Genome-wide Identification Research Articles

Genome-wide identification following functional analysis of amino acid permease and cationic amino acid transporter gene families in maize and their role in drought stress

In maize, the amino acid permease (AAP) and the cationic amino acid transporters (CAT) play a significant role in amino nitrogen (N) uptake, transport, utilization, and homeostasis. Hence, genome-wide analysis of maize AAP and CAT resulted in 24 AAP (1-24) and 14 CAT (1-14) proteins in maize having significant variation in molecular weights. Most proteins are basic and localized in the plasma membrane. AAPs and CATs showed up to 7 and 14 introns respectively. All proteins showed multiple motifs, alpha-helices, transmembrane helices (except ZmAAP23), and coiled in nature. The ZmAAP and ZmCAT promoters consisted of phytohormone, plant growth and development, and stress-related cis-elements. All genes are distributed in different chromosomes. All the above properties are consistent with the same in Arabidopsis, which represent their functional similarities. Significantly higher transcription of some AAPs and CATs in vegetative and/or reproductive tissues reveal their great potential to source-sink transport and reuptake of leaked amino N from the rhizosphere. Interestingly, some members of the above-mentioned families are also upregulated during drought stress revealing their great role in drought tolerance or acclimatization during the stress. For increasing drought tolerance, these transporters might interact with the genes regulating the turgor pressure of the guard cells for increasing stomatal closure and reducing transpiration in leaves through controlling cellular osmotic homeostasis.

Genome-Wide Identification of Calmodulin-Binding Protein 60 Gene Family and the Function of GhCBP60B in Cotton Growth and Development and Abiotic Stress Response

The calmodulin-binding protein 60 (CBP60) family is a gene family unique to plants, and its members play a crucial role in plant defense responses to pathogens and growth and development. Considering that cotton is the primary source of natural cotton textile fiber, the functional study of its CBP60 gene family members is critical. In this research, we successfully identified 162 CBP60 members from the genomes of 21 species. Of these, 72 members were found in four cotton species, divided into four clades. To understand the function of GhCBP60B in cotton in depth, we conducted a detailed analysis of its sequence, structure, cis-acting elements, and expression patterns. Research results show that GhCBP60B is located in the nucleus and plays a crucial role in cotton growth and development and response to salt and drought stress. After using VIGS (virus-induced gene silencing) technology to conduct gene silencing experiments, we found that the plants silenced by GhCBP60B showed dwarf plants and shortened stem nodes, and the expression of related immune genes also changed. In further abiotic stress treatment experiments, we found that GhCBP60B-silenced plants were more sensitive to drought and salt stress, and their POD (peroxidase) activity was also significantly reduced. These results imply the vital role of GhCBP60B in cotton, especially in regulating plant responses to drought and salt stress. This study systematically analyzed CBP60 gene family members through bioinformatics methods and explored in depth the biological function of GhCBP60B in cotton. These research results lay a solid foundation for the future use of the GhCBP60B gene to improve cotton plant type and its drought and salt resistance.

Genome-wide identification and characterization of the sweet orange (Citrus sinensis) basic helix-loop-helix (bHLH) family reveals a role for CsbHLH085 as a regulator of citrus bacterial canker resistance

Citrus bacterial canker (CBC) is a harmful bacterial disease caused by Xanthomonas citri subsp. citri (Xcc), negatively impacting citrus production worldwide. The basic helix-loop-helix (bHLH) transcription factor family plays crucial roles in plant development and stress responses. This study aimed to identify and annotate bHLH proteins encoded in the Citrus sinensis genome and explore their involvement and functional importance in regulating CBC resistance. A total of 135 putative CsbHLHs TFs were identified and categorized into 16 subfamilies. Their chromosomal locations, collinearity, and phylogenetic relationships were comprehensively analyzed. Upon Xcc strain YN1 infection, certain CsbHLHs were differentially regulated in CBC-resistant and CBC-sensitive citrus varieties. Among these, CsbHLH085 was selected for further functional characterization. CsbHLH085 was upregulated in the CBC-resistant citrus variety, was localized in the nucleus, and had a transcriptional activation activity. CsbHLH085 overexpression in Citrus significantly enhanced CBC resistance, accompanied by increased levels of salicylic acid (SA), jasmonic acid (JA), reactive oxygen species (ROS), and decreased levels of abscisic acid (ABA) and antioxidant enzymes. Conversely, CsbHLH085 virus-induced gene silencing resulted in opposite phenotypic and biochemical responses. CsbHLH085 silencing also affected the expression of phytohormone biosynthesis and signaling genes involved in SA, JA, and ABA signaling. These findings highlight the crucial role of CsbHLH085 in regulating CBC resistance, suggesting its potential as a target for biotechnological-assisted breeding citrus varieties with improved resistance against phytopathogens.

Characterization of FBA genes in potato (Solanum tuberosum L.) and expression patterns in response to light spectrum and abiotic stress

Fructose-1, 6-bisphosphate aldolase (FBA) plays vital roles in plant growth, development, and response to abiotic stress. However, genome-wide identification and structural characterization of the potato (Solanum tuberosum L.) FBA gene family has not been systematically analyzed. In this study, we identified nine StFBA gene members in potato, with six StFBA genes localized in the chloroplast and three in the cytoplasm. The analysis of gene structures, protein structures, and phylogenetic relationships indicated that StFBA genes were divided into Class I and II, which exhibited significant differences in structure and function. Synteny analysis revealed that segmental duplication events promoted the expansion of the StFBA gene family. Promoter analysis showed that most StFBA genes contained cis-regulatory elements associated with light and stress responses. Expression analysis showed that StFBA3, StFBA8, and StFBA9 showing significantly higher expression levels in leaf, stolon, and tuber under blue light, indicating that these genes may improve photosynthesis and play an important function in regulating the induction and expansion of microtubers. Expression levels of the StFBA genes were influenced by drought and salt stress, indicating that they played important roles in abiotic stress. This work offers a theoretical foundation for in-depth understanding of the evolution and function of StFBA genes, as well as providing the basis for the genetic improvement of potatoes.

Genome-wide identification and functional profile analysis of long non-coding RNAs in Avicennia marina.

Avicennia marina, known for its remarkable adaptability to the challenging coastal environment, including high salinity, tide, and anaerobic soils, holds pivotal functions in safeguarding the coastal ecosystem. Long non-coding RNAs (lncRNAs) have emerged as significant players in various natural processes of plants such as development. However, lncRNAs in A. marina remain largely unknown and uncharacterized. Here, we employed the transcriptome datasets from multiple tissues, such as root, leaf, and seed, to detect and characterize the lncRNAs of A. marina. Analyzing synthetically, we finally identified 6333 lncRNAs in the A. marina. These lncRNAs exhibited distinct features compared to messenger RNAs, including larger exons, lower guanine-cytosine contents, lower expression levels, and higher tissue specificities. Moreover, we identified thousands of tissue-specific lncRNAs across the examined tissues and further found that these tissue-specific lncRNAs were significantly enriched in biological processes related to the major functions of their corresponding tissues. For instance, leaf-specific lncRNAs showed prominent enrichment in photosynthesis, oxidation-reduction processes, and light harvesting. By providing a comprehensive dataset and functional annotations for A. marina lncRNAs, this study offers a valuable overview of lncRNAs in A. marina and lays the fundamental foundation for further functional exploring of them.

Two maize homologs of mammalian proton-coupled folate transporter, ZmMFS_1–62 and ZmMFS_1–73, are essential to salt and drought tolerance

Folates are essential to the maintenance of normal life activities in almost all organisms. Proton-coupled folate transporter (PCFT), belonging to the major facilitator superfamily, is one of the three major folate transporter types widely studied in mammals. However, information about plant PCFTs is limited. Here, a genome-wide identification of maize PCFTs was performed, and two PCFTs, ZmMFS_1-62 and ZmMFS_1-73, were functionally investigated. Both proteins contained the typical 12 transmembrane helixes with N- and C-termini located in the cytoplasm, and were localized in the plasma membrane. Molecular docking analysis indicated their binding activity with folates via hydrogen bonding. Interference with ZmMFS_1-62 and ZmMFS_1-73 in maize seedlings through virus-induced gene silencing disrupted folate homeostasis, mainly in the roots, and reduced tolerance to drought and salt stresses. Moreover, a molecular chaperone protein, ZmHSP20, was found to interact with ZmMFS_1-62 and ZmMFS_1-73, and interference with ZmHSP20 in maize seedlings also led to folate disruption and increased sensitivity to drought and salt stresses. Overall, this is the first report of functional identification of maize PCFTs, which play essential roles in salt and drought stress tolerance, thereby linking folate metabolism with abiotic stress responses in maize.

Genome-wide identification and expression analysis of the cryptochromes reveal the CsCRY1 role under low-light-stress in cucumber

IntroductionLow-light-stress is a common meteorological disaster that can result in slender seedlings. The photoreceptors play a crucial role in perceiving and regulating plants' tolerance to low-light-stress. However, the low-light-stress tolerance of cucumber has not been effectively evaluated, and the functions of these photoreceptor genes in cucumber, particularly under low-light-stress conditions, are not clear.MethodsHerein, we evaluated the growth characteristics of cucumber seedlings under various LED light treatment. The low-light-stress tolerant cucumber CR and intolerant cucumber CR were used as plant materials for gene expression analysis, and then the function of CsCRY1 was analyzed.ResultsThe results revealed that light treatment below 40 μmol m-2 s-1 can quickly and effectively induce low-light-stress response. Then, cucumber CR exhibited remarkable tolerance to low-light-stress was screened. Moreover, a total of 11 photoreceptor genes were identified and evaluated. Among them, the cryptochrome 1 (CRY1) had the highest expression level and was only induced in the low-light sensitive cucumber CS. The transcript CsaV3_3G047490.1 is predicted to encode a previously unknown CsCRY1 protein, which lacks 70 amino acids at its C-terminus due to alternative 5′ splice sites within the final intron of the CsCRY1 gene.DiscussionCRY1 is a crucial photoreceptor that plays pivotal roles in regulating plants' tolerance to low-light stress. In this study, we discovered that alternative splicing of CsCRY1 generates multiple transcripts encoding distinct CsCRY1 protein variants, providing valuable insights for future exploration and utilization of CsCRY1 in cucumber.

Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis)

BackgroundThe Auxin Responsive Factor (ARF) family plays a crucial role in mediating auxin signal transduction and is vital for plant growth and development. However, the function of ARF genes in Korean pine (Pinus koraiensis), a conifer species of significant economic value, remains unclear.ResultsThis study utilized the whole genome of Korean pine to conduct bioinformatics analysis, resulting in the identification of 13 ARF genes. A phylogenetic analysis revealed that these 13 PkorARF genes can be classified into 4 subfamilies, indicating the presence of conserved structural characteristics within each subfamily. Protein interaction prediction indicated that Pkor01G00962.1 and Pkor07G00704.1 may have a significant role in regulating plant growth and development as core components of the PkorARFs family. Additionally, the analysis of RNA-seq and RT-qPCR expression patterns suggested that PkorARF genes play a crucial role in the development process of Korean pine.ConclusionPkor01G00962.1 and Pkor07G00704.1, which are core genes of the PkorARFs family, play a potentially crucial role in regulating the fertilization and developmental process of Korean pine. This study provides a valuable reference for investigating the molecular mechanism of embryonic development in Korean pine and establishes a foundation for cultivating high-quality Korean pine.

Genome-wide identification of Shaker K+ channel family in Nicotiana tabacum and functional analysis of NtSKOR1B in response to salt stress

Soil salinization poses a mounting global ecological and environmental threat. The identification of genes responsible for negative regulation of salt tolerance and their utilization in crop improvement through gene editing technologies emerges as a swift strategy for the effective utilization of saline-alkali lands. One efficient mechanism of plant salt tolerance is maintaining the proper intracellular K+/Na+ ratio. The Shaker K+ channels play a crucial role in potassium absorption, transport, and intracellular potassium homeostasis in plant cells. Here, the study presents the first genome-wide identification of Shaker K+ channels in Nicotiana tabacum L., along with a detailed bioinformatic analysis of the 20 identified members. Transcriptome analysis revealed a significant up-regulation of NtSKOR1B, an outwardly-rectifying member predominantly expressed in the root tissue of tobacco seedlings, in response to salt stress. This finding was then confirmed by GUS staining of ProNtSKOR1B::GUS transgenic lines and RT-qPCR analysis. Subsequently, NtSKOR1B knockout mutants (ntskor1) were then generated and subjected to salt conditions. It was found that ntskor1 mutants exhibit enhanced salt tolerance, characterized by increased biomass, higher K+ content and elevated K+/Na+ ratios in both leaf and root tissues, compared to wild-type plants. These results indicate that NtSKOR1B knockout inhibits K+ efflux in root and leaf tissues of tobacco seedlings under salt stress, thereby maintaining higher K+/Na+ ratios within the cells. Thus, our study identifies NtSKOR1B as a negative regulator of salt tolerance in tobacco seedlings.

Genome-Wide Identification of the WRKY Gene Family and Functional Characterization of CpWRKY5 in Cucurbita pepo

The WRKY gene family is crucial for regulating plant growth and development. However, the WRKY gene is rarely studied in naked kernel formation in hull-less Cucurbita pepo L. (HLCP), a natural mutant that lacks the seed coat. In this research, 76 WRKY genes were identified through bioinformatics-based methods in C. pepo, and their phylogenetics, conserved motifs, synteny, collinearity, and temporal expression during seed coat development were analyzed. The results showed that 76 CpWRKYs were identified and categorized into three main groups (I−III), with Group II further divided into five subgroups (IIa−IIe). Moreover, 31 segmental duplication events were identified in 49 CpWRKY genes. A synteny analysis revealed that C. pepo shared more collinear regions with cucumber than with melon. Furthermore, quantitative RT-PCR (qRT-PCR) results indicated the differential expression of CpWRKYs across different varieties, with notable variations in seed coat development between HLCP and CP being attributed to differences in CpWRKY5 expression. To investigate this further, CpWRKY5-overexpression tobacco plants were generated, resulting in increased lignin content and an upregulation of related genes, as confirmed by qRT-PCR. This study offers valuable insights for future functional investigations of CpWRKY genes and presents novel information for understanding the regulation mechanism of lignin synthesis.

Genome-Wide Identification and Analysis of the EIN3/EIL Transcription Factor Gene Family in Doubled Haploid (DH) Poplar.

Ethylene (ET) is an important phytohormone that regulates plant growth, development and stress responses. The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) transcription factor family, as a key regulator of the ET signal transduction pathway, plays an important role in regulating the expression of ET-responsive genes. Although studies of EIN3/EIL family members have been completed in many species, their role in doubled haploid (DH) poplar derived from another culture of diploid Populus simonii × P. nigra (donor tree, DT) remains ambiguous. In this study, a total of seven EIN3/EIL gene family members in the DH poplar genome were identified. Basic physical and chemical property analyses of these genes were performed, and these proteins were predicted to be localized to the nucleus. According to the phylogenetic relationship, EIN3/EIL genes were divided into two groups, and the genes in the same group had a similar gene structure and conserved motifs. The expression patterns of EIN3/EIL genes in the apical buds of different DH poplar plants were analyzed based on transcriptome data. At the same time, the expression patterns of PsnEIL1, PsnEIN3, PsnEIL4 and PsnEIL5 genes in different tissues of different DH plants were detected via RT-qPCR, including the apical buds, young leaves, functional leaves, xylem, cambium and roots. The findings presented above indicate notable variations in the expression levels of PsnEIL genes across various tissues of distinct DH plants. Finally, the PsnEIL1 gene was overexpressed in DT, and the transgenic plants showed a dwarf phenotype, indicating that the PsnEIL1 gene was involved in regulating the growth and development of poplar. In this study, the EIN3/EIL gene family of DH poplar was analyzed and functionally characterized, which provides a theoretical basis for the future exploration of the EIN3/EIL gene function.

Genome-Wide Identification and Characterization of Tea SGR Family Members Reveal Their Potential Roles in Chlorophyll Degradation and Stress Tolerance

Photosynthesis plays vital roles in plant growth and development. Stay-green (SGR) proteins are responsible for chlorophyll degradation and photosynthetic metabolism. To identify SGR family members and determine their potential functions in tea plants, we identified and cloned three SGR genes. Phylogenetic analysis revealed that the tea SGR homologs were classified into the SGR subfamily (named CsSGR1 and CsSGR2) and the SGRL subfamily (named CsSGRL). Cis-element analysis indicated that the promoters of CsSGR1, CsSGR2 and CsSGRL contained light-, phytohormone- and stress-related elements. Subcellular localization confirmed that CsSGR1 was localized in the chloroplast, while CsSGR2 and CsSGRL were localized in the chloroplast, membrane and nucleus. The RT-qPCR results showed that the three genes in the matures of albino tea cultivars were expressed higher than in the green tea cultivar. However, only CsSGR2-overexpressing tobacco leaves exhibited a yellowish phenotype and significantly lower Fv/Fm values. CsSGR1 and CsSGR2 exhibited similar expression patterns in different tissues after infection with the pathogen Colletotrichum camelliae, which was opposite to the pattern observed for CsSGRL. In addition, CsSGR1 was significantly induced in response to cold stress, SA, JA and ABA in C. camelliae. These findings identified valuable candidate genes for elucidating the mechanism of leaf albinism, stress response and phytohormone signaling in tea plants.

The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis.

The F-box proteins in fungi perform diverse functions including regulation of cell cycle, circadian clock, development, signal transduction and nutrient sensing. Genome-wide analysis revealed 10 F-box genes in Puccinia triticina, the causal organism for the leaf rust disease in wheat and were characterized using in silico approaches for revealing phylogenetic relationships, gene structures, gene ontology, protein properties, sequence analysis and gene expression studies. Domain analysis predicted functional domains like WD40 and LRR at C-terminus along with the obvious presence of F-box motif in N-terminus. MSA showed amino acid replacements, which might be due to nucleotide substitution during replication. Phylogenetic analysis revealed the F-box proteins with similar domains to be clustered together while some sequences were spread out in different clades, which might be due to functional diversity. The clustering of Puccinia triticina GG705409 with Triticum aestivum TaAFB4/TaAFB5 in a single clade suggested the possibilities of horizontal gene transfer during the coevolution of P. triticina and wheat. Gene ontological annotation categorized them into three classes and were functionally involved in protein degradation through the protein ubiquitination pathway. Protein-protein interaction network revealed F-box proteins to interact with other components of the SCF complex involved in protein ubiquitination. Relative expression analysis of five F-box genes in a time course experiment denoted their involvement in leaf rust susceptible wheat plants. This study provides information on structure elucidation of F-box proteins of a basidiomycetes plant pathogenic fungi and their role during pathogenesis.

Genome-wide identification of oleosin family and expression analysis in response to abiotic stresses in balloon flower (Platycodon grandiflorus)

Genome-wide identification of oleosin family and expression analysis in response to abiotic stresses in balloon flower (<i>Platycodon grandiflorus</i>)

Genome-Wide Identification and Expression Analysis of TGA Family Genes Associated with Abiotic Stress in Sunflowers (Helianthus annuus L.).

Sunflower (Helianthus annuus L.) is an important, substantial global oil crop with robust resilience to drought and salt stresses. The TGA (TGACG motif-binding factor) transcription factors, belonging to the basic region leucine zipper (bZIP) family, have been implicated in orchestrating multiple biological processes. Despite their functional significance, a comprehensive investigation of the TGA family's abiotic stress tolerance in sunflowers remains elusive. In the present study, we identified 14 TGA proteins in the sunflower genome, which were unequally distributed across 17 chromosomes. Employing phylogenetic analysis encompassing 149 TGA members among 13 distinct species, we revealed the evolutionary conservation of TGA proteins across the plant kingdom. Collinearity analysis suggested that both HaTGA01 and HaTGA03 were generated due to HaTGA08 gene duplication. Notably, qRT-PCR analysis demonstrated that HaTGA04, HaTGA05, and HaTGA14 genes were remarkably upregulated under ABA, MeJA, and salt treatments, whereas HaTGA03, HaTGA06, and HaTGA07 were significantly repressed. This study contributes valuable perspectives on the potential roles of the HaTGA gene family under various stress conditions in sunflowers, thereby enhancing our understanding of TGA gene family dynamics and function within this agriculturally significant species.

Genome-wide identification and expression analysis of the ALDH gene family and functional analysis of PaALDH17 in Prunus avium

Genome-wide identification and expression analysis of the ALDH gene family and functional analysis of PaALDH17 in Prunus avium

Exploring the guardian of abiotic stress: Genome-wide identification of the basic helix-loop-helix transcription factor family in Juglans mandshurica

The Basic helix-loop-helix (bHLH) transcription factors are wildly involved in many physiological processes in plants, such as tissue/organ development, metabolite synthesis, signal transduction and abiotic stress response. However, the structure, characteristics, and functions of bHLH genes remain unknown in Juglans mandshurica. This study identified 118 bHLH gene family members using a genome-wide database and classified into 16 subfamilies. Gene structure and conserved motifs analysis revealed that the protein structure of each JmbHLH subfamily was relatively conserved. Four pairs of tandem replication genes (JmbHLH015-JmbHLH016, JmbHLH022-JmbHLH023-JmbHLH024, JmbHLH092-JmbHLH093, and JmbHLH108-JmbHLH109) were identified, which could explain the functional diversity of JmbHLH genes. The Ka/Ks values of the intraspecific collinear gene pairs were less than 1, indicating that the genes were relatively conserved during evolution. Protein interaction network analysis predicted the key genes in the JmbHLH functional network. JmbHLH genes that regulate tissues/organs development and light stress were screened using transcriptomic data, the expression pattern of JmbHLH genes differed significantly. Additionally, twelve JmbHLH genes were expressed differently under drought, salt, and cadmium stress, demonstrating that these genes may have multiple biological functions. The results provide new insights into the characteristics and regulatory functions of JmbHLH genes in J. mandshurica.

Genome-Wide Identification and Expression Analysis of YTH Gene Family for Abiotic Stress Regulation in Camellia chekiangoleosa.

N6-methyladenosine (m6A) is essential for RNA metabolism in cells. The YTH domain, conserved in the kingdom of Eukaryotes, acts as an m6A reader that binds m6A-containing RNA. In plants, the YTH domain is involved in plant hormone signaling, stress response regulation, RNA stability, translation, and differentiation. However, little is known about the YTH genes in tea-oil tree, which can produce edible oil with high nutritional value. This study aims to identify and characterize the YTH domains within the tea-oil tree (Camellia chekiangoleosa Hu) genome to predict their potential role in development and stress regulation. In this study, 10 members of the YTH family containing the YTH domain named CchYTH1-10 were identified from C. chekiangoleosa. Through analysis of their physical and chemical properties and prediction of subcellular localization, it is known that most family members are located in the nucleus and may have liquid-liquid phase separation. Analysis of cis-acting elements in the CchYTH promoter region revealed that these genes could be closely related to abiotic stress and hormones. The results of expression profiling show that the CchYTH genes were differentially expressed in different tissues, and their expression levels change under drought stress. Overall, these findings could provide a foundation for future research regarding CchYTHs in C. chekiangoleosa and enrich the world in terms of epigenetic mark m6A in forest trees.

Genome-wide identification and characterization of flavonol synthase (FLS) gene family in Brassica vegetables and their roles in response to biotic and abiotic stresses

Flavonol synthase (FLS) serves as a pivotal enzyme in the flavonol biosynthesis pathway, contributing to the abundance of flavonol compounds found in Brassica vegetables. Nevertheless, there are limited investigations on the identification and analysis of FLS gene family and their precise roles in responding to biotic and abiotic stresses remain elusive in Brassica vegetables. Herein, a total of 6 (Brassica rapa), 9 (Brassica oleracea), and 14 (Brassica napus) FLS genes were identified and distributed on 4, 5, and 8 chromosomes, respectively. Notably, while FLS genes exhibited considerable variation in sequence, exon-intron structure, and molecular weight, they displayed highly conserved domain and motif compositions. Of the six identified BrFLSs, namely BrFLS1, BrFLS2, BrFLS3.1, BrFLS3.2, BrFLS3.3, and BrFLS4, all were located in the nucleus and cell membrane except for BrFLS4 exclusively in the nucleus. Specifically, BrFLS1, BrFLS3.2, and BrFLS3.3 showed up-regulation after 6-BA, ABA, BR, and GA3 treatments, while BrFLS2 exhibited down-regulation. Intriguingly, BrFLS members displayed distinct expression patterns under diverse abiotic and biotic stresses. Employing the virus-induced gene silencing (VIGS) technology, we validated BrFLS1/BrFLS3.2, BrFLS1/BrFLS3.3, BrFLS2, BrFLS1, and BrFLS1/BrFLS2/BrFLS3.1/BrFLS3.3 as vital candidate genes, contributing to the flavonol biosynthesis pathway under drought, salt, high temperature, low temperature, and anthracnose stresses in Brassica vegetables, respectively, and they enhanced their resistance to stresses by bolstering antioxidant capacity. Overall, our findings shed light on the biological roles of FLS gene family in the flavonoid biosynthesis pathway, offering valuable genetic resources for crop enhancement.

Genome-wide identification and expression analysis of the Nitrile-specifier proteins (NSPs) in Brassica napus

The complete exploitation of Brassica napus plants is a study hotspot, since it is an essential oil crop that is widely cultivated across the world. Glucosinolate is a unique secondary metabolite in the Brassicaceae family, and its content has a substantial influence on rapeseed development and quality. Its degradation products have various physiological functions, among which Nitrile specific proteins (NSPs) can hydrolyze glucosinolate and hence influence the balance of plant immunity and growth. However, the related gene families in B. napus have not been investigated. Here, 72 NSP family members were discovered and described in B. napus based on their sequence structures, physiological correlations, phonological locations, and expression levels. According to collinearity studies, the NSP proteins in B. napus and A. thaliana are closely related. Analysis of BnNSP expression patterns in various tissues revealed that BnNSPs exhibit high tissue specificity, implying that BnNSPs may play distinguish functions in various developmental phases. We discovered that NSPs may be regulated by hormones such as abscisic acid (ABA), gibberellin (GA), and metallic jasmonate (MeJA) based on the expression of NSPs during hormone treatment. The results provide valuable information for the future functional characterization of BnNSP genes.