Genome-wide Expression Analysis Research Articles

Genome-Wide Identification and Expression Analysis of SNAP Gene Family in Wheat

Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution, physicochemical properties, conserved motifs, and cis-acting elements of the TaSNAP family members. Results: The TaSNAP family comprises members that encode proteins ranging between 120 and 276 amino acids, with isoelectric points spanning from 4.87 to 7.92. Phylogenetic analysis elucidated the categorization of the eight TaSNAP into three distinct subfamilies, wherein members of the same subfamily display marked similarities in their gene structures. Chromosomal mapping revealed the distribution of TaSNAP family members across chromosomes 2A, 2B, 2D, 7A, 7B, and 7D. Utilizing the Plant CARE tool, we identified ten elements linked to plant hormones and four associated with stress responses. Expression analysis via qRT-PCR was performed to assess the levels of the eight TaSNAP genes in various tissues and under diverse abiotic stress conditions. The results indicated heightened expression of most genes in roots compared to spikes. Notably, under ABA stress, the majority of genes exhibited upregulation, whereas certain genes were downregulated under PEG stress, implying a substantial role for SNAP protein in wheat growth and development. Conclusions: This study conducted a comprehensive bioinformatics analysis of each member of the wheat SNAP family, laying a crucial foundation for future functional investigations.

The Role of PLATZ6 in Raffinose Family Oligosaccharides Loading of Leaves via PLATZ Family Characterization in Cucumber

The plant AT protein and zinc-binding protein (PLATZ) genes, a novel cluster of plant-specific zinc-finger-dependent DNA-binding proteins, play a crucial role in regulating stress response and plant development. However, there has been little study focus on the role of the cucumber PLATZ family in assimilating loading in leaves. (1) In this study, a total of 12 PLATZ genes were identified from the cucumber genome. The cucumber PLATZ genes were clustered into five groups, and unevenly distributed on five chromosomes. A single pair of cucumber PLATZ genes underwent segmental duplication. (2) The results of genome-wide expression analysis suggested that the cucumber PLATZ genes were widely expressed in a wide range of cucumber tissues, with three PLATZ (PLATZ2, PLATZ6, and PLATZ12) genes exhibiting high expression in the vascular tissues of cucumber leaves. PLATZ2, PLATZ6, and PLATZ12 proteins were primarily located in cytomembrane and nucleus. (3) In VIGS-PLATZ6 plants, the expression of Galactinol synthase 1 (GolS1) and STACHYOSE SYNTHASE (STS), two genes involved in the synthesis of raffinose family oligosaccharides (RFOs) were observed to be decreased in cucumber leaves. In conclusion, the comprehensive analysis of the cucumber PLATZ family and the preliminary functional verification of PLATZ6 lay the foundation for the molecular and physiological functions of cucumber PLATZ genes.

Genome-Wide Identification and Expression Analysis of the BTB Gene Superfamily Provides Insight into Sex Determination and Early Gonadal Development of Alligator sinensis

The BTB gene superfamily is widely distributed among higher eukaryotes and plays a significant role in numerous biological processes. However, there is limited knowledge about the structure and function of BTB genes in the critically endangered species Alligator sinensis, which is endemic to China. A total of 170 BTB genes were identified from the A. sinensis genome, classified into 13 families, and unevenly distributed across 16 chromosomes. Analysis of gene duplication events yielded eight pairs of tandem duplication genes and six pairs of segmental duplication genes. Phylogenetics shows that the AsBTB genes are evolutionarily conserved. The cis-regulatory elements in the AsBTB family promoter region reveal their involvement in multiple biological processes. Protein interaction network analysis indicates that the protein interactions of the AsBTB genes are centered around CLU-3, mainly participating in the regulation of biological processes through the ubiquitination pathway. The expression profile and protein interaction network analysis of AsBTB genes during sex differentiation and early gonadal development indicate that AsBTB genes are widely expressed in this process and involves numerous genes and pathways for regulation. This study provides a basis for further investigation of the role of the BTB gene in sex differentiation and gonadal development in A. sinensis.

Genome-wide characterization and expression analysis of WRKY transcription factors reveals biotic stress response potential mechanisms in Panax notoginseng

WRKY transcription factors (TFs), among the largest families of transcriptional regulators, are essential players in defense responses in plants. Panax notoginseng, a traditional and precious herbal medicine in China, is widely cultivated due to its excellent medicinal and edible value. However, P. notoginseng is frequently affected by various diseases (like Black blot disease, Root rot disease and Viral diseases). Therefore, the present study aimed to identify and characterize PnWRKYs in the P. notoginseng genome, reveal their structural attributes, regulatory elements, and potential functions in defense responses. 68 PnWRKY TFs that have conserved domains and different physicochemical characteristics were identified in the genome. They can be divided into four groups according to phylogenetic relationships and conserved domain structures. Furthermore, Group II WRKY TFs can be classified into five subgroups (IIa, IIb, IIc, IId, and IIe) according to their zinc finger-like motif. The PnWRKY family expands mainly via segmental duplication. Additionally, the promoter regions of PnWRKYs contain many hormone-responsive and stress-responsive elements. Expression patterns under different hormones (salicylic acid, methyl jasmonate, and melatonin) and disease (root rot disease, black blot disease, and virus disease) treatment analysis highlighted their wide involvement in plant hormone-induced disease defense responses. These findings affirmed the potential functions of PnWRKY TFs in disease-mediated defense responses and provided valuable insights for future agricultural applications.

Genome-wide identification and expression analysis of SlKFB gene family (Solanum lycopersicum) and the molecular mechanism of SlKFB16 and SlKFB34 under drought

Environmental stress significantly affects plant growth and productivity. The effects of drought stress on plants are reflected primarily in enzyme activity, membrane systems, and cell-water loss. Here, the Kelch repeat F-box (KFB) protein family in tomato was systematically identified and analysed. Using bioinformatics, we identified 37 SlKFB family members in the tomato genome and analysed their protein structure, phylogenetic relationships, chromosome distribution, and expression under drought or biotic-stress conditions. Transcriptome data revealed that SlKFB members exhibit differential responses to drought stress, with significant differences in SlKFB16 and SlKFB34 expression. Functional analysis revealed that SlKFB16 functions in the cytoplasm and SlKFB34 in the nucleus and cytoplasm. Under drought stress, SlKFB16 and SlKFB34-silencing significantly reduced reactive oxygen species scavenging and resistance to drought stress. These findings provide a reference for further studies of the mechanisms of SlKFB16 and SlKFB34 in drought stress in tomato as well as a foundation for enhancing their resistance to drought stress.

Genome-wide identification and expression analysis of the U-box gene family related to biotic and abiotic stresses in Coffea canephora L.

Plant U-box genes play an important role in the regulation of plant hormone signal transduction, stress tolerance, and pathogen resistance; however, their functions in coffee (Coffea canephora L.) remain largely unexplored. In this study, we identified 47 CcPUB genes in the C. canephora L. genome, clustering them into nine groups via phylogenetic tree. The CcPUB genes were unevenly distributed across the 11 chromosomes of C. canephora L., with the majority (11) on chromosome 2 and none on chromosome 8. The cis-acting elements analysis showed that CcPUB genes were involved in abiotic and biotic stresses, phytohormone responsive, and plant growth and development. RNA-seq data revealed diverse expression patterns of CcPUB genes across leaves, stems, and fruits tissues. qRT-PCR analyses under dehydration, low temperature, SA, and Colletotrichum stresses showed significant up-regulation of CcPUB2, CcPUB24, CcPUB34, and CcPUB40 in leaves. Furthermore, subcellular localization showed CcPUB2 and CcPUB34 were located in the plasma membrane and nucleus, and CcPUB24 and CcPUB40 were located in the nucleus. This study provides valuable insights into the roles of PUB genes in stress responses and phytohormone signaling in C. canephora L., and provided basis for functional characterization of PUB genes in C. canephora L.

Enhancing Retinoic Acid-mediated Effects Through Inhibition of CYP26A1, CYP26B1 and HGF Signaling in Neuroblastoma Cells.

Retinoic acid (RA) induces tumor cell differentiation in diseases like acute promyelocytic leukemia or high-risk neuroblastoma. However, the formation of resistant cells, which results from dysregulation of different signaling pathways, limits therapy success. The present study aimed to characterize basic regulatory processes induced by the application of RA in human neuroblastoma cells, to identify therapeutic targets independent of the often amplified oncogene MYCN. In MYCN-amplified Kelly and MYCN non-amplified SH-SY5Y cells, different assays were employed to quantify the viability and cytotoxicity, while RA-mediated expression changes were examined using genome-wide gene expression analysis followed by quantitative PCR. Enzyme-linked immunoabsorbent assays (ELISA) and western blots were used to determine the levels or activation of the examined proteins. In Kelly cells, treatment with 5 μM RA for 3 days significantly reduced the cell number due to attenuated proliferation, while SH-SY5Y cells were less responsive. An up-regulation of the RA-metabolizing enzymes CYP26A1 and CYP26B1 was observed in both cell lines, and co-treatment with the selective CYP26 inhibitor talarozole markedly decreased cell viability. When RA and ketoconazole, which inhibits CYP26 as well as RA-degrading CYP3A enzymes, were co-administered, not only cell survival was impaired in both cell lines, but also the release of hepatocyte growth factor (HGF). Accordingly, co-application of the c-Met inhibitor tepotinib and RA or ketoconazole substantially decreased cell viability. Independent of MYCN amplification, inhibitors of RA metabolism or HGF signaling might prevent the emergence of RA-resistant neuroblastoma cells when co-applied with RA.

Genome-Wide Identification and Expression Analysis of GST Genes during Light-Induced Anthocyanin Biosynthesis in Mango (Mangifera indica L.)

Anthocyanins are important secondary metabolites contributing to the red coloration of fruits, the biosynthesis of which is significantly affected by light. Glutathione S-transferases (GSTs) play critical roles in the transport of anthocyanins from the cytosol to the vacuole. Despite their importance, GST genes in mango have not been extensively characterized. In this study, 62 mango GST genes were identified and further divided into six subfamilies. MiGSTs displayed high similarity in their exon/intron structure and motif and domain composition within the same subfamilies. The mango genome harbored eleven pairs of segmental gene duplications and ten sets of tandemly duplicated genes. Orthologous analysis identified twenty-nine, seven, thirty-four, and nineteen pairs of orthologous genes among mango MiGST genes and their counterparts in Arabidopsis, rice, citrus, and bayberry, respectively. Tissue-specific expression profiling highlighted tissue-specific expression patterns for MiGST genes. RNA-seq and qPCR analyses revealed elevated expression levels of seven MiGSTs including MiDHAR1, MiGSTU7, MiGSTU13, MiGSTU21, MiGSTF3, MiGSTF8, and MiGSTF9 during light-induced anthocyanin accumulation in mango. This study establishes a comprehensive genetic framework of MiGSTs in mango fruit and their potential roles in regulating anthocyanin accumulation, which is helpful in developing GST-derived molecular markers and speeding up the process of breeding new red-colored mango cultivars.

Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis

Understanding breast cancer genetic risk relies on identifying causal variants and candidate target genes in risk loci identified by genome-wide association studies (GWAS), which remains challenging. Since most loci fall in active gene regulatory regions, we developed a novel approach facilitated by pinpointing the variants with greater regulatory potential in the disease’s tissue of origin. Through genome-wide differential allelic expression (DAE) analysis, using microarray data from 64 normal breast tissue samples, we mapped the variants associated with DAE (daeQTLs). Then, we intersected these with GWAS data to reveal candidate risk regulatory variants and analysed their cis-acting regulatory potential. Finally, we validated our approach by extensive functional analysis of the 5q14.1 breast cancer risk locus. We observed widespread gene expression regulation by cis-acting variants in breast tissue, with 65% of coding and noncoding expressed genes displaying DAE (daeGenes). We identified over 54 K daeQTLs for 6761 (26%) daeGenes, including 385 daeGenes harbouring variants previously associated with BC risk. We found 1431 daeQTLs mapped to 93 different loci in strong linkage disequilibrium with risk-associated variants (risk-daeQTLs), suggesting a link between risk-causing variants and cis-regulation. There were 122 risk-daeQTL with stronger cis-acting potential in active regulatory regions with protein binding evidence. These variants mapped to 41 risk loci, of which 29 had no previous report of target genes and were candidates for regulating the expression levels of 65 genes. As validation, we identified and functionally characterised five candidate causal variants at the 5q14.1 risk locus targeting the ATG10 and ATP6AP1L genes, likely acting via modulation of alternative transcription and transcription factor binding. Our study demonstrates the power of DAE analysis and daeQTL mapping to identify causal regulatory variants and target genes at breast cancer risk loci, including those with complex regulatory landscapes. It additionally provides a genome-wide resource of variants associated with DAE for future functional studies.

Genome-Wide Identification, Expression Analysis, and Transcriptome Analysis of the NPF Gene Family under Various Nitrogen Conditions in Eucalyptus grandis

Genome-Wide Identification, Expression Analysis, and Transcriptome Analysis of the NPF Gene Family under Various Nitrogen Conditions in Eucalyptus grandis

Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package

Background/Objectives: We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature. This tool is applicable to all ploidy levels; we notably provide functionalities to facilitate the visualisation of GWAS results obtained for autotetraploid organisms with the GWASpoly package. Results: We illustrate the capabilities of hidecan with examples from two autotetraploid potato datasets. Conclusions: The hidecan package is implemented in R and is publicly available on the CRAN repository and on GitHub. A description of the package, as well as a detailed tutorial, is made available alongside the package. It is also part of the VIEWpoly tool for the visualisation and exploration of results from polyploids computational tools.

Genome-Wide Identification and Expression Analysis of the Cyclic Nucleotide-Gated Channel Gene Family in Zoysia japonica under Salt Stress.

Salt stress severely inhibits plant growth. Understanding the mechanism of plant salt tolerance is highly important to improving plant salt tolerance. Previous studies have shown that nonselective cyclic nucleotide-gated ion channels (CNGCs) play an important role in plant salt tolerance. However, current research on CNGCs mainly focuses on CNGCs in glycophytic plants, and research on CNGCs in halophytes that exhibit special salt tolerance strategies is still scarce. This study used the halophilic plant Zoysia japonica, an excellent warm-season turfgrass, as the experimental material. Through bioinformatics analysis, 18 members of the CNGC family were identified in Zoysia japonica; they were designated ZjCNGC1 through ZjCNGC18 according to their scaffold-level chromosomal positions. ZjCNGCs are divided into four groups (I-IV), with the same groups having differentiated protein-conserved domains and gene structures. ZjCNGCs are unevenly distributed on 16 scaffold-level chromosomes. Compared with other species, the ZjCNGCs in Group III exhibit obvious gene expansion, mainly due to duplication of gene segments. The collinearity between ZjCNGCs, OsCNGCs, and SjCNGCs suggests that CNGCs are evolutionarily conserved among gramineous plants. However, the Group III ZjCNGCs are only partially collinear with OsCNGCs and SjCNGCs, implying that the expansion of Group III ZjCNGC genes may have been an independent event occurring in Zoysia japonica. Protein interaction prediction revealed that ZjCNGCs, calcium-dependent protein kinase, H+-ATPase, outwardly rectifying potassium channel protein, and polyubiquitin 3 interact with ZjCNGCs. Multiple stress response regulatory elements, including those involved in salt stress, are present on the ZjCNGC promoter. The qPCR results revealed differences in the expression patterns of ZjCNGCs in different parts of the plant. Under salt stress conditions, the expression of ZjCNGCs was significantly upregulated in roots and leaves, with ZjCNGC8 and ZjCNGC13 showing the greatest increase in expression in the roots. These results collectively suggest that ZjCNGCs play an important role in salt tolerance and that their expansion into Group III may be a special mechanism underlying the salt tolerance of Zoysia japonica.

Genome-Wide Identification and Expression Analysis of ‘NanGuo’ Pear Revealed Key MYB Transcription Factor Family Genes Involved in Anthocyanin Accumulation

The MYB gene family, widely distributed across a variety of plants, plays a crucial role in the phenylpropane metabolic pathway. In this study, we identified 146 R2R3-MYB genes in the ‘NanGuo’ pear genome by screening its gene sequences. Phylogenetic analysis divided these genes into seven subfamilies, and we examined each for stability through analyses of conserved structural domains and motifs. In addition, differences in the expression levels between two varieties, the ‘NanGuo’ pear and its red bud sport variant ‘NanHong’ pear, were investigated using quantitative real-time PCR (qRT-PCR). The results revealed that the expression levels of 12 R2R3-MYB transcription factors (TFs) corresponded with the trends in anthocyanin content. Specifically, the expression trends of eight R2R3-MYB TFs positively correlated with anthocyanin accumulation, whereas four exhibited opposite trends, suggesting their negatively regulatory role in anthocyanin accumulation. This study not only enhances our understanding of the MYB gene family in the ‘NanGuo’ pear genome but also lays a solid foundation for future research into the functional roles of PuMYBs.

Genome-Wide Identification and Expression Analysis of MYB Transcription Factor Family in Response to Various Abiotic Stresses in Coconut (Cocos nucifera L.).

Abiotic stresses such as nitrogen deficiency, drought, and salinity significantly impact coconut production, yet the molecular mechanisms underlying coconut's response to these stresses are poorly understood. MYB proteins, a large and diverse family of transcription factors (TF), play crucial roles in plant responses to various abiotic stresses, but their genome-wide characterization and functional roles in coconut have not been comprehensively explored. This study identified 214 CnMYB genes (39 1R-MYB, 171 R2R3-MYB, 2 3R-MYB, and 2 4R-MYB) in the coconut genome. Phylogenetic analysis revealed that these genes are unevenly distributed across the 16 chromosomes, with conserved consensus sequences, motifs, and gene structures within the same subgroups. Synteny analysis indicated that segmental duplication primarily drove CnMYB evolution in coconut, with low nonsynonymous/synonymous ratios suggesting strong purifying selection. The gene ontology (GO) annotation of protein sequences provided insights into the biological functions of the CnMYB gene family. CnMYB47/70/83/119/186 and CnMYB2/45/85/158/195 were identified as homologous genes linked to nitrogen deficiency, drought, and salinity stress through BLAST, highlighting the key role of CnMYB genes in abiotic stress tolerance. Quantitative analysis of PCR showed 10 CnMYB genes in leaves and petioles and found that the expression of CnMYB45/47/70/83/85/119/186 was higher in 3-month-old than one-year-old coconut, whereas CnMYB2/158/195 was higher in one-year-old coconut. Moreover, the expression of CnMYB70, CnMYB2, and CnMYB2/158 was high under nitrogen deficiency, drought, and salinity stress, respectively. The predicted secondary and tertiary structures of three key CnMYB proteins involved in abiotic stress revealed distinct inter-proteomic features. The predicted interaction between CnMYB2/158 and Hsp70 supports its role in coconut's drought and salinity stress responses. These results expand our understanding of the relationships between the evolution and function of MYB genes, and provide valuable insights into the MYB gene family's role in abiotic stress in coconut.

Genome-Wide Characterization and Expression Analysis of CsPALs in Cucumber (Cucumis sativus L.) Reveal Their Potential Roles in Abiotic Stress and Aphid Stress Tolerance.

Phenylalanine ammonia lyase (PAL) is a pivotal enzyme in the phenylalanine metabolic pathway in plants and has a crucial role in the plant's response to environmental stress. Although the PAL family has been widely studied in many plant species, limited is known about its particular role in cucumbers under stress. We investigated the physicochemical properties, gene structure, gene duplication events, conserved motifs, cis-acting elements, protein interaction networks, stress-related transcriptome data, and quantitatively validated key stress-related genes. The main results indicated that 15 PAL genes were grouped into four clades: I, II, and III when arranged in a phylogenetic tree of PAL genes in angiosperms. The analysis of the promoter sequence revealed the presence of multiple cis-acting elements related to hormones and stress responses in the cucumber PAL genes (CsPALs). The analysis of protein interaction networks suggested that CsPAL1 interacts with eight other members of the PAL family through CsELI5 and CsHISNA, and directly interacts with multiple proteins in the 4CL family. Further investigation into the expression patterns of CsPAL genes in different tissues and under various stress treatments (NaCl, Cu2+, Zn2+, PEG6000, aphids) demonstrated significant differential expression of CsPALs across cucumber tissues. In summary, our characterization of the CsPAL family offers valuable insights and provides important clues regarding the molecular mechanisms of CsPALs in managing abiotic and biotic stress interactions in cucumbers.

Genome-wide identification, characterization, and expression analysis of the transient receptor potential gene family in mandarin fish Siniperca chuatsi

BackgroundTemperature is a crucial environmental determinant for the vitality and development of teleost fish, yet the underlying mechanisms by which they sense temperature fluctuations remain largely unexplored. Transient receptor potential (TRP) proteins, renowned for their involvement in temperature sensing, have not been characterized in teleost fish, especially regarding their temperature-sensing capabilities.ResultsIn this study, a genome-wide analysis was conducted, identifying a total of 28 TRP genes in the mandarin fish Siniperca chuatsi. These genes were categorized into the families of TRPA, TRPC, TRPP, TRPM, TRPML, and TRPV. Despite notable variations in conserved motifs across different subfamilies, TRP family members shared common structural features, including ankyrin repeats and the TRP domain. Tissue expression analysis showed that each of these TRP genes exhibited a unique expression pattern. Furthermore, examination of the tissue expression patterns of ten selected TRP genes following exposure to both high and low temperature stress indicated the expression of TRP genes were responsive to temperatures changes. Moreover, the expression profiles of TRP genes in response to mandarin fish virus infections showed significant upregulation for most genes after Siniperca chuatsi rhabdovirus, mandarin fish iridovirus and infectious spleen and kidney necrosis virus infection.ConclusionsThis study characterized the TRP family genes in mandarin fish genome-wide, and explored their expression patterns in response to temperature stress and virus infections. Our work will enhance the overall understanding of fish TRP channels and their possible functions.

Genome-wide identification and expression analysis of the SPL gene family and its response to abiotic stress in barley (Hordeum vulgare L.)

BackgroundSquamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that is widely involved in the regulation of plant growth and development, including flower and grain development, stress responses, and secondary metabolite synthesis. However, this gene family has not been comprehensively evaluated in barley, the most adaptable cereal crop with a high nutritional value.ResultsIn this study, a total of 15 HvSPL genes were identified based on the Hordeum vulgare genome. These genes were named HvSPL1 to HvSPL15 based on the chromosomal distribution of the HvSPL genes and were divided into seven groups (I, II, III, V, VI, VII, and VIII) based on the phylogenetic tree analysis. Chromosomal localization revealed one pair of tandem duplicated genes and one pair of segmental duplicated genes. The HvSPL genes exhibited the highest collinearity with the monocotyledonous plant, Zea mays (27 pairs), followed by Oryza sativa (18 pairs), Sorghum bicolor (16 pairs), and Arabidopsis thaliana (3 pairs), and the fewest homologous genes with Solanum lycopersicum (1 pair). The distribution of the HvSPL genes in the evolutionary tree was relatively scattered, and HvSPL proteins tended to cluster with SPL proteins from Z. mays and O. sativa, indicating a close relationship between HvSPL and SPL proteins from monocotyledonous plants. Finally, the spatial and temporal expression patterns of the 14 HvSPL genes from different subfamilies were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the results, the HvSPL gene family exhibited tissue-specific expression and played a regulatory role in grain development and abiotic stress. HvSPL genes are highly expressed in various tissues during seed development. The expression levels of HvSPL genes under the six abiotic stress conditions indicated that many genes responded to stress, especially HvSPL8, which exhibited high expression under multiple stress conditions, thereby warranting further attention.ConclusionIn this study, 15 SPL gene family members were identified in the genome of Hordeum vulgare, and the phylogenetic relationships, gene structure, replication events, gene expression, and potential roles of these genes in millet development were studied. Our findings lay the foundation for exploring the HvSPL genes and performing molecular breeding of barley.

Genome-wide investigation of the PIF gene family in alfalfa (Medicago sativa L.) expression profiles during development and stress

BackgroundPhytochrome-interacting factors (PIFs) plays an important role in plants as hubs for intracellular signaling regulation. The PIF gene family has been identified and characterized in many plants, but alfalfa (Medicago sativa L.), an important perennial high-quality legume forage, has not been reported on the PIF gene family.ResultsIn this study, we presented the identification and characterization of five MsPIF genes in alfalfa (Medicago sativa L.). Phylogenetic analysis indicated that PIFs from alfalfa and other four plant species could be divided into three groups supported by similar motif analysis. The collinearity analysis of the MsPIF gene family showed the presence of two gene pairs, and the collinearity analysis with AtPIFs showed three gene pairs, indicating that the evolutionary process of this family is relatively conservative. Analysis of cis-acting elements in promoter regions of MsPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Gene expression analyses demonstrated that MsPIFs were primarily expressed in the leaves and were induced by various abiotic stresses.ConclusionThis study conducted genome-wide identification, evolution, synteny analysis, and expression analysis of the PIFs in alfalfa. Our study lays a foundation for the study of the biological functions of the PIF gene family and provides a useful reference for improving abiotic stress resistance in alfalfa.

Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum.

CINNAMYL ALCOHOL DEHYDROGENASE (CAD) catalyzes the NADPH-dependent reduction of cinnamaldehydes into cinnamyl alcohols and is a key enzyme found at the final step of the monolignol pathway. Cinnamyl alcohols and their conjugates are subsequently polymerized in the secondary cell wall to form lignin. CAD genes are typically encoded by multi-gene families and thus traditionally organized into general classifications of functional relevance. In silico analysis of the hexaploid Triticum aestivum genome revealed 47 high confidence TaCAD copies, of which three were determined to be the most significant isoforms (class I) considered bone fide CADs. Class I CADs were expressed throughout development both in RNAseq data sets as well as via qRT-PCR analysis. Of the 37 class II TaCADs identified, two groups were observed to be significantly co-expressed with class I TaCADs in developing tissue and under chitin elicitation in RNAseq data sets. These co-expressed class II TaCADs were also found to be phylogenetically unrelated to a separate clade of class II TaCADs previously reported to be an influential resistance factor to pathogenic fungal infection. Lastly, two groups were phylogenetically identified as class III TaCADs, which possess distinct conserved gene structures. However, the lack of data supporting their catalytic activity for cinnamaldehydes and their bereft transcriptional presence in lignifying tissues challenges their designation and function as CADs. Taken together, our comprehensive transcriptomic analyses suggest that TaCAD genes contribute to overlapping but nonredundant functions during T. aestivum growth and development across a wide variety of agroecosystems and provide tolerance to various stressors.

SOS1 gene family in mangrove (Kandelia obovata): Genome-wide identification, characterization, and expression analyses under salt and copper stress

BackgroundSalt Overly Sensitive 1 (SOS1), a plasma membrane Na+/H+ exchanger, is essential for plant salt tolerance. Salt damage is a significant abiotic stress that impacts plant species globally. All living organisms require copper (Cu), a necessary micronutrient and a protein cofactor for many biological and physiological processes. High Cu concentrations, however, may result in pollution that inhibits the growth and development of plants. The function and production of mangrove ecosystems are significantly impacted by rising salinity and copper contamination.ResultsA genome-wide analysis and bioinformatics techniques were used in this study to identify 20 SOS1 genes in the genome of Kandelia obovata. Most of the SOS1 genes were found on the plasma membrane and dispersed over 11 of the 18 chromosomes. Based on phylogenetic analysis, KoSOS1s can be categorized into four groups, similar to Solanum tuberosum. Kandelia obovata's SOS1 gene family expanded due to tandem and segmental duplication. These SOS1 homologs shared similar protein structures, according to the results of the conserved motif analysis. The coding regions of 20 KoSOS1 genes consist of amino acids ranging from 466 to 1221, while the exons include amino acids ranging from 3 to 23. In addition, we found that the 2.0 kb upstream promoter region of the KoSOS1s gene contains several cis-elements associated with phytohormones and stress responses. According to the expression experiments, seven randomly chosen genes experienced up- and down-regulation of their expression levels in response to copper (CuCl2) and salt stressors.ConclusionsFor the first time, this work systematically identified SOS1 genes in Kandelia obovata. Our investigations also encompassed physicochemical properties, evolution, and expression patterns, thereby furnishing a theoretical framework for subsequent research endeavours aimed at functionally characterizing the Kandelia obovata SOS1 genes throughout the life cycle of plants.