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PubMed2026

Genome-Wide Identification of the Soybean GH5 Gene Family and Functional Analysis of GmGH5-22 in Salt Tolerance.

Plant GH5 family genes function in both cell wall biosynthesis and stress responses. However, comprehensive studies on GH5 genes in the soybean remain limited. Here, we identified 28 GmGH5 genes from the soybean genome. Phylogenetic analysis assigned these genes to three subfamilies (I-III), with no representatives in subfamily IV. The GmGH5 family harbors 15 conserved motifs, which are largely similar within subfamilies but differ across subfamilies. Additionally, exon-intron structures (2-7 introns) exhibit clade-specific patterns, with members within the same clade sharing similar intron numbers and lengths, whereas distinct clades show some variation. The promoter regions of GmGH5 genes contained various cis-acting regulatory elements associated with stress responses and developmental processes. Transcriptome-based expression profiling revealed distinct tissue-specific expression patterns of GmGH5 genes. RT-qPCR further confirmed their differential expression under salt, alkaline, cold, and drought stresses, especially a significant increase in GmGH5-22 expression under salt stress (approximately 22-fold at 6 h, **** p < 0.0001). Furthermore, GmGH5-22 was highly expressed in roots, and transient expression in tobacco leaves showed its peripheral localization, which aligns with its predicted extracellular localization, suggesting that GmGH5-22 is highly likely localized to the cell wall. Overexpression of GmGH5-22 in soybean hairy roots significantly improved tolerance to salt stress. These findings establish a foundation for functional characterization of GmGH5 genes and provide viable targets for molecular breeding to enhance salt tolerance in soybeans.

GH5 family↗

PubMed2026

Genome-Wide Identification of the LdARF Gene Family in Lilium davidii var. unicolor and Transient Functional Analysis of LdARF17 in Bulblet Regeneration.

Auxin response factors (ARFs) are key transcriptional regulators of the auxin signaling pathway and play important roles in plant organogenesis and regeneration. However, the functions of ARF family genes in lily scale-derived bulblet regeneration remain largely unclear. In this study, 24 LdARF genes were identified from the genome of Lilium davidii var. unicolor. Phylogenetic analysis revealed that LdARF proteins showed evolutionary conservation with ARF homologs from other monocot species. Genome-wide identification, phylogenetic analysis, and expression profiling revealed functional divergence among LdARF genes during scale-derived bulblet regeneration. Among them, LdARF17 exhibited a distinct regeneration-associated expression pattern, characterized by rapid induction after scale excision and sustained high expression during subsequent bulblet initiation and formation. Subcellular localization analysis demonstrated that LdARF17 is localized in the nucleus. Transient overexpression of LdARF17 significantly promoted bulblet regeneration and was associated with increased expression of auxin-responsive and regeneration-related genes, including IAA14, LBD16, and LBD29. These findings suggest that LdARF17 acts as a positive regulator of lily scale regeneration and may influence auxin-responsive transcriptional processes associated with early cell proliferation, providing new insights into the molecular mechanisms underlying vegetative regeneration in lilies.

Auxin response factor↗

PubMed2024

Expression pattern of Stlhcb gene family in potato and effects of overexpression of Stcp24 gene on potato photosynthesis.

Potato is one of the four staple food crops in the world. It has a wide range of cultivation, high yield, and high nutritional value. Enhancing the photosynthesis of potato is particularly important as it leads to an increase in the potato yield. The light-harvesting pigment-binding protein complex is very important for plant photosynthesis. We identified 12 Stlhcb gene family members from the potato variety "Atlantic" using transcriptome sequencing and bioinformatics. The proteins encoded by the Stlhcb gene family have between 3358 and 4852 atomic number, a relative molecular weight between 24060.16 and 34624.54 Da, and an isoelectric point between 4.99 and 8.65. The RT-qPCR results showed that the 12 Stlhcb genes were expressed in a tissue-specific and time-dependent fashion under low light. The relative expression of the Stlhcb genes in the leaves was significantly higher than that in the stems and roots, and the relative expression of these genes first increased and then decreased with the prolongation of light exposure time. The Stcp24 gene with the highest expression was cloned, and an expression vector was constructed. A subcellular localization analysis was performed in tobacco and an overexpression experiment was performed in potato using an Agrobacterium-mediated method. The subcellular localization analysis showed that the protein encoded by Stcp24 was located in chloroplasts as expected. Overexpression of Stcp24 in transgenic potato increased the yield of potatoes and the content of chlorophyll a and b; increased the net photosynthetic rate, transpiration rate, stomatal conductance, electron transport efficiency, and semi-saturated light intensity; and promoted photosynthesis and plant growth. This study provides a reference for the study of the function of the potato light-harvesting pigment-binding protein gene family. It lays a foundation for further study of the mechanism of the photosynthesis of potato, improvement of the light energy utilization of potato, and molecular breeding of potato.

Solanum tuberosum↗

PubMed2026

Genome-wide identification and expression analysis of the UGT gene family in honeysuckle.

BACKGROUND: The UGT gene family plays critical roles in regulating plant growth, development, stress responses, and secondary metabolite synthesis. Although UGT proteins have been studied in numerous plant species, research on the UGT family in honeysuckle (Lonicera japonica Thunb.) remains limited. RESULTS: In this study, a comprehensive genome-wide analysis of the UGT gene family was performed in honeysuckle. A total of 224 unique LjUGT genes were identified and classified into 21 distinct subfamilies (T71-T92 without T77) based on the phylogenetic analysis. These genes were unevenly distributed on the 9 chromosomes. Eighteen segmental duplication events and 61 tandem duplications were identified, of which only 3 were positive selection. Integrated analysis of promoter cis-acting elements, transcription factors, targeted miRNAs, and interacting proteins suggested that the expression and function of the LjUGT genes may be regulated by transcription factors and proteins through binding to the various binding sites and cis-acting elements, thereby putatively participating in diverse biological processes, including hormone signaling, stress response, and metabolism. The expression pattern analysis of LjUGTs in different tissues and under stress conditions indicated that Lj2A1135G32, Lj5A236T61, Lj6A350T83, and Lj7A737T47 emerged as candidate genes potentially associated with development, 46 genes showed expression changes under all 6 abiotic stresses, suggesting broad stress responsiveness. Additionally, there 7 genes were identified as candidate hub genes that may correlate with the low temperature stress tolerance in honeysuckle according to the WGCNA results, and further verification by qRT-PCR confirmed that Lj4A99G61 and Lj9A591T82 can be regarded as key candidate genes for in-depth research. CONCLUSIONS: This study systematically identified 224 LjUGT genes in honeysuckle for the first time and characterized their physicochemical properties, phylogenetic relationship, and expression patterns. These findings provide a foundational resource for hypothesis-driven investigations into the functions and action mechanisms of LjUGTs.

Lonicera↗

PubMed2026

Depletion of the Candida albicans TLO gene family reveals a requirement for alpha TLO genes for wild-type virulence.

Candida albicans uniquely possesses an expanded family of genes (the TLO gene family) that encodes 10-15 paralogues of the Med2 component of the transcriptional regulator Mediator. Previous studies have shown that TLO null mutants are unable to form hyphae and are hypersensitive to environmental stress. However, the reason for the TLO gene expansion remains unclear, and the current study aimed to determine if reduction in the TLO family copy number affected virulence. In order to investigate this, we used CRISPR-Cas9 mutagenesis to generate two TLO-depleted mutants: one mutant retaining only TLOβ2 (CaTLO2) and the second mutant containing only TLOγ5 (CaTLO5). Both TLO-depleted mutants exhibited increased filamentous growth, increased susceptibility to specific stresses and reduced virulence in a murine model of oropharyngeal candidiasis (OPC). In vitro, the CaTLO5 mutant also exhibited impaired hyphal escape from macrophages and reduced hyphal invasion of oral keratinocytes. We then investigated if complementation with TLOα1, a gene previously shown to restore wild-type growth in a Δtlo null mutant, could restore virulence. In vitro infection models showed that TLOα1 could restore true hypha formation, epithelial invasion and hyphal escape from macrophages in the CaTLO5 background. The murine OPC model showed that TLOα1 could restore wild-type virulence in both CaTLO2 and CaTLO5 strains, suggesting an essential role for α-TLO in oral mucosal infection. Together, these findings highlight the functional specialization between the α, β and γ TLO gene groups and establish α-TLO as a major regulator of virulence in C. albicans.

Candida albicans↗

PubMed2026

The emergence and diversification of the DUX gene family across placental mammals.

The DUX gene family encodes transcription factors with paired homeodomains. It has critical roles in embryogenesis and disease, including facioscapulohumeral muscular dystrophy (FSHD) and cancer. This study conducts a comparative analysis of the DUX gene family-DUXA, DUXB (including DUXBL), and DUXC (including DUX4 and Dux)-across placental mammals, highlighting their structural diversity within macrosatellite repeat contexts. Using long-read genomes, we explore gene distribution, array patterns, and phylogenetic relationships in various vertebrate species. Our analysis reveals that DUXA and DUXB are highly conserved, with intriguing variations such as intronless forms likely arising from ancestral retrotransposition events. While DUXBL is inconsistently retained across clades, its locus-which in non-placental mammals harbors the ancestral single-homeodomain sDUX gene-served as an evolutionary hub for diversification, giving rise to DUXA, DUXB and DUXC, as well as macrosatellite tandem array structures. Sequence conservation and syntenic analyses demonstrate array adaptability, exemplified by higher-order repeats in orangutans and disrupted patterns of concerted evolution in elephants. Furthermore, analysis of human pseudo-DUX4 arrays indicates their potential role in disease mechanisms, including as possible contributors to rare cases of FSHD, warranting further investigation. This study thus provides insights into DUX-family gene evolution, offering a foundation for future research into developmental roles and disease implications.

Animals↗

PubMed2026

Genome-Wide Identification and Bioinformatics Analysis of the FAD Gene Family in Walnut (Juglans regia L.).

Fatty acid desaturase (FAD) is a core catalytic enzyme in plants for the synthesis of unsaturated fatty acids, profoundly affecting plant growth, development, and adaptability to various environmental stresses. The walnut (Juglans regia L.) is an important woody oil tree species, and its kernel is rich in unsaturated fatty acids. Systematic identification of the walnut FAD gene family and analysis of its function are of great significance for revealing the molecular mechanisms underlying unsaturated fatty acid metabolism in the walnut. Based on walnut whole-genome data, this study used homology alignment and hidden Markov model search methods to identify the JrFAD gene family members. Subsequently, a variety of bioinformatics tools were used to systematically analyze their structural characteristics, evolutionary expansion mechanism, expression regulation, and function. A total of 21 JrFAD gene family members were identified and classified into five subfamilies. The family genes were unevenly distributed on nine chromosomes. WGD/segmental duplication was the main expansion method, and the duplicated gene pairs experienced strong purification selection. The family gene promoter sequence is rich in regulatory elements that respond to light, plant hormones, and various stresses. The expression pattern analysis showed that JrFAD3.1 and JrFAD2.3 showed high expression specifically during the rapid accumulation of walnut kernel oil. This study clarified the composition and evolutionary characteristics of the FAD gene family in the walnut, which provides useful information for in-depth analyses of its functional mechanism in the regulation of lipid metabolism, and also identified potential candidate gene resources for the genetic improvement of walnut varieties with high amounts of unsaturated fatty acids.

Juglans↗

PubMed2026

Comprehensive Identification of WDR Gene Family in Panax ginseng: PgWDR Gene Expression Analysis with Ginsenosides Biosynthesis Under MeJA.

Panax ginseng (Panax ginseng C.A. Mey.) produces pharmacologically valuable ginsenosides. WD40-repeat (WDR) proteins act as versatile regulators of plant specialized metabolism, yet their biological roles under methyl jasmonate (MeJA) elicitation remain largely uncharacterized in ginseng. In this study, we identified 29 PgWDR family members at the whole-genome level, and systematically analyzed their phylogeny, gene structure, cis-acting promoter elements, as well as organ- and development-dependent expression patterns. Six candidate genes potentially associated with ginsenoside biosynthesis were screened through integrating gene-metabolite correlation analysis and gene co-expression analysis. Under MeJA treatment, three of these candidates showed statistically significant expression responses, while the other three exhibited variable expression fluctuations with no statistical significance. PgWDR24 displayed a positive correlation with key ginsenoside biosynthetic enzyme genes, and a negative correlation with protopanaxadiol-type ginsenoside accumulation. Combined with its predicted nuclear localization, we hypothesize that PgWDR24 participates in the negative modulation of protopanaxadiol-type ginsenoside accumulation, although further genetic functional validation is still required. This work provides valuable candidate genes for deciphering ginsenoside regulatory networks and offers support for molecular-assisted breeding of high-quality ginseng.

Panax ginseng C. A. Mey.↗

PubMed2026

Genome-wide identification and characterization of 1-amino-cyclopropane-1- carboxylate synthase (ACS) gene family in Carica papaya and expression insights in response to hormone stress.

ACC-synthase (1-aminocyclopropane-1-carboxylate synthase), also known as the ACS gene, plays a pivotal role in ethylene production, which is of great importance in the fruit ripening process for producing saleable yield (marketable fruit). The ACS gene family presumably controls stress responses, plant growth and development, and particularly fruit ripening. Computational biology was used as an essential tool to identify seven ACS genes in Carica papaya (red hermaphrodite) using an RNA-seq database (NCBI GEO). Further, the phylogenetic relationships of ACS genes determined gene family resemblance in the genomes of Hordeum vulgare, Musa acuminata, C. papaya, and Arabidopsis thaliana; therefore, the identified gene families were further classified into four distinct clades (Type-I, Type-II, Type-III, and Type-IV) in alignment with the well-established Arabidopsis classification. Moreover, encompassing gene structure, domain motifs, cis-element phylogenetic profiling, synteny, and transcriptomic profiling unveiled latent structural and functional attributes within CpACS genes. Through segmental duplication of CpACS, insights into evolutionary duplication events were predicted. The paralogous behavior of ACS genes in C. papaya and a comprehensive transcriptomic analysis demonstrated both up- and down-regulation patterns in response to ethylene treatment at different time points during the fruit ripening process, using the papaya manual handbook V2 (2021). Gene expression showed upregulation of two essential CpACS genes, CpACS5 and CpACS6. RT-qPCR validates the expression of these important genes during fruit ripening. However, one gene, CpACS7, is expressed in the later stages of fruit development. Our results demonstrated novel avenues for understanding the expression pathways of the ACS gene family in red hermaphrodite papaya, and most of these genes were linked to regulating various abiotic stresses, plant growth, and fruit development.

Carica↗

PubMed2026

Recent gene duplication and structural remodeling drive rapid lineage-specific gene family evolution in plants.

Gene duplication promotes the generation of novel gene functions and trait diversity across species. Here, we present DupHIST, a computational pipeline that reconstructs the hierarchical timing of gene duplications by integrating maximum likelihood (ML)-based phylogeny with substitution-derived timing via statistical smoothing. Applied to over 4.5 million genes from 114 plant genomes, we successfully inferred duplication histories across nearly 130,000 orthogroups. This large-scale analysis showed that 53.0% of genes arose from recent, lineage-specific duplications, with high concentrations in particular multi-copy families. Among these, NLR, C48, and P450 families exemplified how recently duplicated genes undergo rapid stepwise structural remodeling. This process was primarily driven by small-scale mutations, including insertions, deletions, and frameshifts, that rapidly accumulated shortly after duplication. By resolving the precise duplication order, we reconstructed these architectural changes, thereby enabling both the inference of putative ancestral structures and the exploration of functional diversification arising from structural remodeling. Structure-based clustering further uncovered that recently duplicated, uncharacterized genes retain core domain structures resembling known functional proteins even across phylogenetically distant species lacking sequence homology. Our findings reveal that recent gene duplications and subsequent structural remodeling represent a widespread and lineage-specific force driving rapid diversification of gene families in plants.

Gene duplication history↗

PubMed2026

Genome-wide identification of olfactory receptor and odorant-binding protein gene families and their roles in Heliothine chemosensory evolution.

Chemosensory systems play key roles in the survival and reproductive success of insects. Two large and diverse chemosensory gene families, odorant receptors (ORs) and odorant-binding proteins (OBPs), play critical roles in insect chemosensation and mediate odour-guided behaviours. In the process of insect chemosensation, odorants from the environment pass through pores in the antennal sensilla and become soluble in the sensillar lymph, either directly on contact or by binding to an OBP. Solubilized odour molecules diffuse through the lymph until they reach and activate their cognate ORs, sending electrophysiological signals to the insect brain. To better understand the evolutionary roles of OR and OBP gene families among members of the Heliothinae, we systematically characterized these two gene families in Chloridea virescens (Lepidoptera: Noctuidae). A total of 81 ORs and 49 OBPs were identified genome-wide. Based on the number and positions of conserved cysteine residues, the OBPs were classified into three types: 34 Classic OBPs, 8 Minus-C OBPs and 7 Plus-C OBPs. Phylogenetic analyses identified potential gene duplications and losses within OR and OBP gene families among members of the Heliothinae, which may be associated with differences in their volatile sensation and olfactory behaviours. Further motif and structural analyses identified a conserved region that was unique among pheromone receptors and predicted as key residues of the binding pocket, implying its critical role in pheromone detection. Future work should focus on experimentally validating its function. Overall, our findings provide important insights into how chemosensory gene evolution contributes to ecological adaptation and reproductive isolation in the Heliothine moths.

Animals↗

PubMed2026

Identification and characterization of the HSP gene family in the Chinese giant salamander: Expression patterns under combined environmental stress.

BACKGROUND: The Chinese giant salamander (Andrias davidianus) is a critically endangered living fossil species that is highly sensitive to changes in water temperature. However, systematic studies on the heat shock protein (HSP) gene family and its response mechanisms to environmental stress in this species remain limited. This study utilized transcriptome data from captive-bred salamanders exposed to combined temperature and pathogen stress. Bioinformatics tools were employed to identify the HSP gene family of A. davidianus (AndHSP) and to analyze their evolution, structure, and function, thereby revealing their regulatory mechanisms in response to environmental stress. RESULTS: A total of 72 AndHSPs were identified and classified into five subfamilies. Phylogenetic analysis revealed that each subfamily is evolutionarily conserved and functionally related. Gene expression analysis demonstrated that pathogen infection induced the expression of AndHSPs, and elevated temperature significantly intensified this response. Nine key differentially expressed genes were identified, predominantly from the AndHSP70 subfamily, with AndHSP70-18 exhibiting rapid heat-induced expression. Tissue-specific analysis showed high expression of AndHSP60 in the spleen. A qPCR validation confirmed the reliability of the transcriptome expression results. CONCLUSIONS: This study presents the first systematic identification of the AndHSP gene family and elucidates its cooperative stress response mechanisms under combined temperature and pathogen stress. These findings provide a molecular basis for understanding the species' environmental adaptation and have important implications for its conservation and artificial breeding.

Animals↗

PubMed2025

Identification of BoRR gene family in cauliflower: roles in curd development and salt tolerance.

BACKGROUND: Cauliflower, as an important vegetable crop, the research on its curd formation mechanism and stress-responsive gene networks is of great significance for improving its quality, yield and abiotic stress tolerance. The response regulator (RR) gene family plays a crucial role in the regulation of various life processes of many organisms. In this research, a comprehensive analysis of the BoRR gene family in cauliflower was carried out. RESULTS: A Total of 57 BoRR genes were identified in cauliflower and classified into seven subtypes (type A/B-I/B-II/B-IV/C/B-PRR/Clock PRR) based on sequence homology. Chromosomal mapping showed even distribution across genomes, while physicochemical analysis revealed diverse protein properties (134-915 amino acids, pI 4.51-9.19) with predominant nuclear localization. Structural analyses found all BoRR proteins contain REC-type domains, with subtype-specific features: type A has REC_typeA_ARR, type B harbors REC_typeB_ARR domains, and Clock PRR shows circadian-related psREC_RR domains. Exon numbers range from 2 to 10, with type A BoRR genes having shorter CDS lengths. Collinearity analysis identified 28 pairs of gene duplicates (26 inter-chromosomal). Comparative analysis showed 133 collinear pairs with Brassica napus, 96 with Brassica. rapa, and only 1 with monocots specie (rice and maize). Promoter analysis identified hormone-responsive motifs (ABRE, TGACG), development-related elements (ARE), and stress-responsive sequences (e.g., MBS for drought tolerance) in the promoters of BoRR genes. GO enrichment linked BoRR genes to phosphorelay signaling, cytokinin/ethylene response, and developmental processes like meristem maintenance. Expression profiling during curd development showed type A genes (BoRR23/27/34/38/45) up-regulated in vegetative-reproductive transition, BoRR3/6/12/32/54 in curd enlargement, and several genes like BoRR49 in flower bud differentiation. Salt stress (1.5% NaCl) induced transient expression in 8 of 9 selected BoRR genes at day 1 after treatment. qRT-PCR validated their roles in developmental regulation and salt tolerance. CONCLUSION: This study provides valuable insights into the BoRR gene family in cauliflower, laying a foundation for further understanding its genetic mechanisms and potentially guiding efforts to enhance curd quality and salt tolerance in cauliflower.

Salt Tolerance↗

PubMed2026

Genome-wide identification of the expansin gene family in Rosa rugosa and overexpression of RrEXPA1 contributes to drought and salt stress tolerance in Arabidopsis.

The expansin (EX) gene family plays a crucial role in the growth and development of various plants, as well as responses to biotic and abiotic stresses. However, genome-wide analysis of the EX gene family and their functions in drought and salt stress tolerance has not been examined in Rosa rugosa. In this study, a total of 30 RrEX genes were identified and located on seven different chromosomes. Phylogenetic analysis classified these genes into four subfamilies: EXPA (24 members), EXPB (3 members), EXLA (1 member), and EXLB (2 members). The average amino acid length was 269.17 aa, with isoelectric points ranging from 4.79 to 9.97. Most members exhibited high aliphatic indices and protein stability, suggesting their adaptability to diverse environments. The synteny analysis provided insights into the evolution of the EX gene family in rose. Toxicity and autoactivation assays confirmed that BD-RrEXPA1 was non-toxic to yeast cells and lacked autoactivation activity, indicating its suitability for yeast two-hybrid screening. The transgenic Arabidopsis lines overexpressing RrEXPA1 improved seed germination and root length under abiotic stress. In addition, the overexpression lines showed reduced malondialdehyde (MDA) levels and increased chlorophyll content and superoxide dismutase (SOD) activity. These results suggest that RrEXPA1 may enhance stress tolerance by promoting root elongation and modulating physiological responses. This study provides important insights into the role of RrEXs in salt and drought stress and lays the foundation for further studies on the regulatory mechanisms of abiotic stress.

Drought stress↗

PubMed2026

Genome-Wide Analysis of Triticum aestivum Root Meristem Growth Factor (RGF) Gene Family Highlights TaRGF5 as a Putative Component of Root-Associated Signaling.

Wheat (Triticum aestivum), a key global crop, faces rising drought stress that limits root growth and water uptake. Root meristem growth factors (RGFs) are small peptides that regulate root stem cell maintenance, meristem activity, and lateral root formation in model plants, yet the RGF gene family remains unexplored in wheat. Here, we performed a comprehensive genome-wide analysis of the TaRGF gene family, identifying 15 genes distributed across the A, B, and D subgenomes and classified into five homeologous groups (TaRGF1-TaRGF5), predominantly located on chromosomes 2 and 6. All TaRGFs contained a characteristic RGF motif, with dibasic cleavage sites and Asp-Tyr motifs indicating conserved maturation mechanisms. Based on the phylogenetic analysis, the TaRGF5 homeologs showed the highest similarity to Arabidopsis thaliana RGF5. Tested RNA-seq data revealed predominantly root-enriched expression for all TaRGF genes, with TaRGF5 exhibiting the most root-preferential and downregulation under drought stress. Quantitative real-time PCR (qRT-PCR) confirmed that drought stress suppressed the expression of TaRGF5A, TaRGF5B, and TaRGF5D in roots of wheat cultivar Sids-13 across all time points, unlike the higher accumulation seen in controls. Promoter analysis predicted a unique BES1 transcription factor binding site exclusively in TaRGF5B, linking brassinosteroid signaling to peptide-mediated root regulation. Structural modeling and molecular docking predicted an interaction between wheat TaRGF5 homeologs and root growth factor-insensitive receptor kinase (TaRGI3), characterized by conserved sulfotyrosine-mediated binding and favorable interaction energetics. Based on this characterization of the wheat RGF gene family, particularly the potential role of TaRGF5 in root development and drought-adaptation signaling, we propose targeting this gene for functional analysis to improve wheat resilience under water-limited conditions.

Triticum↗

PubMed2026

Genome-Wide Identification and Expression Pattern of the ANK Gene Family in Sorghum bicolor Under Salt Stress.

The Ankyrin-repeat proteins (ANKs) play a key role in plant development and in response to abiotic stress. This research identified family members of the ANK genes in Sorghum bicolor at the whole-genome level, analyzed their sequence characteristics, evolutionary relationships, and expression patterns, and provided a scientific basis for elucidating the functionality of SbANK genes and for salt-tolerant breeding. Using bioinformatics methods, this study conducted a comprehensive identification of the SbANK gene family, analyzing its physicochemical properties, domain composition, chromosomal distribution, colinearity relationships, promoter cis-acting elements, and conserved protein motifs. Transcriptomic data and qRT-PCR were used to detect changes in their expression under salt stress. A total of 186 ANK family members were identified in the Sorghum bicolor genome, classified into 13 subfamilies and unevenly distributed across 10 chromosomes. Intra-species colinearity analysis revealed 7 pairs of duplicated genes, while inter-species colinearity analysis showed that S. bicolor and Oryza sativa share 88 pairs of orthologs, far exceeding the number found in Arabidopsis thaliana (11 pairs). Promoter analysis indicated that SbANK genes are enriched with cis-acting elements associated with hormone responses (particularly MeJA elements, accounting for 51.7%) and stress responses (particularly anaerobic-inducible elements, accounting for 60.9%). Transcriptomic expression analysis revealed that SbANK genes exhibit distinct tissue specificity, with the ANK-IQ subfamily highly expressed in leaves and the ANK-M subfamily showing the most widespread response under salt stress. Expression levels of the 10 candidate genes showing the most significant responses to salt stress were analyzed using qRT-PCR. The results indicated that SbANK91, SbANK135, and SbANK136 were significantly upregulated under 200 mmol/L NaCl treatment. The SbANK family is distinguished by a large number of member genes and structural diversity, with the ANK-M subfamily being the primary group responding to salt stress. SbANK91, SbANK135, and SbANK136 are identified as putative candidate genes for salt stress responses.

Sorghum↗

PubMed2025

Genome-wide identification and expression profiling of the MADS-box gene family in Lavandula angustifolia.

BACKGROUND: MADS-box genes encode transcription factors critical for plant development, particularly floral organogenesis, flowering time regulation, and adaptation to environmental stresses. Among these, the MIKCC-type genes are pivotal regulators in floral developmental processes. Although the evolutionary diversification and functional dynamics of MADS-box genes have been extensively characterized in model plants such as Arabidopsis thaliana and Oryza sativa, their evolutionary relationships and functional profiles in Lavandula angustifolia, an economically significant aromatic plant, remain poorly understood. RESULTS: Genome-wide analysis identified 173 MADS-box genes in L. angustifolia, categorized into type I (Mα: 26; Mβ: 0; Mγ: 10) and type II (MIKCC: 125; MIKC*: 12) based on phylogenetic comparisons with A. thaliana. The MIKCC subgroup was further subdivided into 12 subclasses, including genes central to the ABCDE model of floral organ specification. Structural analyses revealed distinct conserved motifs and exon-intron configurations specific to each subgroup, indicative of functional divergence. Synteny analysis demonstrated Whole Genome Duplication (WGD) and segmental duplications as major contributors to MIKCC gene family expansion, notably among genes linked to floral organ development. Expression profiling via RNA-seq and quantitative real-time PCR (qPCR) showed type II MADS-box genes exhibited higher expression levels with pronounced tissue-specific and developmental stage-specific expression patterns compared to type I genes. Many type II genes displayed significant associations with floral organogenesis, floral transition, and abiotic stress responses, underscoring their essential roles in reproductive development and environmental adaptability in L. angustifolia. CONCLUSIONS: The identification and comprehensive characterization of 173 MADS-box genes in L. angustifolia highlight the significant expansion of the MIKCC subgroup driven primarily by WGD and segmental duplications. The distinct structural features and specific expression patterns observed provide insights into the functional divergence and complexity of these genes, particularly regarding floral organogenesis and adaptation to environmental stress. This study establishes a robust molecular basis for further functional analysis and genetic improvement of aromatic plants.

MADS Domain Proteins↗

PubMed2026

Genome-wide characterization of the FOX gene family reveals sex-biased expression and FoxO-associated regulation during gonadal development in Bellamya aeruginosa.

Forkhead box (FOX) transcription factors are important regulators of development and reproduction, but their roles in molluscan gonadal development remain unclear. In this study, the FOX gene family was systematically identified in the freshwater gastropod Bellamya aeruginosa, and comparative gonadal transcriptomic analyses were performed across sexes and developmental stages.A total of 35 FOX genes were identified and classified into 19 subfamilies. Phylogenetic and synteny analyses indicated that the FOX gene family is generally conserved among mollusks, whereas FoxG and FoxL2 showed lineage-specific expansion. Structural analyses demonstrated that most BaeFOX proteins retained the conserved Forkhead domain architecture. Transcriptomic analyses revealed that gene expression divergence between testes and ovaries was markedly greater than that between developmental stages within the same gonad, indicating that sexual dimorphism is the major source of gonadal transcriptional variation. Functional enrichment consistently identified the FoxO signaling pathway in sex-biased comparisons. Several FOX genes also displayed clear gonad-biased expression patterns, and network analyses suggested that BaeFoxO, BaeFoxL2, and BaeFoxG may play central regulatory roles in gonadal development. These findings provide the first comprehensive characterization of the FOX gene family in B. aeruginosa and suggest that FOX-related regulatory networks potentially participate in gonadal development in gastropod mollusks.

Animals↗