-element architecture in promoter regions of TCP genes have driven the function divergence of duplicated gene pairs. Three and four AcTCP genes significantly affected kiwifruit responses to the ethylene treatment and Psa invasion, respectively. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit TCPs.

Genome-wide identification of SIMILAR to RCD ONE (SRO) gene family in rapeseed (Brassica napus L.) reveals their role in drought stress response

Rapeseed (Brassica napus L.) is an important oilseed crop widely cultivated worldwide, and drought is the main environmental factor limiting its yield enhancement and the expansion of planted areas. SIMILAR TO RCD ONE (SRO) is a plant-specific small gene family that plays a crucial role in plant growth, development, and responses to abiotic stresses such as drought. However, the functional role of SROs in rapeseed remains poorly understood. In this study, 19 BnaSROs were identified from the rapeseed genome, with 9, 10, 10, 18, and 20 members identified from the genomes of Brassica rapa, Brassica nigra, Brassica oleracea, Brassica juncea, and Brassica carinata, respectively. We then analyzed their sequence characteristics, phylogenetic relationships, gene structures, and conserved domains, and explored the collinearity relationships of the SRO members in Brassica napus and Brassica juncea. Next, we focused on the analysis of tissue expression and stress-responsive expression patterns of rapeseed SRO members and examined their expression profiles under ABA, MeJA and water-deficit drought treatments using qPCR. Transcriptome data analysis and qPCR detection indicated that BnaSROs exhibit multiple stress-responsive expression patterns. BnaSRO1 and BnaSRO11, which are likely to function through interactions with NAC transcription factors, were screened as major drought-regulated members. Our results provide a solid foundation for functional analysis of the role of the SRO gene family in abiotic stress responses, especially drought stress responses, in rapeseed.

Genome-wide identification of YABBY gene family and its expression pattern analysis in Astragalus mongholicus

During plant growth and development, the YABBY gene plays a crucial role in the morphological structure, hormone signaling, stress resistance, crop breeding, and agricultural production of plant lateral organs, leaves, flowers, and fruits. Astragalus mongholicus is a perennial herbaceous plant in the legume family, widely used worldwide due to its high medicinal and edible value. However, there have been no reports of the YABBY gene family in A. mongholicus. This study used bioinformatics methods, combined with databases and analysis websites, to systematically analyze the AmYABBY gene family in the entire genome of A. mongholicus and verified its expression patterns in different tissues of A. mongholicus through transcriptome data and qRT-PCR experiments. A total of seven AmYABBY genes were identified, which can be divided into five subfamilies and distributed on three chromosomes. Two pairs of AmYABBY genes may be involved in fragment duplication on three chromosomes. All AmYABBY proteins have a zinc finger YABBY domain, and members of the same group have similar motif composition and intron - exon structure. In the promoter region of the genes, light-responsive and MeJa-response cis-elements are dominant. AmYABBY is highly expressed in stems and leaves, especially AmYABBY1, AmYABBY2, and AmYABBY3, which play important roles in the growth and development of stems and leaves. The AmYABBY gene family regulates the growth and development of A. mongholicus. In summary, this study provides a theoretical basis for in-depth research on the function of the AmYABBY gene and new insights into the molecular response mechanism of the growth and development of the traditional Chinese medicine A. mongholicus.

Genome-wide analysis of the NYN domain gene family in Brassica napus and its function role in plant growth and development

The NYN domain gene family consists of genes that encode ribonucleases that are characterized by a newly identified NYN domain. Members of the family were widely distributed in all life kingdoms and play a crucial role in various RNA regulation processes, although the wide genome overview of the NYN domain gene family is not yet available in any species. Rapeseed (Brassica napus L.), a polyploid model species, is an important oilseed crop. Here, the phylogenetic analysis of these BnaNYNs revealed five distinct groups strongly supported by gene structure, conserved domains, and conserved motifs. The survey of the expansion of the gene family showed that the birth of BnaNYNs is explained by various duplication events. Furthermore, tissue-specific expression analysis, protein-protein interaction prediction, and cis-element prediction suggested a role for BnaNYNs in plant growth and development. Interestingly, the data showed that three tandem duplicated BnaNYNs (TDBs) exhibited distinct expression patterns from those other BnaNYNs and had a high similarity in protein sequence level. Furthermore, the analysis of one of these TDBs, BnaNYN57, showed that overexpression of BnaNYN57 in Arabidopsis thaliana and B. napus accelerated plant growth and significantly increased silique length, while RNA interference resulted in the opposite growth pattern. It suggesting a key role for the TDBs in processes related to plant growth and development.

Genome-Wide Characterization of ABC Transporter Genes and Expression Profiles in Red Macroalga Pyropia yezoensis Expose to Low-Temperature

Pyropia yezoensis is an important economic macroalga widely cultivated in the East Asia countries of China, Korea, and Japan. The ATP-binding cassette (ABC) transporter gene family is one of the largest transporter families in all forms of life involved in various biological processes. The characteristics of ABC transporter genes in P. yezoensis (PyABC) and their functions in stress resistance, however, remain largely unknown. In this study, PyABCs were identified and characterized their expression patterns under low-temperature stress. A total of 48 PyABCs transporters were identified and divided into eight subfamilies, which are mostly predicted as membrane-binding proteins. The cis-elements of phytohormone and low-temperature response were distinguished in promoter sequences of PyABCs. Transcriptome analysis showed that PyABCs are involved in response to low-temperature stress. Among them, 12 PyABCs were significantly up-regulated after 24 h of exposure to low temperature (2 °C). Further quantitative RT-PCR analysis corroborated the highest expression happened at 24 for detected genes of PyABCC8, PyABCF3, and PyABCI1, extraordinarily for PyABCF3, and followed by decreased expression at 48 h. The expression of PyABCI1 was generally low in all tested strains. Whereas, in a strain of P. yezoensis with lower tolerance to low temperature, the expression was observed higher in PyABCC1, PyABCC8, and remarkably high in PyABCF3. This study provided valuable information on ABC gene families in P. yezoensis and their functional characteristics, especially on low-temperature resistance, and would help to understand the adaptive mechanisms of P. yezoensis to adverse environments.

Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo

Long terminal repeat retroelements (LTR-REs) have profound effects on DNA methylation and gene regulation. Despite the vast abundance of LTR-REs in the genome of Moso bamboo (Phyllostachys edulis), an industrial crop in underdeveloped countries, their precise implication of the LTR-RE mobility in stress response and development remains unknown. We investigated the RNA and DNA products of LTR-REs in Moso bamboo under various developmental stages and stressful conditions. Surprisingly, our analyses identified thousands of active LTR-REs, particularly those located near genes involved in stress response and developmental regulation. These genes adjacent to active LTR-REs exhibited an increased expression under stress and are associated with reduced DNA methylation that is likely affected by the induced LTR-REs. Moreover, the analyses of simultaneous mapping of insertions and DNA methylation showed that the LTR-REs effectively alter the epigenetic status of the genomic regions where they inserted, and concomitantly their transcriptional competence which might impact the stress resilience and growth of the host. Our work unveils the unusually strong LTR-RE mobility in Moso bamboo and its close association with (epi)genetic changes, which supports the co-evolution of the parasitic DNAs and host genome in attaining stress tolerance and developmental robustness.

Leaf starch degradation by β-amylase ZmBAM8 influences drought tolerance in maize

As a typical C4 plant and important crop worldwide, maize is susceptible to drought. In maize, transitory starch (TS) turnover occurs in the vascular bundle sheath of leaves, differing from that in Arabidopsis (a C3 plant). This process, particularly its role in drought tolerance and the key starch-hydrolyzing enzymes involved, is not fully understood. We discovered that the expression of the β-amylase (BAM) gene ZmBAM8 is highly upregulated in the drought-tolerant inbred line Chang7-2t. Inspired by this finding, we systematically investigated TS degradation in maize lines, including Chang7-2t, Chang7-2, B104, and ZmBAM8 overexpression (OE) and knockout (KO) lines. We found that ZmBAM8 was significantly induced in the vascular bundle sheath by drought, osmotic stress, and abscisic acid. The stress-induced gene expression and chloroplast localization of ZmBAM8 align with the tissue and subcellular sites where TS turnover occurs. The recombinant ZmBAM8 was capable of effectively hydrolyzing leaf starch. Under drought conditions, the leaf starch in ZmBAM8-OE plants substantially decreased under light, while that in ZmBAM8-KO plants did not decrease. Compared with ZmBAM8-KO plants, ZmBAM8-OE plants exhibited increased drought tolerance. Our study provides insights into the significance of leaf starch degradation in C4 crops and contributes to the development of drought-resistant maize.

Systematic analysis of the ARF gene family in Fagopyrum dibotrys and its potential roles in stress tolerance

The auxin response factor (ARF) is a plant-specific transcription factor that regulates the expression of auxin response genes by binding directly to their promoters. They play an important role in the regulation of plant growth and development, as well as in the response to biotic and abiotic stresses. However, the identification and functional analysis of ARFs in Fagopyrum dibotrys are still unclear. In this study, a total of 26 FdARF genes were identified using bioinformatic methods. Their chromosomal location, gene structure, physical and chemical properties of their encoded protein, subcellular location, phylogenetic tree, conserved motifs and cis-acting elements in FdARF promoters were analyzed. The results showed that 26 FdARF genes were unevenly distributed on 8 chromosomes, with the largest distribution on chromosome 4 and the least distribution on chromosome 3. Most FdARF proteins are located in the nucleus, except for the proteins FdARF7 and FdARF21 located to the cytoplasm and nucleus, while FdARF14, FdARF16, and FdARF25 proteins are located outside the chloroplast and nucleus. According to phylogenetic analysis, 26 FdARF genes were divided into 6 subgroups. Duplication analysis indicates that the expansion of the FdARF gene family was derived from segmental duplication rather than tandem duplication. The prediction based on cis-elements of the promoter showed that 26 FdARF genes were rich in multiple stress response elements, suggesting that FdARFs may be involved in the response to abiotic stress. Expression profiling analysis showed that most of the FdARF genes were expressed in the roots, stems, leaves, and tubers of F. dibotrys, but their expression exhibits a certain degree of tissue specificity. qRT-PCR analysis revealed that most members of the FdARF gene were up- or down-regulated in response to abiotic stress. The results of this study expand our understanding of the functional role of FdARFs in response to abiotic stress and lay a theoretical foundation for further exploration of other functions of FdARF genes.

Genome-wide identification and expression analysis of the GAD family reveal their involved in embryogenesis and hormones responses in Dimocarpus longan Lour

Glutamate decarboxylase (GAD) is involved in GABA metabolism and plays an essential regulatory role in plant growth, abiotic stresses, and hormone response. This study investigated the expression mechanism of the GAD family during longan early somatic embryogenesis (SE) and identified 6 GAD genes based on the longan genome. Homology analysis indicated that DlGAD genes had a closer relationship with dicotyledonous plants. The analysis of cis-acting elements in the promoter region suggests that the GAD genes were associated with various stress responses and hormones. RNA sequencing (RNA-Seq) and the qRT-PCR data indicated that most DlGAD genes were highly expressed in the incomplete compact pro-embryogenic cultures (ICpEC) and upregulated in longan embryogenic callus (EC) after treatments with 2,4-D, high temperature (35 °C), IAA, and ABA. Moreover, the RNA-Seq analysis also revealed that DlGADs exhibit different expression patterns in various tissues and organs. The subcellular localization results showed that DlGAD5 was localized in the cytoplasm, suggesting that it played a role in the cytoplasm. Transient overexpression of DlGAD5 enhanced the expression levels of DlGADs and increased the activity of glutamate decarboxylase in longan embryogenic callus (EC), while the content of glutamic acid decreased. Thus, the DlGAD gene can play an important role in the early somatic embryogenesis of longan by responding to hormones such as IAA and ABA. DlGAD5 can affect the growth and development of longan by stimulating the expression of the DlGAD gene family, thereby increasing the GAD activity in the early SE of longan, participating in hormone synthesis and signaling pathways.

Exploring the GRAS gene family in Taraxacum kok-saghyz Rodin：characterization, evolutionary relationships, and expression analyses in response to abiotic stresses

The GRAS gene is an important specific transcription factor in plants, which has multiple functions such as signal transduction, cell morphogenesis and stress response. Although it is widely distributed in plants and has been characterized in several species, however, information about the GRAS family in Taraxacum kok-saghyz Rodin remains unknown. Here, TkGRAS family members were identified and analyzed for molecular characterization, tissue expression patterns and induced expression patterns. A total of 64 GRAS family members were identified at the genome-wide level, which could be categorized into 14 subfamilies by phylogenetic analysis. Most TkGRASs were intronless and had essentially the same gene structure in the same subfamily. Meanwhile, there were multiple response elements found in the promoters of TkGRASs. Tissue expression patterns and induced expression patterns showed that TkGRASs were expressed in different tissues and induced by abiotic stresses. Notably, the expression level of TkGRAS20 was up-regulated under different stresses, suggesting that this gene plays a pivotal role in the stress response. TkGRAS20 showed transcriptional activity in yeast cells and localized in the nucleus and plasma membrane. In conclusion, our study provided valuable insights into the genetic mechanisms underlying stress tolerance in TKS, and several key genes may be used for genetic breeding to improve stress tolerance.

Genome-wide identification and expression analysis of the ZRT, IRT-like protein (ZIP) family in Nicotiana tabacum

Iron (Fe) and Zinc (Zn) are essential micronutrients for plant growth and development. ZIP (ZRT, IRT-like protein) transporters, known for their role in the regulation of Zinc and Iron uptake, are pivotal in facilitating the absorption, transport, and maintenance of Fe/Zn homeostasis in plants. Nicotiana tabacum has been widely used as a model plant for gene function analysis; however, the tobacco ZIP genes have not been identified systematically. In this study, we have identified a comprehensive set of 32 NtZIP genes, which were phylogenetically categorized into three distinct clades. The gene structures, characterized by their exon/intron organization, and the protein motifs are relatively conserved, particularly among genes within the same clade. These NtZIP genes exhibit an uneven distribution across 12 chromosomes. The gene localization analysis revealed the presence of 11 pairs of homeologous locus genes and 7 pairs of tandem duplication genes within the genome. To further explore the functionality of these genes, real-time quantitative reverse transcription PCR was employed to assess their expression levels in roots subjected to metal deficiency. The results indicated that certain NtZIP genes are specifically upregulated in response to either Fe or Zn deficiency. Additionally, the presence of specific cis-elements within their promoter regions, such as the E-box associated with Fe deficiency response and the ZDRE box linked to Zn deficiency response, was identified. This study lays a foundational groundwork for future research into the biological functions of NtZIP genes in tobacco in micronutrient regulation and homeostasis.

ZmHsp18 screened from the ZmHsp20 gene family confers thermotolerance in maize

Heat stress has become one of the abiotic stresses that pose an increasing threat to maize production due to global warming. The Hsp20 gene family confers tolerance to various abiotic stresses in plants. However, very few Hsp20s have been identified in relation to maize thermotolerance. In this study, we conducted a comprehensive study of Hsp20s involved in thermotolerance in maize. A total of 33 maize Hsp20 genes (ZmHsp20s) were identified through scanning for a conserved α-crystalline domain (ACD), and they were categorized into 14 subfamilies based on phylogenetic analysis. These genes are distributed across all maize chromosomes and nine of them are in regions previously identified as heat-tolerance quantitative trait loci (hrQTL). These hrQTL-associated ZmHsp20s show variation in tissue-specific expression profiles under normal conditions, and seven of them possess 1-5 heat stress elements in their promoters. The integration of RNA-seq data with real-time RT-PCR analysis indicated that ZmHsp23.4, ZmHsp22.8B and ZmHsp18 were dramatically induced under heat stress. Additionally, these genes exhibited co-expression patterns with key ZmHsfs, which are crucial in the heat tolerance pathway. When a null mutant carrying a frame-shifted ZmHsp18 gene was subjected to heat stress, its survival rate decreased significantly, indicating a critical role of ZmHsp18 in maize thermotolerance. Our study lays the groundwork for further research into the roles of ZmHsp20s in enhancing maize's thermotolerance.

Chromosome-scale genome assembly of Apocynum pictum, a drought-tolerant medicinal plant from the Tarim Basin

Apocynum pictum Schrenk is a semishrub of the Apocynaceae family with a wide distribution throughout the Tarim Basin that holds significant ecological, medicinal, and economic values. Here, we report the assembly of its chromosome-level reference genome using Nanopore long-read, Illumina HiSeq paired-end, and high-throughput chromosome conformation capture sequencing. The final assembly is 225.32 Mb in length with a scaffold N50 of 19.64 Mb. It contains 23,147 protein-coding genes across 11 chromosomes, 21,148 of which (91.36%) have protein functional annotations. Comparative genomics analysis revealed that A. pictum diverged from the closely related species Apocynum venetum approximately 2.2 million years ago and has not undergone additional polyploidizations after the core eudicot WGT-γ event. Karyotype evolution analysis was used to characterize interchromosomal rearrangements in representative Apocynaceae species and revealed that several A. pictum chromosomes were derived entirely from single chromosomes of the ancestral eudicot karyotype. Finally, we identified 50 members of the well-known stress-responsive WRKY transcription factor family and used transcriptomic data to document changes in their expression at 2 stages of drought stress, identifying a number of promising candidate genes. Overall, this study provides high-quality genomic resources for evolutionary and comparative genomics of the Apocynaceae, as well as initial molecular insights into the drought adaptation of this valuable desert plant.

New insights into the evolution analysis of trihelix gene family in eggplant (Solanum melongena L.) and expression analysis under abiotic stress

BACKGROUND

Trihliex transcription factors (TFs) play crucial roles in plant growth and development, stress response, and plant hormone signaling network transmission. In order to comprehensively investigate the functions of trihliex genes in eggplant development and the abiotic stress response, we conducted an extensive analysis of the trihliex gene family in the eggplant genome.

RESULTS

In this study, 30 trihelix gene family members were unevenly distributed on 12 chromosomes. On the basis of their phylogenetic relationships, these genes were conserved in different plant species and could be divided into six subfamilies, with trihelix genes within the same subfamily sharing similar structures. The promoter regions of trihelix genes contained cis-acting elements related to plant growth and development, plant hormones, and abiotic stress responses, suggesting potential applications in the development of more resistant crops. Selective pressure assessments indicated that trihliex genes have undergone purifying selection pressure. Expression analysis on the basis of transcriptomic profiles revealed that SmGT18, SmGT29, SmGT6, and SmGT28 are highly expressed in roots, leaves, flowers, and fruits, respectively. Expression analysis via quantitative real-time PCR (qRT‒PCR) revealed that most trihelix genes respond to low temperature, abscisic acid (ABA), and salicylic acid (SA), with SmGT29 exhibiting significant upregulation under cold stress conditions. The SmGT29 gene was subsequently successfully cloned from eggplant, which was located in the nucleus, robust transcriptional activity, and a protein molecular weight of 74.59 kDa. On the basis of these findings, SmGT29 was postulated to be a pivotal candidate gene that actively responds to biotic stress stimuli, thereby supporting the plant's innate stress resistance mechanisms.

CONCLUSION

In summary, this study was the first report on trihelix genes and their potential roles in eggplant plants. These results provided valuable insights for enhancing stress resistance and quality traits in eggplant breeding, thereby serving as a crucial reference for future improvement efforts.

EARLY FLOWERING3-1 represses Grain number, plant height, and heading date7 to promote ABC1 REPRESSOR1 and regulate nitrogen uptake in rice

The extensive use of nitrogen fertilizer boosts rice (Oryza sativa) production but also harms ecosystems. Therefore, enhancing crop nitrogen use efficiency is crucial. Here, we performed map-based cloning and identified the EARLY FLOWERING3 (ELF3) like protein-encoding gene OsELF3-1, which confers enhanced nitrogen uptake in rice. OsELF3-1 forms a ternary complex (OsEC) with OsELF4s and OsLUX, the putative orthologs of ELF4 and LUX ARRHYTHMO (LUX) in Arabidopsis (Arabidopsis thaliana), respectively. OsEC directly binds to the promoter of Grain number, plant height, and heading date7 (Ghd7) and represses its expression. Ghd7 encodes a transcription factor that has major effects on multiple agronomic traits. Ghd7 is also a transcriptional repressor and directly suppresses the expression of ABC1 REPRESSOR1 (ARE1), a negative regulator of nitrogen use efficiency. Therefore, targeting the OsEC-Ghd7-ARE1 module offers an approach to enhance nitrogen uptake, presenting promising avenues for sustainable agriculture.

Genome-wide analyses of Ariadne family genes reveal their involvement in abiotic stress responses in apple

E3 ligases are essential for ubiquitination and play a role in regulating various aspects of eukaryotic life. Ariadne (ARI) proteins, a subfamily of RBR (RING-between-RING) proteins, have been recognized as a new class of RING-finger E3 ligases. Recent research has shed light on their potential involvement in plants' responses to abiotic stress. However, comprehensive studies on ARI genes in apple (Malus domestica) are still lacking. This study identified ten MdARI genes in the apple genome, and examined intraspecific and interspecific collinearity to explore the evolutionary relationships of ARI family members. Phylogenetic analyses classified MdARIs into two subfamilies (A and B), and by integrating gene structure, conserved motifs, and sequence comparison results, subfamily B was further divided into two subgroups (I and II). Tissue expression analyses revealed varied expression patterns of MdARI genes in different tissues, and subcellular localization showed that MdARI1-1, MdARI1-2, and MdARI9-1 were located in the nucleus, while the other seven MdARIs were distributed throughout the cell. Analyses of promoter cis-elements and expression patterns under cold, salt, and drought treatments indicated the involvement of MdARIs in abiotic stress responses. Several proteins crucial to the plant stress response were predicted to be potential MdARIs-interacting proteins based on the protein interaction network. Additionally, the interaction between UBC11 (E2) and MdARI7-2 was confirmed by a yeast two-hybrid (Y2H) experiment, suggesting that MdARI7-2 may function as an E3. These findings will greatly benefit future research on the role and mechanisms of ARI proteins in apple stress response.

A pearl millet plasma membrane protein, PgPM19, facilitates seed germination through the negative regulation of abscisic acid-associated genes under salinity stress in Arabidopsis thaliana

MAIN CONCLUSION

The pearl millet gene PgPM19 inhibits seed dormancy by negatively regulating the ABA biosynthesis and ABA signaling pathways in response to salinity stress in Arabidopsis. Abscisic acid (ABA) plays a pivotal role in orchestrating plant stress responses and development. However, how the ABA signal is transmitted in response to stresses remains primarily uncertain, particularly in monocotyledonous plants. In this study, PgPM19, a gene whose expression is induced by drought, salinity, heat, and ABA in both leaf and root tissues, was isolated from pearl millet. The expression of PgPM19 in yeast cells did not influence their growth when subjected to mannitol, sorbitol, or NaCl stress. However, Arabidopsis plants overexpressing PgPM19 (PgPM19_OE plants) exhibited increased germination rates, greater fresh weights and longer roots under salinity stress during germination, compared to wild-type (WT) plants. Conversely, the pm19L1 (SALK_075435) mutant, featuring a transfer DNA insertion in a closely related PgPM19 homolog (AT1G04560) in Arabidopsis, demonstrated reduced germination rates and smaller fresh weights under salinity-stressed condition than did WT and PgPM19_OE plants. A pivotal ABA biosynthesis gene, NCED3, ABA signaling pathway genes, such as PYL6 and SnRK2.7, alongside downstream ABI genes and stress-responsive genes RAB28 and RD29, were downregulated in PgPM19_OE plants, as evidenced by both transcriptome analysis and quantitative reverse transcription-PCR. These findings raise the possibility that PgPM19 is involved in regulating seed germination by mediating ABA biosynthesis and signaling pathway in response to salinity stress in Arabidopsis. This study contributes to a better understanding of PgPM19 in response to salinity stress and establishes a foundation for unraveling the crosstalk of stress responses and ABA in Arabidopsis and other plant species.

Genome wide analysis of HMA gene family in Hydrangea macrophylla and characterization of HmHMA2 in response to aluminum stress

Aluminum toxicity poses a significant threat to plant growth, especially in acidic soils. Heavy metal ATPases (HMAs) are crucial for transporting heavy metal ions across plant cell membranes, yet their role in Al3+ transport remains unexplored. This study identified eight HmHMA genes in the genome of Hydrangea macrophylla, categorizing them into two major clades based on phylogenetic relationships. These genes were found unevenly distributed across six chromosomes. Detailed analysis of their physicochemical properties, collinearity, and gene structure was conducted. RNA-seq and qRT-PCR analyses revealed that specific HmHMA genes, notably HmHMA2, were predominantly expressed in roots and flowers under Al3+ stress, indicating their potential role in Al3+ tolerance. HmHMA2 showed significant expression in roots, especially under Al3+ stress conditions, and when expressed in yeast cells, it conferred resistance to aluminum and zinc but increased sensitivity to cadmium. Overexpression of HmHMA2 in hydrangea leaf discs significantly improved Al3+ tolerance, reduced oxidative stress markers like hydrogen peroxide and malondialdehyde, and enhanced antioxidant enzyme activity such as SOD, POD and CAT compared to controls. These findings shed lights on the potential role of HmHMAs in Al transport and tolerance in H. macrophylla.

Overexpression of the Poa pratensis GA2ox gene family significantly reduced the plant height of transgenic Arabidopsis thaliana and Poa pratensis

Gibberellin (GAs) is an important plant hormone that plays a key role in plant growth and development. Gibberellin 2-oxidase (GA2ox) catalyzes the inactivation of biologically active GA or their direct precursors. In this study, five GA2ox genes were isolated from the wild type Poa pratensis 'Baron', named PpGA2ox3, PpGA2ox4, PpGA2ox5, PpGA2ox8, and PpGA2ox9. Phylogenetic tree analysis showed that PpGA2ox3, PpGA2ox4, PpGA2ox5, and PpGA2ox8 belong to class I GA2ox genes, while PpGA2ox9 belongs to class III GA2ox genes. They expressed in all tissues of Poa pratensis, in each plant tissue and growth stage, the expression patterns were different. After GA3 spraying treatment, the expression of each gene showed different patterns. Subcellular localization showed that PpGA2ox3 was located in chloroplasts, while PpGA2ox5 and PpGA2ox9 were located in the cytoplasm. When PpGA2ox3 and PpGA2ox9 were overexpressed in Arabidopsis thaliana, they all led to a typical dwarf phenotype, as well as low plant height, small leaves and late flowering. Similarly, when they overexpressed in P. pratensis, the transgenic plants also exhibited a dwarf phenotype with a lower leaf length/width ratio. Hormone analysis suggested that these dwarfing traits might be caused by a decrease in GA4 content. These studies indicated that the PpGA2ox gene family played an important role in studying the mechanism of plant dwarfism and also had the potential to become important genes for the breeding of P. pratensis.

Genome-wide identification of the OVATE family proteins and functional analysis of BhiOFP1, BhiOFP5, and BhiOFP18 during fruit development in wax gourd (Benincasa hispida)

OVATE family proteins (OFPs) are transcriptional regulators in plants. They have a common domain called the OVATE domain and control the development of leaves, fruits, and flowers in plants. Although the OFP gene family has been widely explored in the plant kingdom, the identification and characterization of this family have not yet been performed in wax gourd. In this study, we conducted a genome-wide investigation of the OFP gene family and identified 18 OFP (BhiOFP) genes in wax gourd. Next, we discovered their evolutionary relationships, conserved motifs, gene structures, cis-acting elements, and expression patterns. The BhiOFP genes were irregularly distributed on nine chromosomes, with only two BhiOFP genes containing introns. The BhiOFP gene promoters contained cis-acting elements in response to phytohormones and environmental signals. The majority of BhiOFP genes were derived from whole-genome duplication events. Expression analysis demonstrated that the BhiOFP genes showed disparate modes of expression and some of them were highly expressed in fruits. Overexpression of BhiOFP1, BhiOFP5, and BhiOFP18 in Arabidopsis resulted in dwarf plants, small rosette leaves, and shortened siliques, while the BhiOFP1 overexpression plants displayed a more severe phenotype. In summary, our study systematically analyzed the wax gourd OFP gene family, facilitated the functional research of BhiOFP1, BhiOFP5, and BhiOFP18, and offered a theoretical foundation for the improvement of wax gourd varieties with appropriate fruit length.

Role of auxin and gibberellin under low light in enhancing saffron corm starch degradation during sprouting

The mechanisms by which low light accelerates starch macromolecules degradation by auxin and gibberellin (GA) in geophytes during sprouting remain largely unknown. This study investigated these mechanisms in saffron, grown under low light (50 μmol m-2 s-1) and optimal light (200 μmol m-2 s-1) during the sprouting phase. Low light reduced starch concentration in corms by 34.0 % and increased significantly sucrose levels in corms, leaves, and leaf sheaths by 19.2 %, 9.8 %, and 134.5 %, respectively. This was associated with a 33.3 % increase in GA3 level and enhanced auxin signaling. Leaves synthesized IAA under low light, which was transported to the corms to promote GA synthesis, facilitating starch degradation through a 228.7 % increase in amylase activity. Exogenous applications of GA and IAA, as well as the use of their synthesis or transport inhibitors, confirmed the synergistic role of these phytohormones in starch metabolism. The unigenes associated with GA biosynthesis and auxin signaling were upregulated under low light, highlighting the IAA-GA module role in starch degradation. Moreover, increased respiration rate and invertase activity, crucial for ATP biosynthesis and the tricarboxylic acid cycle, were consistent with the upregulation of related unigenes, suggesting that auxin signaling accelerates starch degradation by promoting energy metabolism. Upregulated of auxin signaling (CsSAUR32) and starch metabolism (CsSnRK1) genes under low light suggests that auxin directly regulate starch degradation in saffron corms. This study elucidates that low light modulates auxin and GA interactions to accelerate starch degradation in saffron corms during sprouting, offering insights for optimizing agricultural practices under suboptimal light conditions.

Identification and analysis of flavonoid pathway genes in responsive to drought and salinity stress in Medicago truncatula

Flavonoid compounds are widely present in various organs and tissues of different plants, playing important roles when plants are exposed to abiotic stresses. Different types of flavonoids are biosynthesized by a series of enzymes that are encoded by a range of gene families. In this study, a total of 63 flavonoid pathway genes were identified from the genome of Medicago truncatula. Gene structure analysis revealed that they all have different gene structure, with most CHS genes containing only one intron. Additionally, analysis of promoter sequences revealed that many cis-acting elements responsive to abiotic stress are located in the promoter region of flavonoid pathway genes. Furthermore, analysis on M. truncatula gene chip data revealed significant changes in expression level of most flavonoid pathway genes under the induction of salt or drought treatment. qRT-PCR further confirmed significant increase in expression level of several flavonoid pathway genes under NaCl and mannitol treatments, with CHS1, CHS9, CHS10, F3'H4 and F3'H5 genes showing significant up-regulation, indicating they are key genes in response to abiotic stress in M. truncatula. In summary, our study identified key flavonoid pathway genes that were involved in salt and drought response, which provides important insights into possible modification of flavonoid pathway genes for molecular breeding of forage grass with improved abiotic resistance.

Molecular characterization of cassava zinc finger-homeodomain (ZF-HD) transcription factors reveals their role in disease resistance

The production of cassava (Manihot esculenta Crantz) is constantly threatened by cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm). Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes widely implicated in various developmental and physiological processes in plants. Despite their importance, a comprehensive analysis of ZF-HD genes, particularly those involved in disease resistance, has not been performed for cassava. In the present study, we utilized bioinformatics methods to identify 21 ZF-HD genes distributed across 11 chromosomes of cassava genome, with the majority exhibiting gene structure without introns. Phylogenetic analysis categorized these genes into two major groups (MIF and ZHD) with five subgroups. We observed fourteen pairs of duplicated genes, suggesting that segmental duplication has likely facilitated the expansion of the cassava ZF-HD gene family. Comparative orthologous analyses between cassava and other plant species shed light on the evolutionary trajectory of this gene family. Promoter analyses revealed multiple hormone- and stress-related elements, indicative of a functional role in stress responses. Expression profiling through RNA-seq and quantitative real-time PCR (qRT-PCR) demonstrated that certain cassava ZF-HD genes are up-regulated in response to Xpm infection, suggesting their involvement in defense mechanisms. Notably, MeZHD7 gene was identified via virus induced gene silencing (VIGS) as potentially crucial in conferring resistance against CBB. Results from subcellular localization experiments indicated that MeZHD7 was localized in the nucleus. The Luciferase reporter assay demonstrated an interaction between MeZHD7 and MeMIF5. These findings may lay the foundation for further cloning and functional analyses of cassava ZF-HD genes, particularly those associated with pathogen resistance.

Comprehensive studies of the serine carboxypeptidase-like (SCPL) gene family in Carya cathayensis revealed the roles of SCPL4 in epigallocatechin-3-gallate (EGCG) synthesis and drought tolerance

Hickory (Carya cathayensis) nuts are rich in epigallocatechin-3-gallate (EGCG) with multiple health functions. EGCG also regulates plant growth, development and stress responses. However, research on the synthesis mechanism of EGCG and its function in hickory is currently limited. Herein, 44 serine carboxypeptidase-like (SCPL) members were identified from the hickory genome and classified into three major categories: SCPL-I, SCPL-II, and SCPL-III. In the CcSCPLs-IA branch, CcSCPL3/4/5/8/9/11/13 showed differential expression patterns in various tissues, especially with relatively high expression levels in plant roots, female flowers and seed coat. These proteins have a catalytic triad composed of serine (Ser), aspartic acid (Asp) and histidine (His). Ser-His in the triad and arginine (Arg) mediated the docking of CcSCPL3/4/5/11 with 1-O-galloyl-β-d-glucose (βG) and epigallocatechin (EGC), whereas the Asp of the triad did not. CcSCPL4 was further confirmed to promote the synthesis of EGCG in tobacco leaves. CcSCPL4 may function as monomer and be mainly localized within cellular structures outside the nucleus. Notably, the expression level of CcSCPL4 significantly changed after drought, cold, and salt stress, with the highest expression level under drought stress. Meanwhile CcSCPL4 over-expression could enhance the drought resistance of Saccharomyces cerevisiae and Arabidopsis. This study elucidates key enzymes for EGCG synthesis and their role in drought resistance, providing insights into the EGCG synthesis pathway and molecular breeding of hickory in future.

Overexpressing CsPSY1 Gene of Tea Plant, Encoding a Phytoene Synthase, Improves α-Carotene and β-Carotene Contents in Carrot

Tea plants (Camellia sinensis (L.) O. Kuntze) belong to Theaceae family, in the section Thea. Tea plants are widely distributed in subtropical and tropical regions in the word. α-carotene and β-carotene in the tea leaves belong to carotenoids, which are associated with the aroma and color of the tea. Phytoene synthase (PSY) is a rate-limiting enzyme in carotenoids biosynthesis. We identified three CsPSY genes in 'Shuchazao', named CsPSY1, CsPSY2, and CsPSY3. Structural analysis of three CsPSY genes showed that CsPSY1 had a longer intro structure. The cis-acting elements of CsPSYs promoter were mainly associated with light-responsiveness, abiotic stress-responsiveness, and hormone-responsiveness. CsPSY1 exhibited expression in all tissues of the tea plants, whereas CsPSY2 and CsPSY3 were trace expression levels in all tissues. The positive expression of CsPSY1 under hormonal and abiotic stresses suggested its role in plant development and defense responses. The amino acid sequence of CsPSY1 was highly conserved in eight tea cultivars. The recombinant vector pCAMBIA1301-CsPSY1 was constructed to stabilize the overexpression of CsPSY1 in carrot. The contents of α-carotene and β-carotene in transgenic carrot callus were significantly increased. This study provides a foundational basis for further research on the function of CsPSYs and carotenoids accumulation in tea plants.

Characterisation and evolution of the PRC2 complex and its functional analysis under various stress conditions in rice

The polycomb repressive complex 2 (PRC2) is a chromatin-associated methyltransferase responsible for catalysing the trimethylation of H3K27, an inhibitory chromatin marker associated with gene silencing. This enzymatic activity is crucial for normal organismal development and the maintenance of gene expression patterns that preserve cellular identity, subsequently influencing plant growth and abiotic stress responses. Therefore, in this study, we investigated the evolutionary characteristics and functional roles of PRC2 in plants. We identified 209 PRC2 genes, including E(z), Su(z), Esc, and Nurf55 families, using 18 representative plant species and revealed that recent gene replication events have led to an expansion in the Nurf55 family, resulting in a greater number of members compared to the E(z), Su(z), and Esc families. Furthermore, protein structure and motif composition analyses highlighted the potential functional site regions within PRC2 members. In addition, we selected rice, a representative monocotyledonous plant, as the model species for food crops. Our findings revealed that SDG711, SDG718, and MSI1-5 genes were induced by abscisic acid (ABA) and/or methyl jasmonate (MeJA) hormones, suggesting that these genes play an important role in abiotic stress and disease resistance. Further experiments involving rice blast fungus treatments confirmed that the expression of SDG711 and MSI1-5 was induced by Magnaporthe oryzae strain GUY11. Multiple protein interaction assays revealed that the M. oryzae effector AvrPiz-t interacts with PRC2 core member SDG711 to increase H3K27me3 levels. Notably, inhibition of PRC2 or mutation of SDG711 enhanced rice resistance to M. oryzae. Collectively, these results provide new insights into PRC2 evolution in plants and its significant functions in rice.

Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses: insights from comparative analysis of Brassica type-A response regulators

Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development and adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of the MSP cascade and cytokinin primary response genes, are thought to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, transcriptional data also suggest the involvement of RRA genes in stress-related responses. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRA genes, we identified five and 38 novel putative RRA genes in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassicaceae. We categorized RRA genes based on the kinetics of their cytokinin-mediated up-regulation and observed both similarities and specificities in this type of response across Brassicaceae species. Using bioinformatic analysis and experimental data demonstrating the cytokinin and abiotic stress responsiveness of the A. thaliana-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin- and stress-mediated up-regulation of RRA genes in B. rapa and B. napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus further demonstrating the role of cytokinin signaling in crop adaptive responses.

Over-expression of SiADCL1 in Arabidopsis modulates folate and amino acid metabolism to impact on flowering time

Foxtail millet is a C4 crop rich in folate (FA). This study explores the roles of the 4-amino-4-deoxychorismate lyase (ADCL) - a member of the transaminase IV group of enzymes - in FA metabolism and conferred phenotypes. Phylogenetic comparisons identified diversity in the transaminase IV/ADCL gene family in the foxtail millet genome which was associated with genomic duplications. Molecular docking studies suggested that SiADCL1 bound most strongly to aminodeoxychorismate (ADC) and most likely had the highest catalytic activities. SiADCL1 which was highly expressed in roots, peduncles and flag leaves. Over-expression of SiADCL1 in Arabidopsis significantly increased total FA content (1.14-1.84 fold) and this was linked to a delayed flowering time. Metabolomic and transcriptomic characterization of the derived over-expression lines, found that FA promotes the change of methylation-related genes, ethylene synthesis, amino acid metabolism and flowering-related genes. This study revealed a potential gene coexpression network linked with FA and targeted key genes that could be exploited in foxtail millet breeding programs.

WHIRLY proteins, multi-layer regulators linking the nucleus and organelles in developmental and stress-induced senescence of plants

Plant senescence is an integrated programme of plant development that aims to remobilize nutrients and energy from senescing tissues to developing organs under developmental and stress-induced conditions. Upstream in the regulatory network, a small family of single-stranded DNA/RNA-binding proteins known as WHIRLYs occupy a central node, acting at multiple regulatory levels and via trans-localization between the nucleus and organelles. In this review, we summarize the current progress on the role of WHIRLY members in plant development and stress-induced senescence. WHIRLY proteins can be traced back in evolution to green algae. WHIRLY proteins trade off the balance of plant developmental senescence and stress-induced senescence through maintaining organelle genome stability via R-loop homeostasis, repressing the transcription at a configuration condition, and recruiting RNA to impact organelle RNA editing and splicing, as evidenced in several species. WHIRLY proteins also act as retrograde signal transducers between organelles and the nucleus through protein modification and stromule or vesicle trafficking. In addition, WHIRLY proteins interact with hormones, reactive oxygen species and environmental signals to orchestrate cell fate in an age-dependent manner. Finally, prospects for further research and promotion to improve crop production under environmental constraints are highlighted.

Genome-wide identification and expression analysis of two-component system genes in switchgrass (Panicum virgatum L.)

The two-component system (TCS) consists of histidine kinase (HK), histidine phosphate transfer protein (HP), and response regulatory factor (RR). It is one of the most crucial components of signal transduction in plants, playing a significant role in regulating plant growth, development, and responses to various abiotic stresses. Although TCS genes have been extensively identified in a variety of plants, the genome-wide recognition and examination of TCS in switchgrass remain unreported. Accordingly, this study identified a total of 87 TCS members in the genome of switchgrass, comprising 20 HK(L)s, 10 HPs, and 57 RRs. Detailed analyses were also conducted on their gene structures, conserved domains, and phylogenetic relationships. Moreover, this study analysed the gene expression profiles across diverse organs and investigated their response patterns to adverse environmental stresses. Results revealed that 87 TCS genes were distributed across 18 chromosomes, with uneven distribution. Expansion of these genes in switchgrass was achieved through both fragment and tandem duplication. PvTCS members are relatively conservative in the evolutionary process, but the gene structure varies significantly. Various cis-acting elements, varying in types and amounts, are present in the promoter region of PvTCSs, all related to plant growth, development, and abiotic stress, due to the TCS gene structure. Protein-protein interaction and microRNA prediction suggest complex interactions and transcriptional regulation among TCS members. Additionally, most TCS members are expressed in roots and stems, with some genes showing organ-specific expression at different stages of leaf and inflorescence development. Under conditions of abiotic stress such as drought, low temperature, high temperature, and salt stress, as well as exogenous abscisic acid (ABA), the expression of most TCS genes is either stimulated or inhibited. Our systematic analysis could offer insight into the characterization of the TCS genes, and further the growth of functional studies in switchgrass.

Genome-wide identification of alcohol dehydrogenase (ADH) gene family in oilseed rape (Brassica napus L.) and BnADH36 functional verification under salt stress

BACKGROUND

Alcohol dehydrogenase (ADH) is an enzyme that binds to zinc, facilitating the interconversion of ethanol and acetaldehyde or other corresponding alcohols/aldehydes in the pathway of ethanol fermentation. It plays a pivotal role in responding to environmental stress. However, the response of the ADH family to abiotic stress remains unknown in rapeseed.

RESULT

In this study, we conducted a comprehensive genome-wide investigation of the ADH family in rapeseed, encompassing analysis of their gene structure, replication patterns, conserved motifs, cis-acting elements, and response to stress. A total of 47 ADH genes were identified within the rapeseed genome. Through phylogenetic analysis, BnADHs were classified into four distinct clades (I, II, IV, V). Prediction of protein domains revealed that all BnADH members possessed a GroES-like (ADH_N) domain and a zinc-bound (ADH_zinc_N) domain. Analysis of promoter sequences demonstrated that BnADHs contained numerous cis-acting elements associated with hormone and stress responses, indicating their widespread involvement in various biological regulatory processes. Expression profiling under different concentrations of salt stress treatments (0%, 0.4%, 0.8%, 1.0% NaCl) further highlighted the significant role played by the BnADH family in abiotic stress response mechanisms. Overexpression of BnADH36 in rapeseed significantly improved the salt tolerance of rapeseed.

CONCLUSION

The features of the BnADH family in rapeseed was comprehensively characterized in this study, which could provide reference to the research of BnADHs in abiotic stress response.

Genome-wide computational analysis of the dirigent gene family in Solanum lycopersicum

BACKGROUND

Dirigent (DIR) genes play a key role in the development of organic products in plants. They confer conformational influence on processes that lack stereoselectivity and regioselectivity through processes that are mostly understood. They are required to produce lignans, which are a unique and widely distributed family of plant secondary metabolites with intriguing pharmacological characteristics and potential role in plant development. DIR genes are implicated in the process of lignification and protect plants from environmental stresses, including biotic and abiotic stresses. Nevertheless, no research has been performed on the DIR gene family in Solanum lycopersicum. This study provides detailed information on the DIR gene family in S. lycopersicum.

METHODS AND RESULTS

The conserved domain analysis, phylogenetic analysis, evolutionary adaptation, cis-acting elements, proteomic analysis, signal peptide detection, transmembrane potential analysis, sequence identity and similarity analysis, gene assembly, genomic localization, duplication of gene analysis, and evolutionary linkage of 31 potential DIR genes were studied. All these analyses provide a deep understanding of DIR genes in the S. lycopersicum genome that will provide a useful reference for further functional analysis of the DIR genes in S. lycopersicum.

CONCLUSION

This research provides an in-depth and comprehensive explanation of the detailed process and structural characterization of DIR genes in the genome of S. lycopersicum, laying the groundwork for future plant genetic engineering and crop development exploration. This work will provide valuable information for identifying DIR genes in higher plants and support future research on the DIR gene family.

Characterization of ATP-dependent phosphofructokinase genes during ripening and their modulation by phytohormones during postharvest storage of citrus fruits (Citrus reticulata Blanco.)

The level of sweetness in citrus fruit is crucial for consumer appeal and market competitiveness, determined mainly by soluble sugars and organic acids. ATP-dependent 6-phosphofructokinase is central to regulating sugar metabolism, yet its role in citrus fruit ripening and postharvest storage remains underexplored. We characterized phosphofructokinase genes in citrus, identifying eight genes classified into pyrophosphate-dependent phosphofructokinase (PFP) and ATP-dependent 6-phosphofructokinase (PFK) subgroups using phylogenetic analysis, genomic architectures, and protein motifs. Comparative genomic analysis with other plants highlighted significant protein homology among CitPFKs. The motif analysis indicated conserved phosphofructokinase domains in CitPFK sequences, with upstream promoter regions containing diverse cis-regulatory elements, most notably light-responsive (LREs). The gene expression profiling throughout fruit development and ripening revealed differential patterns, with responses to gibberellic acid and salicylic acid phytohormones during postharvest indicating their roles in regulating CitPFK genes. The analysis of the transcriptome showed high expression of ATP-dependent 6-phosphofructokinase 3 (CitPFK3) during fruit development, indicating a positive role in fruit maturation. Consequently, silencing CitPFK3 through virus-induced gene silencing (VIGS) increased hexose sugar content, suggesting its function in sugar accumulation. These findings improve our understanding of PFKs in citrus, particularly CitPFK3's pivotal role in regulating hexose sugar dynamics and their modulation by exogenous phytohormones after harvest. This study provides a foundation for optimizing soluble sugar regulation to enhance fruit quality and postharvest handling in citrus production.

Genome-wide analysis of the SWEET gene family and its response to powdery mildew and leaf spot infection in the common oat (Avena sativa L.)

The nutritional quality and yield of oats (Avena sativa) are often compromised by plant diseases such as red leaf, powdery mildew, and leaf spot. Sugars Will Eventually be Exported Transporters (SWEETs) are newly identified sugar transporters involved in regulating plant growth and stress responses. However, the roles of SWEET genes in biotic stress responses remain uncharacterized in oats. In this study, 13 AsSWEET genes were identified across nine chromosomes of the oat genome, all of which were predicted to contain seven transmembrane regions. Phylogenetic analysis revealed four clades of AsSWEET proteins, with high homology to SWEET proteins in the Poaceae family. Collinearity analysis demonstrated strong relationships between oat and Zea mays SWEETs. Using subcellular localization prediction tools, AsSWEET proteins were predicted to localize to the plasma membrane. Promoter analysis revealed cis-acting elements associated with light response, growth, and stress regulation. Six AsSWEET proteins were predicted to interact in a network centered on AsSWEET1a and AsSWEET11. Gene expression analysis of two oat varieties, 'ForagePlus' and 'Molasses', indicated significant expression differences in several AsSWEET genes following infection with powdery mildew or leaf spot, including AsSWEET1a, AsSWEET1b, AsSWEET2b, AsSWEET3a, AsSWEET11, and AsSWEET16. These SWEET genes are potential candidates for disease resistance in oats. This study provides a foundation for understanding the regulatory mechanisms of AsSWEET genes, particularly in response to powdery mildew and leaf spot, and offers insights for enhancing oat molecular breeding.

MYB transcription factors, their regulation and interactions with non-coding RNAs during drought stress in Brassica juncea

BACKGROUND

Brassica juncea (L.) Czern is an important oilseed crop affected by various abiotic stresses like drought, heat, and salt. These stresses have detrimental effects on the crop's overall growth, development and yield. Various Transcription factors (TFs) are involved in regulation of plant stress response by modulating expression of stress-responsive genes. The myeloblastosis (MYB) TFs is one of the largest families of TFs associated with various developmental and biological processes such as plant growth, secondary metabolism, stress response etc. However, MYB TFs and their regulation by non-coding RNAs (ncRNAs) in response to stress have not been studied in B. juncea. Thus, we performed a detailed study on the MYB TF family and their interactions with miRNAs and Long non coding RNAs.

RESULTS

Computational investigation of genome and proteome data presented a comprehensive picture of the MYB genes and their protein architecture, including intron-exon organisation, conserved motif analysis, R2R3 MYB DNA-binding domains analysis, sub-cellular localization, protein-protein interaction and chromosomal locations. Phylogenetically, BjuMYBs were further classified into different subclades on the basis of topology and classification in Arabidopsis. A total of 751 MYBs were identified in B. juncea corresponding to 297 1R-BjuMYBs, 440 R2R3-BjuMYBs, 12 3R-BjuMYBs, and 2 4R-BjuMYBs types. We validated the transcriptional profiles of nine selected BjuMYBs under drought stress through RT-qPCR. Promoter analysis indicated the presence of drought-responsive cis-regulatory components. Additionally, the miRNA-MYB TF interactions was also studied, and most of the microRNAs (miRNAs) that target BjuMYBs were involved in abiotic stress response and developmental processes. Regulatory network analysis and expression patterns of lncRNA-miRNA-MYB indicated that selected long non-coding RNAs (lncRNAs) acted as strong endogenous target mimics (eTMs) of the miRNAs regulated expression of BjuMYBs under drought stress.

CONCLUSIONS

The present study has established preliminary groundwork of MYB TFs and their interaction with ncRNAs in B. juncea and it will help in developing drought- tolerant Brassica crops.

A highly potential Zn biofortification tool: MTP1 in Triticum aestivum

TaMTPs belong to metal tolerance proteins (MTPs) family in common wheat and have significant potential to address the "hidden hunger" caused by inadequate dietary intake of a key micronutrient (Zn). In this study, a total of 33 MTP members in Triticum aestivum were identified, among which six TaMTP1-likes were closely related to Arabidopsis thaliana MTP1 and were designated as TaMTP1-A/B/D and TaMTP1.1-A/B/D. When heterologously expressed in yeast mutants, TaMTP1-likes complemented their hypersensitivity to Zn and Co, and three of the most metal-resistant members, TaMTP1-A, TaMTP1-D and TaMTP1.1-B, were selected for further subcellular localization and functional experiment in Arabidopsis and rice. The results showed that all three proteins were localized in the vacuole membrane, that TaMTP1-D was more resistant to Zn and less resistant to Co than other TaMTP1-like members, and that TaMTP1-D was expressed at a higher level in the endosperm than other members. All results reveal that the use of TaMTP1-D for biofortification can substantially increase the content of Zn in the edible part of wheat and avoid the overaccumulation of Co, suggesting that TaMTP1-D is a potential Zn biofortifier / bioreinforcement.

Predicting the role of β-GAL genes in bean under abiotic stress and genome-wide characterization of β-GAL gene family members

Β-Gals are a subgroup of the glycoside hydrolase (GH) family of enzymes, which possess the Glyco_hydro_35 (GH35) domain. Although studies have been conducted on the β-Gal gene family in numerous plant species, no such research has been conducted on beans. The purpose of this study was to determine the gene expression levels of β-Gal genes in the leaf tissue of P. vulgaris under salt and drought stress using quantitative real-time polymerase chain reaction (qRT-PCR) and to perform a comprehensive analysis of β-Gal gene family members using bioinformatics tools. In the bean genome, 25 Pvul-βGAL proteins with amino acid numbers ranging from 291 to 1119, molecular weights from 32.94 to 126.56 kDa, and isoelectric points from 5.46 to 9.08 were identified. Both segmental and tandem duplication have occurred in β-Gal genes in the bean genome, and Pvul-BGAL genes have been subject to negative selection in the evolutionary process. For a deeper comprehension of the evolutionary proximity of Pvul-BGAL genes, a phylogenetic tree and synteny map were drawn together with Arabidopsis thaliana and Glycine max β-Gal genes. The expression profiles of β-Gal genes in different tissues of the bean were determined in silico. In addition, the expression profiles of β-Gal genes in the leaves of bean plants subjected to drought and salt stress were analyzed, and the role of β-Gal genes in salt and drought stress was estimated. In this study, the role of β-Gal gene family in abiotic stress response and the characterization of β-Gal genes in beans were determined for the first time and will provide a basis for future functional genomics studies.

Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean

BACKGROUND

Calmodulin-binding transcription activator (CAMTA) is comprised of a group of transcription factors and plays an important role in the Ca2+ signaling pathway, mediating various molecular responses via interactions with other transcription factors and binding to the promoter region of specific genes. Mung beans (Vigna radiata) are one of the most commonly consumed commodities in Asia. To date, CAMTA proteins have not been characterized in this important crop plant.

RESULTS

Eight paralogous VrCAMTA genes were identified and found to be distributed on five of the 11 chromosomes. The proteins possessed CG-1 DNA-binding domains with bipartite NLS signals, ankyrin domains, CaM-binding IQ motifs, and CaM-binding domain (CaMBD). The 2 kb upstream regions of VrCAMTA genes contained sequence motifs of abscisic acid-responsive elements (ABRE) and ethylene-responsive elements (ERE), and binding sites for transcription factors of the bZIP and bHLH domains. Analysis of RNA-seq data from a public repository revealed ubiquitous expression of the VrCAMTA genes, as VrCAMTA1 was expressed at the highest level in seedling leaves, whereas VrCAMTA8 was expressed at the lowest level, which agreed with the RT-qPCR analysis performed on the first true leaves. On day four after leaf emergence, all VrCAMTA genes were upregulated, with VrCAMTA1 exhibiting the highest degree of upregulation. In darkness on day 4, upregulation was not observed in most VrCAMTA genes, except VrCAMTA7, for which a low degree of upregulation was found, whereas no difference was found in VrCAMTA8 expression between light and dark conditions. Treatment with calcium ionophores enhanced VrCAMTA expression under light and/or dark conditions at different times after leaf emergence, suggesting that calcium signaling is involved in the light-induced upregulation of VrCAMTA gene expression.

CONCLUSIONS

The expression dependence of nearly all VrCAMTA genes on light and calcium signaling suggests their possible differential but likely complementary roles during the early stages of mung bean growth and development.

Genome-wide analysis and expression profile of the bZIP gene family in Neopyropia yezoensis

The basic leucine zipper (bZIP) family consists of conserved transcription factors which are widely present in eukaryotes and play important regulatory roles in plant growth, development, and stress responses. Neopyropia yezoensis is a red marine macroalga of significant economic importance; however, their bZIP family members and functions have not been systematically identified and analyzed. In the present study, the bZIP gene family in Ny. yezoensis was characterized by investigating gene structures, conserved motifs, phylogenetic relationships, chromosomal localizations, gene duplication events, cis-regulatory elements, and expression profiles. Twenty-three Ny. yezoensis bZIP (NyybZIP) genes were identified and sorted into 13 out of 30 groups, which were classified based on the bZIPs of Ny. yezoensis and 15 other red algae species. Phylogenetic analysis revealed that bZIP genes may have a complex evolutionary pattern in red algae. Cross-species collinearity analysis indicated that the bZIP genes in Ny. yezoensis, Neoporphyra haitanensis, and Porphyra umbilicalis are highly evolutionarily conserved. In addition, we identified four main categories of cis-elements, including development-related, light-responsive, phytohormone-responsive and stress-responsive promoter sequences in NyybZIP genes. Finally, RNA sequencing data and quantitative real-time PCR (qRT-PCR) showed that NyybZIP genes exhibited different expression patterns depending on the life stage. NyybZIP genes were also found to be involved in the nitrogen stress response. We thought that bZIP genes may be involved in Ny. yezoensis growth and development, and play a significant role in nitrogen deficiency response. Taken together, our findings provide new insights into the roles of the bZIP gene family and provide a basis for additional research into its evolutionary history and biological functions.

Comprehensive analysis of PLATZ family genes and their responses to abiotic stresses in Barley

BACKGROUND

Plant A/T-rich protein and zinc-binding protein (PLATZ) transcription factors are pivotal regulators in various aspects of plant biology, including growth, development, and responses to environmental stresses. While PLATZ genes have been extensively studied and functionally characterized in various plants, limited information is available for these genes in barley.

RESULTS

Here, we discovered a total of 11 PLATZ genes distributed across seven chromosomes in barley. Based on phylogenetic and conserved motif analysis, we classified PLATZ into five subfamilies, comprising 3, 1, 2, 1 and 4 genes, respectively. Analysis of gene structure demonstrated that these 11 HvPLATZ genes typically possessed two to four exons. Most HvPLATZ genes were found to possess at least one ABRE cis-element in their promoter regions, and a few of them also contained LTR, CAT-box, MRE, and DRE cis-elements. Then, we conducted an exploration of the expression patterns of HvPLATZs, which displayed notable differences across various tissues and in response to abiotic stresses. Functional analysis of HvPLATZ6 and HvPLATZ8 in yeast cells showed that they may be involved in drought tolerance. Additionally, we constructed a regulatory network including miRNA-targeted gene predictions and identified two miRNAs targeting two HvPLATZs, such as hvu-miR5053 and hvu-miR6184 targeting HvPLATZ2, hvu-miR6184 targeting HvPLATZ10.

CONCLUSION

In summary, these findings provide valuable insights for future functional verification of HvPLATZs and contribute to a deeper understanding of the role of HvPLATZs in response to stress conditions in barley.

Metallothionein family genes in kiwifruit: characterization and determining their roles in plant's response to different stresses

Kiwifruit growth and development are severely affected by various biotic and abiotic stresses, especially cold stress and the bacterial disease caused by Pseudomonas syringae pv. actinidiae (Psa). Metallothioneins (MTs) are a group of cysteine-rich proteins that play crucial roles in stress response, metal detoxification, and homeostasis in plants. However, the protective role of these MTs in kiwifruit remains to be elucidated. In the present study, four AcMT genes were identified in the Hongyang kiwifruit genome, namely, two Type 2 isoforms (AcMT2 and AcMT2a) and two Type 3 isoforms (AcMT3a and AcMT3b) located separately on four different chromosomes. The hormones and stress response cis-elements within the promoter regions of these AcMTs were characterized. It was revealed that the four AcMT genes exhibited different expression patterns in different tissues: AcMT2 and AcMT2a were expressed at much higher levels in the fruit, male flower, female flower, root, and bark, while AcMT3a was expressed mainly in the fruit and AcMT3b was expressed highly in the bark. The expression patterns of these AcMT genes after exposure to Psa infection and different phytohormones, including gibberellic acid A3(GA3), ethylene (ET), and abscisic acid (ABA), were evaluated. It was revealed that in response to Psa infection, the main AcMTs in each tissue (those with expression levels higher compared to the other MTs in that tissue) were downregulated during the early stage in kiwifruits, followed by a recovery phase. In addition, most AcMTs were downregulated after exposure to ET and GA3, while type 2 AcMTs (AcMT2 and AcMT2a) were upregulated after treatment with ABA. The overexpression of AcMTs in Escherichia coli presented a higher tolerance to H2O2, heavy metals, low temperature, and high temperature. Collectively, these findings demonstrated the protective roles of AcMTs in terms of stress resistance conferred through plant hormone-related signal pathways.

Genome-wide identification of rice CXE gene family and mining of alleles for potential application in rice improvement

Carboxylesterases (CXE, EC 3.1.1.1), a class of hydrolases with an α/β folding domain, play important roles in plant growth and development and stress response. Here, we identified 32, 63, 41, and 45 CXE genes in Oryza sativa Japonica (Nipponbare), Oryza sativa Indica (93-11), Oryza sativa Indica (Xian-1B1 var.IR64), and Oryza sativa Japonica (Geng-sbtrp var.ChaoMeo), respectively. Then, we analyzed the chromosomal location, physical and chemical properties, subcellular localization, collinearity, and selection pressure of CXE genes in four rice varieties. We also analyzed the functional interaction network, cis-regulatory elements, evolutionary relationship, and protein tertiary structure, and performed gene expression profiling and qPCR verification under abiotic stress, as well as diversity analysis of 3010 gene-CDS-haplotype (gcHap) rice samples, aiming to understand the potential function of the 32 OsCXE genes. Our results indicated that fragment replication is the main reason for amplification of the CXE gene family in rice, and the gene family has undergone strong purification selection. OsCXE3.1, OsCXE3.2, OsCXE3.3, OsCXE5.1, and OsCXE7.3 may be used to improve the tolerance of rice to abiotic stress. OsCXE play important roles in rice population differentiation and improvement, and the major gcHaps at most OsCXE locus are significantly associated with yield traits. Therefore, natural variations of most OsCXE locus have great potential value for improvement of rice productivity.

Genome-Wide Identification of the Maize Chitinase Gene Family and Analysis of Its Response to Biotic and Abiotic Stresses

BACKGROUND/OBJECTIVES

Chitinases, enzymes belonging to the glycoside hydrolase family, play a crucial role in plant growth and stress response by hydrolyzing chitin, a natural polymer found in fungal cell walls. This study aimed to identify and analyze the maize chitinase gene family, assessing their response to various biotic and abiotic stresses to understand their potential role in plant defense mechanisms and stress tolerance.

METHODS

We employed bioinformatics tools to identify 43 chitinase genes in the maize B73_V5 genome. These genes were characterized for their chromosomal positions, gene and protein structures, phylogenetic relationships, functional enrichment, and collinearity. Based on previous RNA-seq data, the analysis assessed the expression patterns of these genes at different developmental stages and under multiple stress conditions.

RESULTS

The identified chitinase genes were unevenly distributed across maize chromosomes with a history of tandem duplications contributing to their divergence. The ZmChi protein family was predominantly hydrophilic and localized mainly in chloroplasts. Expression analysis revealed that certain chitinase genes were highly expressed at specific developmental stages and in response to various stresses, with ZmChi31 showing significant responsiveness to 11 different abiotic and biotic stresses.

CONCLUSIONS

This study provides new insights into the role of chitinase genes in maize stress response, establishing a theoretical framework for exploring the molecular basis of maize stress tolerance. The identification of stress-responsive chitinase genes, particularly ZmChi31, offers potential candidates for further study in enhancing maize resistance to environmental challenges.

Genome-Wide Identification of the RALF Gene Family and Expression Pattern Analysis in Zea mays (L.) under Abiotic Stresses

Rapid Alkalization Factor (RALF) is a signaling molecule in plants that plays a crucial role in growth and development, reproductive processes, and responses to both biotic and abiotic stresses. Although RALF peptides have been characterized in Arabidopsis and rice, a comprehensive bioinformatics analysis of the ZmRALF gene family in maize is still lacking. In this study, we identified 20 RALF genes in the maize genome. Sequence alignment revealed significant structural variation among the ZmRALF family genes. Phylogenetic analysis indicates that RALF proteins from Arabidopsis, rice, and maize can be classified into four distinct clades. Duplication events suggest that the expansion of the RALF gene family in maize primarily relies on whole-genome duplication. ZmRALF genes are widely expressed across various tissues; ZmRALF1/15/18/19 are highly expressed in roots, while ZmRALF6/11/14/16 are predominantly expressed in anthers. RNA-seq and RT-qPCR demonstrated that the expression levels of ZmRALF7, ZmRALF9, and ZmRALF13 were significantly up-regulated and down-regulated in response to PEG and NaCl stresses, respectively. Overall, our study provides new insights into the role of the RALF gene family in abiotic stress.

Genome-wide analysis of Triticum aestivum bromodomain gene family and expression analysis under salt stress

MAIN CONCLUSION

This study identified 82 wheat BRD genes, revealing both conserved evolutionary and functional characteristics across plant species and novel features specific to wheat. GTE8-12 cluster TaBRDs were found as positive response to salt stress. Bromodomain-containing proteins (BRDs) are crucial in histone acetylation "reading" and chromatin remodeling in eukaryotes. Despite some of their members showing importance in various biological processes in plants, our understanding of the BRD family in wheat (Triticum aestivum) remains limited. This study comprehensively analyzes the T. aestivum BRD (TaBRD) family. We identified 82 TaBRD genes in wheat genome encoding hydrophobic proteins with a conserved pocket structure. Phylogenetic analysis classified these genes into 16 distinct clusters, with conserved protein motifs and gene structures within clusters but diverse patterns across clusters. Gene duplication analysis revealed that whole-genome or segmental duplication events were the primary expansion mechanism for the TaBRD family, with purifying selection acting on these genes. Subcellular localization and Gene Ontology (GO) analyses indicated that TaBRD proteins are predominantly nuclear-localized and involved in transcription regulation and RNA metabolism. Promoter analysis and interaction network prediction suggested diverse regulatory mechanisms for TaBRDs. Notably, TaBRDs from the GTE8-12 cluster were enriched with cis-elements responsive to abscisic acid (ABA), methyl jasmonate (MeJA), and light, implying their involvement in physiological functions and abiotic stress responses. Expression analysis confirmed tissue-specific patterns and responsiveness to salinity stress. This comprehensive study enhances our understanding of the BRD family in higher plants and provides a foundation for developing salt-tolerant wheat varieties.

Genome-wide identification, expression analysis of the R2R3-MYB gene family and their potential roles under cold stress in Prunus sibirica

BACKGROUND

The R2R3-MYB transcription factors in plants participate in various physiological and biochemical processes and responds to various external stimuli. Prunus sibirica (known as Siberian apricot) is a drupe tree species that produces extremely high nutritional value kernels. However, it is susceptiblility to frost damage during the flowering period, results in a marked reduction in kernel yield.

RESULTS

In this study, the MYB gene family of P. sibirica (PsMYB) was systematically analyzed, and 116 R2R3-MYB genes that were distributed unevenly over eight chromosomes were ultimately screened. Phylogenetic analysis divided these 116 genes into 30 subgroups. We discovered that 37 PsMYBs had cold stress-responsive promoters, and six PsMYBs were annotated to be associated with cold response. Intraspecific homology analysis identified segmental duplication as the primary gene amplification mechanism, and homology analysis of the PsMYB genes with those of five other species revealed phylogenetic relationships with Rosaceae species. Protein interaction studies revealed collaborative regulation of the PsMYB proteins with Arabidopsis protein, and transcriptome analysis identified PsMYB genes that were highly expressed at low temperatures. Additionally, the expression levels of 22 PsMYBs in different tissue parts of P. sibirica and under different low-temperature stress conditions were evaluated using quantitative real-time PCR, with the results verifying that PsMYBs are specifically expressed in different plant parts and may be involved in the growth and development of P. sibirica species. Genes upregulated after exposure to low-temperature stress and likely involved in cold response were identified.

CONCLUSION

This study lays a foundation for understanding the molecular biology of PsMYBs in P. sibirica and provides a theoretical basis for the future study of transgenic lines with cold resistance during the flowering period of this tree.

Genome-wide profiling of bZIP transcription factors in Camelina sativa: implications for development and stress response

BACKGROUND

The bZIP transcription factor family, characterized by a bZIP domain, plays vital roles in plant stress responses and development. While this family has been extensively studied in various plant species, its specific functions in Camelina sativa (False Flax) remain underexplored.

METHODS AND RESULTS

This study identified 71 bZIP transcription factors in C. sativa, classified into nine distinct groups based on phylogenetic analysis. Subcellular localization predicted a nucleus-specific expression for these bZIPs. Analysis of GRAVY scores revealed a range from 0.469 to -1.256, indicating a spectrum from hydrophobic to hydrophilic properties. Motif analysis uncovered 10 distinct motifs, with one motif being universally present in all CsbZIPs. Conserved domain analysis highlighted several domains beyond the core bZIP domain. Protein-protein interaction predictions suggested a robust network involving CsbZIPs. Moreover, promoter analysis revealed over 60 types of cis-elements, including those responsive to stress. Expression studies through RNA-seq and Real-time RT-qPCR demonstrated high expression of CsbZIPs in roots, leaves, flowers, and stems. Specifically, CsbZIP01, CsbZIP02, CsbZIP44, and CsbZIP60 were consistently up-regulated under cold, salt, and drought stresses, whereas CsbZIP34 and CsbZIP35 were down-regulated.

CONCLUSION

This study presents the first comprehensive genome-wide profiling of bZIP transcription factors in Camelina sativa, providing novel insights into their roles in plant development and stress response mechanisms. By identifying and characterizing the bZIP gene family in C. sativa, this research offers new opportunities for improving stress tolerance and crop resilience through targeted genetic approaches, addressing key challenges in agriculture under changing environmental conditions.

Genome-wide identification of the NAC family in Hemerocallis citrina and functional analysis of HcNAC35 in response to abiotic stress in watermelon

Introduction

NAC (NAM, ATAF, and CUC) transcription factor family, one of the important switches of transcription networks in plants, functions in plant growth, development, and stress resistance. Night lily (Hemerocallis citrina) is an important horticultural perennial monocot plant that has edible, medicinal, and ornamental values. However, the NAC gene family of night lily has not yet been analyzed systematically to date.

Methods

Therefore, we conducted a genome-wide study of the HcNAC gene family and identified a total of 113 HcNAC members from the Hemerocallis citrina genome.

Results

We found that 113 HcNAC genes were unevenly distributed on 11 chromosomes. Phylogenetic analysis showed that they could be categorized into 16 instinct subgroups. Proteins clustering together exhibited similar conserved motifs and intron-exon structures. Collinearity analysis indicated that segmental and tandem duplication might contribute to the great expansion of the NAC gene family in night lily, whose relationship was closer with rice than Arabidopsis. Additionally, tissue-specific pattern analysis indicated that most HcNAC genes had relatively higher expression abundances in roots. RNA-Seq along with RT-qPCR results jointly showed HcNAC genes expressed differently under drought and salinity stresses. Interestingly, HcNAC35 was overexpressed in watermelon, and the stress resilience of transgenic lines was much higher than that of wild-type watermelon, which revealed its wide participation in abiotic stress response.

Conclusion

In conclusion, our findings provide a new prospect for investigating the biological roles of NAC genes in night lily.