The emergence and evolution of intron-poor and intronless genes in intron-rich plant gene families

Abiotic stress-regulated LEA gene mediates the response to drought, salinity, and cold stress in Medicago sativa L

Late embryogenesis abundant (LEA) proteins are typical stress-related proteins widely distributed across various organisms. Their anti-stress functions in higher plants have garnered significant attention and have been extensively studied; however, no such studies have been reported on the entire protein family in Medicago sativa. In this study, we identified a total of 83 MsLEA proteins in M. sativa and conducted a comprehensive analysis to elucidate their functions in response to abiotic stresses. The results indicated that these proteins could be classified into seven groups and were distributed across eight chromosomes. Collineation analysis revealed that segmental duplication primarily drove the expansion of MsLEA genes. Furthermore, the promoters of MsLEA genes were found to be enriched with cis-acting elements associated with various stress responses. Through transcriptome and quantitative real-time PCR analysis, nine MsLEA genes related to drought, salinity, and cold stress were identified, with MsLEA69 selected for further validation. The ectopic expression of MsLEA69 improves osmotic and extreme temperature tolerance by increasing the activity of stress-related enzymes in both prokaryotic and eukaryotic cells. These comprehensive analyses and identifications lay the groundwork for future research into the functional mechanisms of MsLEA proteins and offer potential candidate genes for enhancing resistance breeding in M. sativa.

Evolutionary trajectories and subfunctionalization of 2 key methyltransferase regulator subfamilies in plants

DNA methylation, a conserved epigenetic mark in both plants and animals, plays a critical role in growth, development, and adaptability. This study explores the origin, evolution, and functional diversification of 2 key methyltransferase regulators, DNAJ-domain-containing protein 1/2/3 (DNAJ1/2/3) and SU(VAR)3-9 HOMOLOG 1/3 (SUVH1/3), in plants. By analyzing genomic data from 21 algae and 86 land plants, we discovered that DNAJ1/2/3 originated within Magnoliopsida, while SUVH1/3 emerged in ferns and evolved through retrotransposition. Both protein families have undergone multiple duplication events and positive selection throughout plant evolution, resulting in their expansion and functional divergence. In dicotyledons, DNAJ1/2/3 diverged into 3 subclades, whereas SUVH1/3 underwent a common duplication event in its ancestral lineage, resulting in 2 subgroups. Structural domain analysis revealed that the evolution of PHD fingers in DNAJ1/2/3 and AT domains in SUVH1/3, under selective pressure, enhanced their interaction capabilities and contributed to the formation of complexes involved in DNA methylation and demethylation regulation. Expression profile analysis across various plant taxa demonstrated tissue-specific expression patterns, with higher expression levels observed in meristematic tissues and active cell regions. These findings elucidate the evolutionary patterns of DNAJ1/2/3 and SUVH1/3 and offer insights into their functional diversification in plants.

Identification of the Dof Gene Family in Quinoa and Its Potential Role in Regulating Flavonoid Synthesis Under Different Stress Conditions

Quinoa (Chenopodium quinoa Willd.), often referred to as the "golden grain", is a highly nutritious crop that has garnered significant global attention due to its exceptional nutritional profile and health benefits. Flavonoids present in quinoa have been shown to possess antioxidant, anti-inflammatory, antiviral, anticancer, and antidepressant properties. The DNA binding with one finger (Dof) transcription factor is crucial for regulating growth, development, and stress responses. However, the identification of the Dof family using the latest quinoa genomic data and its function in abiotic stress response have not been fully elucidated. Here, 36 CqDof genes were identified from the quinoa genome and classified into ten subfamilies through phylogenetic analysis. Physicochemical property analysis predicted that CqDofs predominantly encode basic, hydrophilic, and unstable nuclear proteins. CqDofs were distributed across 15 chromosomes, with segmental duplication being the primary driver of their expansion. Subsequently, basic information on CqDofs was systematically analyzed, including conserved motifs, gene structure, cis-acting elements, and expression patterns. Notably, the promoter regions of all CqDof genes were enriched with cis-acting elements related to light responsiveness. Further analysis revealed that red and blue light significantly affected CqDof expression and flavonoid accumulation (epigallocatechin, rutin, naringenin, morin, pinocembrin, quercetin-7-O-rutinoside, quercetin-3-O-glucoside, and naringenin), in which 5 CqDofs exhibited a pronounced response to both light conditions and showed a significant correlation with flavonoid levels. Finally, RT-PCR analysis indicated that the expression levels of CqDofs (except CqDof21) were significantly upregulated under drought, salt, and saline-alkali stresses. These findings lay the groundwork for future studies on how CqDofs regulate flavonoid biosynthesis under different light qualities and function in abiotic stress.

Genome-Wide Identification of β-Ketoacyl CoA Synthase Gene Family in Melon (Cucumis melo L.) and Its Expression Analysis in Autotoxicity, Saline-Alkali, and Microplastic Exposure Environments

β-ketoacyl CoA synthase (KCS) is a key enzyme in the synthesis of long-chain fatty acids. It affects plant stress resistance by regulating the chain length of fatty acid elongation products, the wax deposition in plant epidermis, and the formation of suberization layers. Through a comprehensive, genome-wide analysis, we identified members of the melon KCS (CmKCS) family and characterized their sequence features, phylogenetic relationships, and expression profiles under three abiotic stress conditions, employing bioinformatics tools and methods. Fifteen CmKCSs were identified in the melon genome and found to be unevenly distributed across eight chromosomes. The subcellular localization of most members is located on the cytoplasmic membrane and chloroplasts. The CmKCS family amplifies its members in a tandem repeat manner, which is more closely related to the cucumber KCS and has similar gene functions. Subfamilies I, IV, and VI exhibit variations in conserved domain sequences, which may indicate specific functional differentiation. The promoter region harbors various cis-acting elements related to plant hormones and abiotic stress responses. Among these, the most abundant are elements responsive to abscisic acid, methyl jasmonate, salicylic acid, and anaerobic induction. CmKCS5, CmKCS6, CmKCS10, and CmKCS12 showed high expression in autotoxicity, saline-alkali stress, and microplastic exposure environments. These four CmKCSs may play important roles in melon development and stress response. In conclusion, this study provides a comprehensive analysis of the CmKCS gene family, revealing its potential roles in melon's response to abiotic stresses and laying a foundation for further functional characterization of these genes in stress tolerance mechanisms.

Identification and role of CmLhcb2.1 in regulating low-light stress resistance in Chinese chestnut (Castanea mollissima)

Chinese chestnut (Castanea mollissima) is a significant woody food plant that has garnered increasing attention due to its potential role in addressing food security challenges. However, low yield remains a critical issue facing the Chinese chestnut industry. One contributing factor to this low yield is insufficient light, particularly since Chinese chestnuts predominantly grow in mountainous regions. Therefore, the present study aims to investigate the intrinsic mechanisms underlying chestnut resistance to light stress, identify and validate genes associated with low light stress tolerance, and provide a foundation for targeted breeding of chestnut varieties that can withstand light stress. Studies have demonstrated that the light-harvesting chlorophyll a/b (Lhca/b) proteins play key roles in regulating the adaptation of plants to low-light stress. However, there have been no reports on the role of the Lhca/b gene family in the chestnut under light stress. We initially identified 17 CmLhca/b gene members across the chestnut genome and constructed a phylogenetic tree that divided them into five subgroups: the Lhca, the Lhcb, the CP24, the CP26, and the CP29 groups. CmLhcb2.1 and CmLhcb2.2 were grouped on the same branch with GhLhcb2.3 of upland cotton that involved in chlorophyll synthesis.The chestnut leaves exhibited phenotypic and transcriptomic differences under low and normal light conditions. By the 10th day of shading treatment, the leaves showed signs of damage, with the extent of damage intensifying as shading intensity increased. Additionally, the leaf color darkened due to the gradual increase in chlorophyll b content, which was correlated with increased shading intensity. The gene CmLhcb2.1 was upregulated across all shading intensities. Specifically, quantitative reverse transcription PCR (qRT-PCR) confirmed the upregulation of CmLhcb2.1 in chestnut under low-light stress. Overexpression studies in tobacco indicated that CmLhcb2.1 enhances chestnut resistance to low-light stress by promoting chlorophyll b synthesis. Finally, yeast one-hybrid and dual-luciferase reporter assays confirmed that the transcription factor CmGLK positively regulated CmLhcb2.1. These findings lay a theoretical foundation for exploring how CmLhcb2.1 regulates chestnut resistance to low-light stress.

Genome-Wide Identification and Expression Analysis of Phytosulfokine Peptide Hormone Genes in Camellia sinensis

Phytosulfokine (PSK) is a tyrosine-sulfated pentapeptide found throughout the plant kingdom, playing key roles in plant growth, development, and responses to biotic and abiotic stresses. However, there is still a lack of a comprehensive analysis of the CsPSK gene family in Camellia sinensis. In this study, we conducted a genome-wide identification and characterized 14 CsPSK genes in tea plants, which are unevenly distributed across seven chromosomes. CsPSK genes encode proteins ranging from 75 to 124 amino acids in length, all belonging to the PSK-α type and containing conserved PSK domains. A synteny analysis revealed that the expansion of the CsPSK gene family is primarily attributed to whole-genome duplication, with homology to Arabidopsis thaliana PSK genes. A promoter region analysis identified cis-regulatory elements related to hormone and stress responses. An expression profile analysis showed that CsPSK genes are highly expressed in roots, stems, flowers, and leaves, and are induced by both biotic and abiotic stresses. Furthermore, an RT-qPCR assay demonstrated that the expression levels of CsPSK8, CsPSK9, and CsPSK10 are significantly upregulated following Discula theae-sinensis infection. These findings establish a basis for further research into the role of the CsPSK gene family in tea plant disease resistance and underlying molecular mechanisms, offering valuable perspectives for developing novel antimicrobial peptides.

The parsley genome assembly and DNA methylome shed light on apigenin biosynthesis in the Apiaceae

Parsley [Petroselinum crispum (Mill.)] is a medicinal and edible vegetable of the Apiaceae family that is rich in apigenin. The Apiaceae family is well known for its diverse secondary metabolites. As a high-quality reference genome is lacking for parsley, the evolution and apigenin biosynthesis in Apiaceae have remained unexplored. Here, we report the chromosome-level genome sequence of parsley, consisting of 1.85 Gb that mainly arose from the expansion of long terminal repeats. Whole-genome bisulfite sequencing revealed a significantly higher number of hypermethylated differentially expressed genes in leaf blades and petioles than in root tissues. Moreover, we identified and characterized chalcone isomerase (CHI) genes, encoding key enzymes involved in apigenin biosynthesis in parsley. We also established that the APETALA2 family transcription factor Pcrispum_6.2855 (PcAP2) binds to the (Pcrispum_11.4764) PcCHI promoter and promotes apigenin accumulation. In conclusion, our work presents a multiomics data resource for understanding apigenin biosynthesis and its transcriptional regulation in parsley, in addition to shedding light on the evolution of parsley within the Apiaceae.

SlMYB1R1-SlSWEET12c module synergistically promotes sugar accumulation in tomato fruits

Tomato (Solanum lycopersium), a globally significant vegetable crop prized for its distinctive flavor, relies on efficient sugar allocation for fruit development. Despite this, the molecular module underlying the translocation of sugars from sources to sinks within the tomato remains elusive. Sugar will eventually be exported transporters (SWEETs), a class of proteins known to mediate sugar transport, have been implicated in the process. Here, we discovered that SlSWEET12c, belonged to subfamily III, which was markedly upregulated during the development of tomato fruits. The subcellular localization of SlSWEET12c-GFP to the plasma and vacuolar membrane supported its putative role in apoplasmic sucrose transport. Complementary growth in a yeast (Saccharomyces cerevisiae) mutant strain SUSY7/ura3 confirmed SlSWEET12c with sucrose transport activity. Overexpressing and CRISPR/Cas9-mediated knockdown of SlSWEET12c in tomato plants demonstrated its role in promoting sugar accumulation in fruits. Additionally, the MYB transcription factor SlMYB1R1 was obtained by screening the cDNA library of tomato, which was highly expressed during tomato fruit development with a similar pattern to SlSWEET12c. The SlMYB1R1 could bind to the SlSWEET12c promoter and regulate its activity, thereby positively promoting sugar accumulation in tomato fruits. Collectively, our findings presented a novel role for the SlMYB1R1-SlSWEET12c module in facilitating sugar accumulation and provided a basis for future efforts to breed crops with enhanced sugar content.

Genome-Wide Identification and Expression Analysis of TCP Transcription Factors Responding to Multiple Stresses in Arachis hypogaea L

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING-CELL-FACTOR (TCP) gene family, a plant-specific transcription factor family, plays pivotal roles in various processes such as plant growth and development regulation, hormone crosstalk, and stress responses. However, a comprehensive genome-wide identification and characterization of the TCP gene family in peanut has yet to be fully elucidated. In this study, we conducted a genome-wide search and identified 51 TCP genes (designated as AhTCPs) in peanut, unevenly distributed across 17 chromosomes. These AhTCPs were phylogenetically classified into three subclasses: PCF, CIN, and CYC/TB1. Gene structure analysis of the AhTCPs revealed that most AhTCPs within the same subclade exhibited conserved motifs and domains, as well as similar gene structures. Cis-acting element analysis demonstrated that the AhTCP genes harbored numerous cis-acting elements associated with stress response, plant growth and development, plant hormone response, and light response. Intraspecific collinearity analysis unveiled significant collinear relationships among 32 pairs of these genes. Further collinear evolutionary analysis found that peanuts share 30 pairs, 24 pairs, 33 pairs, and 100 pairs of homologous genes with A. duranensis, A. ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Moreover, we conducted a thorough analysis of the transcriptome expression profiles in peanuts across various tissues, under different hormone treatment conditions, in response to low- and high-calcium treatments, and under low-temperature and drought stress scenarios. The qRT-PCR results were in accordance with the transcriptome expression data. Collectively, these studies have established a solid theoretical foundation for further exploring the biological functions of the TCP gene family in peanuts, providing valuable insights into the regulatory mechanisms of plant growth, development, and stress responses.

Analysis of the CHS Gene Family Reveals Its Functional Responses to Hormones, Salinity, and Drought Stress in Moso Bamboo (Phyllostachys edulis)

Chalcone synthase (CHS), the first key structural enzyme in the flavonoid biosynthesis pathway, plays a crucial role in regulating plant responses to abiotic stresses and hormone signaling. However, its molecular functions remain largely unknown in Phyllostachys edulis, which is one of the most economically and ecologically important bamboo species and the most widely distributed one in China. This study identified 17 CHS genes in Phyllostachys edulis and classified them into seven subgroups, showing a closer evolutionary relationship to CHS genes from rice. Further analysis of PeCHS genes across nine scaffolds revealed that most expansion occurred through tandem duplications. Collinearity analysis indicated strong evolutionary conservation among CHS genes. Motif and gene structure analyses confirmed high structural similarity, suggesting shared functional characteristics. Additionally, cis-acting element analysis demonstrated that PeCHS genes are involved in hormonal regulation and abiotic stress responses. RNA-Seq expression profiles in different bamboo shoot tissues and heights, under various hormone treatments (gibberellin (GA), naphthaleneacetic acid (NAA), abscisic acid (ABA), and salicylic acid (SA)), as well as salinity and drought stress, revealed diverse response patterns among PeCHS genes, with significant differential expression, particularly under hormone treatments. Notably, PeCHS14 consistently maintained high expression levels, suggesting its key role in stress response mechanisms. qRT-PCR analysis further validated the expression differences in five PeCHS genes under GA and ABA treatments. Subcellular localization analysis demonstrated that PeCHS14 and PeCHS15 proteins are localized in the nucleus. This study provides a foundation for investigating the potential functions of PeCHS genes and identifies candidate genes for future research on the responses of Phyllostachys edulis to abiotic stresses and hormone signaling.

Genome-wide identification of the ATP-dependent zinc metalloprotease (FtsH) in Triticeae species reveals that TaFtsH-1 regulates cadmium tolerance in Triticum aestivum

The ATP-dependent zinc metalloprotease (FtsH) protein gene family is essential for plant growth, development, and stress responses. Although FtsH genes have been identified in various plant species, the FtsH gene family in wheat (Triticum aestivum) remains unstudied. In this study, we identified 11 TaFtsH genes with uneven chromosomal distribution, significant variations in gene sequence length, and differing intron numbers among individual members. Additionally, these proteins exhibit similar physicochemical characteristics as well as secondary and tertiary structures. The FtsH genes can be classified into eight groups, each characterized by similar structures and conserved motifs. Intraspecific and interspecific comparisons further revealed extensive gene duplications within the TaFtsH gene family, indicating a closer relationship to maize. Analysis of cis-acting elements in the promoter regions of TaFtsH genes revealed developmental and stress-responsive elements in most of the genes. Expression pattern analysis showed that TaFtsH genes are expressed in all wheat tissues, though with varying patterns. TaFtsH genes displayed differential responses to CdCl2, ZnSO4, and MnSO4 stress treatments. Gene Ontology (GO) enrichment analysis indicated that TaFtsH genes are involved in protein hydrolysis. Barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) technology confirmed the function of TaFtsH-1, indicating that silencing TaFtsH-1 enhances common wheat's resistance to cadmium (Cd) toxicity. In summary, this study offers an in-depth understanding of the FtsH gene family in wheat, establishing a solid basis for comprehending its functions, genetic mechanisms, and improving wheat's tolerance to heavy metal contamination.

Genome-Wide Identification and Analysis of BrTCP Transcription Factor Family Genes Involved in Cold Stress Tolerance in Winter Rapeseed (Brassica rapa L.)

TCP transcription factors are important during plant growth and stress responses. However, their role in the cold stress response of Brassica rapa L. remains poorly understood. In this research, we identified the TCPs gene family in B. rapa to learn the features of the BrTCP gene family, functionally annotating the interacting proteins of TCP4 and analyzing their expression levels. Our results illustrated the presence of 19 members of the BrTCPs family in B. rapa, exhibiting molecular weights ranging from 27,367.45 to 59,433.64 Da. All identified proteins were classified as unstable, with isoelectric points ranging from 5.5 to 9.48. Subcellular localization forecasted that TCP proteins were all positioned in the nucleus. The BrTCP gene structure is relatively simple, with only seven members possessing introns, and none of the members contain UTR regions. BrTCPs comprise hormone-, light-, and stress-responsive elements. We found that the frequency of photoresponsive elements was greatest in the promoter region, suggesting that BrTCP genes are regulated by light signals and function synergistically with plant growth and development. In addition, five candidate interaction proteins of BrTCP4 were identified using yeast two-hybrid screening. RNA-Seq and q-PCR analyses of the interacting genes revealed differential expression of BrTCP family genes across various tissues following cold stress. Significant responses were observed under low-temperature stress, drought stress, and rehydration treatment, suggesting that these genes play crucial roles as regulators of the molecular network mechanisms responding to stress. This study enhances our understanding of the BrTCP family and provides significant insights into the stress tolerance mechanisms of B. rapa.

Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron-Exon Gene Structures Across Eukaryotic Lineages

Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still only partially understood. Here, we explore the evolution of the eukaryotic intron-exon gene structure by focusing on several key features such as the intron length, the number of introns, and the intron-to-exon length ratio in protein-coding genes. We utilize whole-genome data from 590 species covering the main eukaryotic taxonomic groups and analyze them within a statistical phylogenetic framework. We found that the basic gene structure differs markedly among the main eukaryotic groups, with animals, and particularly chordates, displaying intron-rich genes, compared with plants and fungi. Reconstruction of gene structure evolution suggests that these differences evolved prior to the divergence of the main phyla and have remained mostly conserved within groups. We revisit the previously reported association between the genome size and the mean intron length and report that this association differs considerably among phyla. Analyzing a large and diverse dataset of species with whole-genome information while applying advanced modeling techniques allowed us to obtain a global evolutionary perspective. Our findings may indicate that introns play different molecular and evolutionary roles in different organisms.

Identification of the FBN gene family in tomato and functional analysis of SlFBN11 in the electron transport under low night temperature

FBNs are lipid-associated proteins that play a critical role in plant growth and stress response. However, the mechanisms of how FBNs proteins participate in the low night temperature response in tomato still unclear. Here we conducted a comprehensive genome-wide analysis of the FBN gene family in Solanum lycopersicum. In total, 14 SlFBN genes were identified, and information on their gene structures, protein motifs, phylogenetic relationships, and stress-related cis-regulatory elements (CREs) was provided. Among these, SlFBN11 was selected as a promising candidate for further functional characterization. The silencing of SlFBN11 destroys the redox balance of the PSI reaction center under low night temperature (LNT) stress, which led to increased ROS accumulation. Surprisingly, we found that the silencing of SlFNR2 also displayed an imbalance in electron transport of the PSI under LNT stress. Further experiments showed SlFBN11 can interact with SlFNR2 to positively response electron transport low night temperature. Collectively, the study provides a comprehensive analysis of the FBN genes family in Solanum lycopersicum and provides a theoretical basis for our understanding of the function of FBN genes in adaptation to LNT stresses.

Genome-Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi-Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves

Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point, and so forth. Furthermore, we combined genome-wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS-type) and Maker00003187 (P-type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1 and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1, and rpoC2 in our previous study and the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNA pull-down assays revealed that Maker00002998 PPR protein might be involved in the post-transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.

Genome-Wide Identification of FCS-Like Zinc Finger (FLZ) Family Genes in Three Brassica Plant Species and Functional Characterization of BolFLZs in Chinese Kale Under Abiotic Stresses

FCS-like zinc finger (FLZ) proteins are plant-specific regulatory proteins, which contain a highly conserved FLZ domain, and they play critical roles in plant growth and stress responses. Although the FLZ family has been systematically characterized in certain plants, it remains underexplored in Brassica species, which are vital sources of vegetables, edible oils, and condiments for human consumption and are highly sensitive to various abiotic stresses. Following the whole-genome triplication events (WGT) in Brassica, elucidating how the FLZ genes have expanded, differentiated, and responded to abiotic stresses is valuable for uncovering the genetic basis and functionality of these genes. In this study, we identified a total of 113 FLZ genes from three diploid Brassica species and classified them into four groups on the basis of their amino acid sequences. Additionally, we identified 109 collinear gene pairs across these Brassica species, which are dispersed among different chromosomes, suggesting that whole-genome duplication (WGD) has significantly contributed to the expansion of the FLZ family. Subcellular localization revealed that six representative BolFLZ proteins are located in the nucleus and cytoplasm. Yeast two-hybrid assays revealed that 13 selected BolFLZs interact with BolSnRK1α1 and BolSnRK1α2, confirming the conservation of the SnRK1α-FLZ module in Brassica species. Expression profile analysis revealed differential expression patterns of BolFLZ across various tissues. Notably, the expression levels of seven BolFLZ genes out of the fifteen genes analyzed changed significantly following treatment with various abiotic stressors, indicating that the BolFLZ genes play distinct physiological roles and respond uniquely to abiotic stresses in Brassica species. Together, our results provide a comprehensive overview of the FLZ gene family in Brassica species and insights into their potential applications for enhancing stress tolerance and growth in Chinese kale.

Research progress on plant stress-associated protein (SAP) family: Master regulators to deal with environmental stresses

Every year, unfavorable environmental factors significantly affect crop productivity and threaten food security. Plants are sessile; they cannot move to escape unfavorable environmental conditions, and therefore, they activate a variety of defense pathways. Among them are processes regulated by stress-associated proteins (SAPs). SAPs have a specific zinc finger domain (A20) at the N-terminus and either AN1 or C2H2 at the C-terminus. SAP proteins are involved in many biological processes and in response to various abiotic or biotic constraints. Most SAPs play a role in conferring transgenic stress resistance and are stress-inducible. The emerging field of SAPs in abiotic or biotic stress response regulation has attracted the attention of researchers. Although SAPs interact with various proteins to perform their functions, the exact mechanisms of these interactions remain incompletely understood. This review aims to provide a comprehensive understanding of SAPs, covering their diversity, structure, expression, and subcellular localization. SAPs play a pivotal role in enabling crosstalk between abiotic and biotic stress signaling pathways, making them essential for developing stress-tolerant crops without yield penalties. Collectively, understanding the complex regulation of SAPs in stress responses can contribute to enhancing tolerance against various environmental stresses through several techniques such as transgenesis, classical breeding, or gene editing.

Genome-wide analysis of the AP2/ERF gene family in Pennisetum glaucum and the negative role of PgRAV_01 in drought tolerance

APETALA2/ethylene-responsive (AP2/ERF) plays crucial roles in resisting diverse stresses and in regulating plant growth and development. However, little is known regarding the structure and function of the AP2/ERF genes in pearl millet (Pennisetum glaucum). The AP2/ERF gene family may be involved in the development and maintenance of P. glaucum resilience to abiotic stresses, central to its role as a vital forage and cereal crop. In this study, PgAP2/ERF family members were identified and comprehensive bioinformatics analyses were performed, including determination of phylogenetic relationships, gene structures, conserved motifs, chromosomal localization, gene duplication, expression pattern, protein interaction network, and functional characterization of PgRAV_01 (Related to ABI3/VP1). In total, 78 PgAP2/ERF members were identified in the P. glaucum genome and classified into five subfamilies: AP2, ERF, DREB, RAV, and soloist. Members within the same clade of the PgAP2/ERF family showed similar gene structures and motif compositions. Six duplication events were identified in the PgAP2/ERF family; calculation of Ka/Ks values showed that purification selection dominated the evolution of PgAP2/ERFs. Subsequently, a potential interaction network of PgAP2/ERFs was generated to predict the interaction relationships. Additionally, abiotic stress expression analysis showed that most PgAP2/ERFs were induced in response to drought and heat stresses. Furthermore, overexpression of PgRAV_01 negatively regulated drought tolerance in Nicotiana benthamiana by reducing its antioxidant capacity and osmotic adjustment. Taken together, these results provide valuable insights into the characteristics and functions of PgAP2/ERF genes, with implications for abiotic stress tolerance, and will ultimately contribute to the genetic improvement of cereal crop breeding.

Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus

Platycodon grandiflorus stands as one of the most extensively utilized traditional Chinese medicinal herbs, with triterpenoids and their derivatives serving as its primary medicinal components. Oxido squalene cyclase (OSC), serving as a crucial enzyme in the triterpenoid synthesis pathway, has the capability to enzymatically generate significant quantities of sterols and triterpenoid intermediates. While the OSC gene family has been identified in numerous species, bioinformatics research on this family remains scant. Presently, the specific members of this gene family in Platycodon grandiflorus have yet to be definitively determined. In this study, we successfully identified a total of 15 PgOSC genes within the genome of Platycodon grandiflorus by conducting homology comparisons. These genes were discovered to be unevenly distributed across the five chromosomes of the species, organized in the form of gene clusters. Subsequently, we conducted a thorough analysis of the OSC gene family's evolutionary relationship by constructing a phylogenetic tree. Other characteristics of PgOSC family members, including gene structure, conserved motifs, protein three-dimensional structure, subcellular localization, and cis-acting elements were thoroughly characterized. Furthermore, We analyzed the expression of PgOSC gene in different tissues of Platycodon grandiflorus by qRT-PCR, and found that the expression of PgOSC genes in root was higher than that in stem and leaf. Upon comparing the effects of salt, heat, and drought treatments, we observed a significant induction of PgOSC gene expression in Platycodon grandiflorus specifically under salt stress conditions. In summary, this study comprehensively identified and analyzed the OSC gene family, aiming to provide basic biological information for exploring the members of PgOSC gene family.

Genome-Wide Identification and Analysis of Phospholipase C Gene Family Reveals Orthologs, Co-Expression Networks, and Expression Profiling Under Abiotic Stress in Sorghum bicolor

Phospholipase C (PLC) is an essential enzyme involved in lipid signaling pathways crucial for regulating plant growth and responding to environmental stress. In sorghum, 11 PLC genes have been identified, comprising 6 PI-PLCs and 5 NPCs. Through phylogenetic and interspecies collinearity analyses, structural similarities between SbPLCs and ZmPLCs proteins have been observed, with a particularly strong collinearity between SbPLCs and OsPLCs. Promoter function analysis has shown that SbPLCs are significantly enriched under abiotic stress and hormonal stimuli, like ABA, jasmonic acid, drought, high temperature, and salt. Gene co-expression networks, constructed using a weighted gene co-expression network analysis (WGCNA), highlight distinct expression patterns of SbPLC1, SbPLC3a, and SbPLC4 in response to abiotic stress, providing further insights into the expression patterns and interactions of SbPLCs under various environmental stimuli. qRT-PCR results reveal variations in expression levels among most SbPLCs members under different stress conditions (drought, NaCl, NaHCO3), hormone treatments (ABA), and developmental stages, indicating both specific and overlapping expression patterns. This comprehensive analysis offers valuable insights into the roles of SbPLCs in sorghum, shedding light on their specific expression patterns, regulatory elements, and protein interactions across different environmental stimuli and developmental stages.

Large-scale analysis of the PAC domain structure of arogenate dehydratases reveals their evolutionary patterns in angiosperms

Arogenate dehydratase (ADT) is the key limiting enzyme of plant phenylalanine biosynthesis, but some ADTs display a prephenate decarboxylase/dehydratase activity-conferring (PAC) domain. The genome resources of 70 species were employed to identify genes and outline their characteristics, especially the number and type of PAC domain structures. We obtained 522 ADTs, and their size, exon number, amino acid number and putative protein isoelectric point greatly varied from 306 to 2520 bp, 1 to 15, 101 to 839 and 4.37 to 11.18, respectively. We classified the ADTs into Class α (without a PAC domain) (115, 22.0 %), β (with a type I PAC domain) (244, 46.7 %) and γ (with a type II PAC domain) (163, 31.2 %), and their distribution frequencies exhibited large differences among various branches of angiosperms. We found that Class γ members are more conserved than Class β members, although they commonly experienced multiple duplication events and strong purifying selection, which resulted in a small number, and the putative origin order was from Class α to β and then to γ. In addition, the co-occurrence of both Class β and γ members could ensure the survival of angiosperms, while their optimized composition and strategically intertwined regulation may facilitate core eudicot success.

Genome-wide identification and comprehensive analysis of the AP2/ERF gene family in Prunus sibirica under low-temperature stress

BACKGROUND

AP2/ERF transcription factors are involved in the regulation of growth, development, and stress response in plants. Although the gene family has been characterized in various species, such as Oryza sativa, Arabidopsis thaliana, and Populus trichocarpa, studies on the Prunus sibirica AP2/ERF (PsAP2/ERF) gene family are lacking. In this study, PsAP2/ERFs in P. sibirica were characterized by genomic and transcriptomic analyses.

RESULTS

In the study, 112 PsAP2/ERFs were identified and categorized into 16 subfamilies. Within each subfamily, PsAP2/ERFs exhibited similar exon-intron structures and motif compositions. Additionally, 50 pairs of segmentally duplicated genes were identified within the PsAP2/ERF gene family. Our experimental results showed that 20 PsAP2/ERFs are highly expressed in leaves, roots, and pistils under low-temperature stress conditions. Among them, the expression of PsAP2/ERF21, PsAP2/ERF56 and PsAP2/ERF88 was significantly up-regulated during the treatment period, and it was hypothesised that members of the PsAP2/ERF family play an important role inlow temperature stress tolerance.

CONCLUSIONS

This study improves our understanding of the molecular basis of development and low-temperature stress response in P. sibirica and provides a solid scientific foundation for further functional assays and evolutionary analyses of PsAP2/ERFs.

Identification and characterization of NHX gene family for their role under salt stress in Vigna mungo

In the current study, we have performed a comprehensive analysis of the Sodium Hydrogen Exchanger (NHX) gene family in Vigna mungo, and a total of 44 NHX genes were identified. A bimodal distribution based on domains, gene structure and phylogenetic analysis was evident. All intronpoor and intron-rich genes were clustered in clades I and II, respectively. Interestingly, all genes of subclade IIb were localized to vacuoles and possess only the NHX domain. The isoelectric point and trans-membrane domain analysis reflect the wide distribution of the NHX genes. Interestingly, Vm_NHX2 and Vm_NHX3 lacked trans-membrane domain but were found to interact with other NHX genes as well as vital salinity pathway genes, including calcium-mediated salt-responsive genes. The comparison of the mRNA sequences with that of V. marina, a halophytic species, reflects their independent evolution, majorly supporting the convergent evolution. The Ka/Ks ratio reflects the abundance of purifying selection supporting their conserved function during evolution. In our analysis, several abiotic stress and hormone-responsive elements and transcription factor binding sites were present in the promoter of the NHX genes. Further, the ion partitioning of a tolerant (K90) and a susceptible (K49) variety of V. mungo suggested that K90 managed the Na+/K+ ratio more affluently, which was also supported by profiling of superoxide radicals, hydrogen peroxide, phenol, peroxidase activity and superoxide dismutase activity. From the expression, we identified five candidate Vm_NHX genes, four of which, i.e. Vm_NHX16, Vm_NHX17, Vm_NHX29 and Vm_NHX33, were localized to the vacuolar and lysosomal membrane.

Comprehensive analysis of pepper (Capsicum annuum) RAV genes family and functional identification of CaRAV1 under chilling stress

BACKGROUND

Despite its known significance in plant abiotic stress responses, the role of the RAV gene family in the response of Capsicum annuum to chilling stress remains largely unexplored.

RESULTS

In this study, we identified and characterized six members of the CaRAV gene subfamily in pepper plants through genome-wide analysis. Subsequently, the CaRAV subfamily was classified into four branches based on homology with Arabidopsis thaliana, each exhibiting relatively conserved domains within the branch. We discovered that light response elements accounted for the majority of CaRAVs, whereas low-temperature response elements were specific to the NGA gene subfamily. After pepper plants were subjected to chilling stress, qRT‒PCR analysis revealed that CaRAV1, CaRAV2 and CaNGA1 were significantly induced in response to chilling stress, indicating that CaRAVs play a role in the response to chilling stress. Using virus-induced gene silencing (VIGS) vectors, we targeted key members of the CaRAV gene family. Under normal growth conditions, the MDA content and SOD enzyme activity of the silenced plants were slightly greater than those of the control plants, and the REC activity was significantly greater than that of the control plants. The levels of MDA and electrolyte leakage were greater in the silenced plants after they were exposed to chilling stress, and the POD and CAT enzyme activities were significantly lower than those in the control, which was particularly evident under repeated chilling stress. In addition, the relative expression of CaPOD and CaCAT was greater in V2 plants upon repeated chilling stress, especially CaCAT was significantly greater in V2 plants than in the other two silenced plants, with 3.29 and 1.10 increases within 12 and 24 h. These findings suggest that CaRAV1 and CaNGA1 positively regulate the response to chilling stress.

CONCLUSIONS

Silencing of key members of the CaRAV gene family results in increased susceptibility to chilling damage and reduced antioxidant enzyme activity in plants, particularly under repeated chilling stress. This study provides valuable information for understanding the classification and putative functions of RAV transcription factors in pepper plants.

Identification and expression analysis of XIP gene family members in rice

Xylanase inhibitor proteins (XIP) are widely distributed in the plant kingdom, and also exist in rice. However, a systematic bioinformatics analysis of this gene family in rice (OsXIP) has not been conducted to date. In this study, we identified 32 members of the OsXIP gene family and analyzed their physicochemical properties, chromosomal localization, gene structure, protein structure, expression profiles, and interaction networks. Our results indicated that OsXIP genes exhibit an uneven distribution across eight rice chromosomes. These genes generally feature a low number of introns or are intronless, all family members, except for OsXIP20, contain two highly conserved motifs, namely Motif 8 and Motif 9. In addition, it is worth noting that the promoter regions of OsXIP gene family members feature a widespread presence of abscisic acid response elements (ABRE) and gibberellin response elements (GARE-motif and TATC-box). Quantitative Real-time PCR (qRT-PCR) analysis unveiled that the expression of OsXIP genes exhibited higher levels in leaves and roots, with considerable variation in the expression of each gene in these tissues both prior to and following treatments with abscisic acid (ABA) and gibberellin (GA3). Protein interaction studies and microRNA (miRNA) target prediction showed that OsXIP engages with key elements within the hormone-responsive and drought signaling pathways. The qRT-PCR suggested osa-miR2927 as a potential key regulator in the rice responding to drought stress, functioning as tissue-specific and temporally regulation. This study provides a theoretical foundation for further analysis of the functions within the OsXIP gene family.

Genome-wide characterization of LEA gene family reveals a positive role of BnaA.LEA6.a in freezing tolerance in rapeseed (Brassica napus L.)

BACKGROUND

Freezing stress is one of the major abiotic stresses that causes extensive damage to plants. LEA (Late embryogenesis abundant) proteins play a crucial role in plant growth, development, and abiotic stress. However, there is limited research on the function of LEA genes in low-temperature stress in Brassica napus (rapeseed).

RESULTS

Total 306 potential LEA genes were identified in B. rapa (79), B. oleracea (79) and B. napus (148) and divided into eight subgroups. LEA genes of the same subgroup had similar gene structures and predicted subcellular locations. Cis-regulatory elements analysis showed that the promoters of BnaLEA genes rich in cis-regulatory elements related to various abiotic stresses. Additionally, RNA-seq and real-time PCR results indicated that the majority of BnaLEA family members were highly expressed in senescent tissues of rapeseed, especially during late stages of seed maturation, and most BnaLEA genes can be induced by salt and osmotic stress. Interestingly, the BnaA.LEA6.a and BnaC.LEA6.a genes were highly expressed across different vegetative and reproductive organs during different development stages, and showed strong responses to salt, osmotic, and cold stress, particularly freezing stress. Further analysis showed that overexpression of BnaA.LEA6.a increased the freezing tolerance in rapeseed, as evidenced by lower relative electrical leakage and higher survival rates compared to the wild-type (WT) under freezing treatment.

CONCLUSION

This study is of great significance for understanding the functions of BnaLEA genes in freezing tolerance in rapeseed and offers an ideal candidate gene (BnaA.LEA6.a) for molecular breeding of freezing-tolerant rapeseed cultivars.

Genome-Wide Identification and Expression Analysis of Bx Involved in Benzoxazinoids Biosynthesis Revealed the Roles of DIMBOA during Early Somatic Embryogenesis in Dimocarpus longan Lour

Benzoxazinoids (BXs) are tryptophan-derived indole metabolites and play a role in various physiological processes, such as auxin metabolism. Auxin is essential in the process of somatic embryogenesis (SE) in plants. In this study, we used bioinformatics, transcriptome data, exogenous treatment experiments, and qPCR analysis to study the evolutionary pattern of Bx genes in green plants, the regulatory mechanism of DlBx genes during early SE, and the effect of 2,4-dihydroxy-7-methoxy-1,4-benzoxazine-3-one (DIMBOA) on the early SE in Dimocarpus longan Lour. The results showed that 27 putative DlBxs were identified in the longan genome; the Bx genes evolved independently in monocots and dicots, and the main way of gene duplication for the DlBx was tandem duplication (TD) and the DlBx were strongly constrained by purification selection during evolution. The transcriptome data indicated varying expression levels of DlBx during longan early SE, and most DlBxs responded to light, temperature, drought stress, and 2,4-dichlorophenoxyacetic acid (2,4-D) treatment; qRT-PCR results showed DlBx1, DlBx6g and DlBx6h were responsive to auxin, and treatment with 0.1mg/L DIMBOA for 9 days significantly upregulated the expression levels of DlBx1, DlBx3g, DlBx6c, DlBx6f, DlB6h, DlBx7d, DlBx8, and DlBx9b. The correlation analysis showed a significantly negative correlation between the expression level of DlBx1 and the endogenous IAA contents; DIMBOA significantly promoted the early SE and significantly changed the endogenous IAA content, and the IAA content increased significantly at the 9th day and decreased significantly at the 13th day. Therefore, the results suggested that DIMBOA indirectly promote the early SE by changing the endogenous IAA content via affecting the expression level of DlBx1 and hydrogen peroxide (H2O2) content in longan.

The high-quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae

Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well-known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high-quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single-cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species-specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high-quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology.

Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection

Plant cells undergo extensive transcriptional reprogramming following pathogen infection, with these reprogramming patterns becoming more complex when pathogens, such as hemibiotrophs, exhibit different lifestyles. These transcriptional changes are often orchestrated by MYB, WRKY and AP2/ERF transcription factors (TFs), which modulate both growth and defence-related gene expression. Transcriptional analysis of defence-related genes in avocado (Persea americana) infected with Phytophthora cinnamomi indicated differential immune response activation when comparing a partially resistant and susceptible rootstock. This study identified 226 MYB, 82 WRKY, and 174 AP2/ERF TF-encoding genes in avocado, using a genome-wide approach. Phylogenetic analysis revealed substantial sequence conservation within TF groups underscoring their functional significance. RNA-sequencing analysis in a partially resistant and susceptible avocado rootstock infected with P. cinnamomi was indicative of an immune response switch occurring in either rootstock after 24 and 6 h post-inoculation, respectively. Different clusters of co-expressed TF genes were observed at these times, suggesting the activation of necrotroph-related immune responses at varying intervals between the two rootstocks. This study aids our understanding of avocado immune response activation following P. cinnamomi infection, and the role of the TFs therein, elucidating the transcriptional reprogramming disparities between partially resistant and susceptible rootstocks.

Molecular characterization and evolutionary relationships of DOFs in four cherry species and functional analysis in sweet cherry

The DOF (DNA binding with one finger) has multiple functions in plants. However, it has received little attention in the research field of cherries. In this study, the evolutionary relationship and molecular characterization of DOF in four cherry species were analyzed, revealing its expression pattern in sweet cherry. There are 23 members in Prunus avium cv. 'Tieton', 88 in Prunus cerasus, 53 in Cerasus × yedoensis, and 27 in Cerasus serrulata. Most of these genes are intron-less or non-intron, with a conserved C2-C2 domain. Due to heterozygosity and chromosomal ploidy, whole-genome duplication (WGD) events occur to varying degrees, and DOF genes are contracted during evolution. Furthermore, these genes are affected by purifying selection pressure. Under low-temperature treatment, the expression of PavDOF2 and PavDOF18 were significantly up-regulated, while that of PavDOF16 is significantly down-regulated. The expression of PavDOF9, PavDOF12, PavDOF14, PavDOF16, PavDOF17, PavDOF18, and PavDOF19 exhibits an increasing trend during flower development and varies during sweet cherry fruit development. PavDOF1, PavDOF8, PavDOF9, and PavDOF15 are localized in the nucleus but is not transcriptionally active. The findings systemically demonstrate the molecular characteristics of DOF in different cherry varieties, providing a basis for further research on the functions of these genes.

CiAP2/ERF65 and CiAP2/ERF106, a pair of homologous genes in pecan (Carya illinoensis), regulate plant responses during submergence in transgenic Arabidopsis thaliana

When plants are entirely submerged, photosynthesis and respiration are severely restricted, affecting plant growth and potentially even causing plant death. The AP2/ERF superfamily has been widely reported to play a vital role in plant growth, development and resistance to biotic and abiotic stresses. However, no relevant studies exist on flooding stress in pecan. In this investigation, we observed that CiAP2/ERF65 positively modulated the hypoxia response during submergence, whereas CiAP2/ERF106 was sensitive to submergence. The levels of physiological and biochemical indicators, such as POD, CAT and among others, in CiAP2/ERF65-OE lines were significantly higher than those in wild-type Arabidopsis thaliana, indicating that the antioxidant capacity of CiAP2/ERF65-OE lines was enhanced under submergence. The RNA-seq results revealed that the maintenance of the expression levels of the antenna protein gene, different signaling pathways for regulation, as well as the storage and consumption of ATP, might account for the opposite phenotypes of CiAP2/ERF65 and CiAP2/ERF106. Furthermore, the expression of some stress-related genes was altered during submergence and reoxygenation. Overall, these findings enhance our understanding of submergence stress in pecan, providing important candidate genes for the molecular design and breeding of hypoxia resistant in plants.

Genome-wide identification of the PFK gene family and their expression analysis in Quercus rubra

The glycolytic pathway involves phosphofructokinase (PFK), a rate-limiting enzyme that catalyzes the phosphorylation of fructose-6-phosphate. In plants, the two PFK members are ATP-dependent phosphofructokinase (PFK) and pyrophosphate-fructose-6-phosphate phosphotransferase (PFP). However, the functions of the PFK family members in Quercus rubra are not well understood. The purpose of this study was to investigate the genome-wide distribution of the PFK family members and their roles in Q. rubra by performing a systematic study of the phylogenetic relationships, molecular characteristics, motifs, chromosomal and subcellular locations, and cis-elements of QrPFKs. We identified 14 QrPFK genes in the genome of Q. rubra, followed by examining their expression in different tissues, including the roots, stems, and leaves. The phylogenetic tree divided the 14 QrPFK genes into two groups: 11 belonging to PFK and three belonging to PFP. The expression profiles of all 14 proteins were relatively the same in leaves but differed between stems and roots. Four genes (Qurub.02G189400.1, Qurub.02G189400.2, Qurub.09G134300.1, and Qurub.09G134300.2) were expressed at very low levels in both stems and roots, while two (Qurub.05G235500.1 and Qurub.05G235500.1) were expressed at low levels and the others showed relatively high expression in all tissues.

Introns and Their Therapeutic Applications in Biomedical Researches

Context

Although for a long time, it was thought that intervening sequences (introns) were junk DNA without any function, their critical roles and the underlying molecular mechanisms in genome regulation have only recently come to light. Introns not only carry information for splicing, but they also play many supportive roles in gene regulation at different levels. They are supposed to function as useful tools in various biological processes, particularly in the diagnosis and treatment of diseases. Introns can contribute to numerous biological processes, including gene silencing, gene imprinting, transcription, mRNA metabolism, mRNA nuclear export, mRNA localization, mRNA surveillance, RNA editing, NMD, translation, protein stability, ribosome biogenesis, cell growth, embryonic development, apoptosis, molecular evolution, genome expansion, and proteome diversity through various mechanisms.

Evidence Acquisition

In order to fulfill the objectives of this study, the following databases were searched: Medline, Scopus, Web of Science, EBSCO, Open Access Journals, and Google Scholar. Only articles published in English were included.

Results & Conclusions

The intervening sequences of eukaryotic genes have critical functions in genome regulation, as well as in molecular evolution. Here, we summarize recent advances in our understanding of how introns influence genome regulation, as well as their effects on molecular evolution. Moreover, therapeutic strategies based on intron sequences are discussed. According to the obtained results, a thorough understanding of intron functional mechanisms could lead to new opportunities in disease diagnosis and therapies, as well as in biotechnology applications.

Hemibiotrophic Phytophthora infestans Modulates the Expression of SWEET Genes in Potato (Solanum tuberosum L.)

Sugar Efflux transporters (SWEET) are involved in diverse biological processes of plants. Pathogens have exploited them for nutritional gain and subsequently promote disease progression. Recent studies have implied the involvement of potato SWEET genes in the most devastating late blight disease caused by Phytophthora infestans. Here, we identified and designated 37 putative SWEET genes as StSWEET in potato. We performed detailed in silico analysis, including gene structure, conserved domains, and phylogenetic relationship. Publicly available RNA-seq data was harnessed to retrieve the expression profiles of SWEET genes. The late blight-responsive SWEET genes were identified from the RNA-seq data and then validated using quantitative real-time PCR. The SWEET gene expression was studied along with the biotrophic (SNE1) and necrotrophic (PiNPP1) marker genes of P. infestans. Furthermore, we explored the co-localization of P. infestans resistance loci and SWEET genes. The results indicated that nine transporter genes were responsive to the P. infestans in potato. Among these, six transporters, namely StSWEET10, 12, 18, 27, 29, and 31, showed increased expression after P. infestans inoculation. Interestingly, the observed expression levels aligned with the life cycle of P. infestans, wherein expression of these genes remained upregulated during the biotrophic phase and decreased later on. In contrast, StSWEET13, 14, and 32 didn't show upregulation in inoculated samples suggesting non-targeting by pathogens. This study underscores these transporters as prime P. infestans targets in potato late blight, pivotal in disease progression, and potential candidates for engineering blight-resistant potato genotypes.

Bioinformatics Analysis of MSH1 Genes of Green Plants: Multiple Parallel Length Expansions, Intron Gains and Losses, Partial Gene Duplications, and Alternative Splicing

MutS homolog 1 (MSH1) is involved in the recombining and repairing of organelle genomes and is essential for maintaining their stability. Previous studies indicated that the length of the gene varied greatly among species and detected species-specific partial gene duplications in Physcomitrella patens. However, there are critical gaps in the understanding of the gene size expansion, and the extent of the partial gene duplication of MSH1 remains unclear. Here, we screened MSH1 genes in 85 selected species with genome sequences representing the main clades of green plants (Viridiplantae). We identified the MSH1 gene in all lineages of green plants, except for nine incomplete species, for bioinformatics analysis. The gene is a singleton gene in most of the selected species with conserved amino acids and protein domains. Gene length varies greatly among the species, ranging from 3234 bp in Ostreococcus tauri to 805,861 bp in Cycas panzhihuaensis. The expansion of MSH1 repeatedly occurred in multiple clades, especially in Gymnosperms, Orchidaceae, and Chloranthus spicatus. MSH1 has exceptionally long introns in certain species due to the gene length expansion, and the longest intron even reaches 101,025 bp. And the gene length is positively correlated with the proportion of the transposable elements (TEs) in the introns. In addition, gene structure analysis indicated that the MSH1 of green plants had undergone parallel intron gains and losses in all major lineages. However, the intron number of seed plants (gymnosperm and angiosperm) is relatively stable. All the selected gymnosperms contain 22 introns except for Gnetum montanum and Welwitschia mirabilis, while all the selected angiosperm species preserve 21 introns except for the ANA grade. Notably, the coding region of MSH1 in algae presents an exceptionally high GC content (47.7% to 75.5%). Moreover, over one-third of the selected species contain species-specific partial gene duplications of MSH1, except for the conserved mosses-specific partial gene duplication. Additionally, we found conserved alternatively spliced MSH1 transcripts in five species. The study of MSH1 sheds light on the evolution of the long genes of green plants.

Genome-Wide Comparison and Functional Characterization of HMGR Gene Family Associated with Shikonin Biosynthesis in Lithospermum erythrorhizon

3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), as the rate-limiting enzyme in the mevalonate pathway, is essential for the biosynthesis of shikonin in Lithospermum erythrorhizon. However, in the absence of sufficient data, the principles of a genome-wide in-depth evolutionary exploration of HMGR family members in plants, as well as key members related to shikonin biosynthesis, remain unidentified. In this study, 124 HMGRs were identified and characterized from 36 representative plants, including L. erythrorhizon. Vascular plants were found to have more HMGR family genes than nonvascular plants. The phylogenetic tree revealed that during lineage and species diversification, the HMGRs evolved independently and intronless LerHMGRs emerged from multi-intron HMGR in land plants. Among them, Pinus tabuliformis and L. erythrorhizon had the most HMGR gene duplications, with 11 LerHMGRs most likely expanded through WGD/segmental and tandem duplications. In seedling roots and M9 cultured cells/hairy roots, where shikonin biosynthesis occurs, LerHMGR1 and LerHMGR2 were expressed significantly more than other genes. The enzymatic activities of LerHMGR1 and LerHMGR2 further supported their roles in catalyzing the conversion of HMG-CoA to mevalonate. Our findings provide insight into the molecular evolutionary properties and function of the HMGR family in plants and a basis for the genetic improvement of efficiently produced secondary metabolites in L. erythrorhizon.

Genome-Wide Analyses of SlFWL Family Genes and Their Expression Profiles under Cold, Heat, Salt and Drought Stress in Tomato

PLAC8 is a cysteine-rich protein that serves as a central mediator of tumor evolution in mammals. PLAC8 motif-containing proteins widely distribute in fungi, algae, higher plants and animals that have been described to be implicated in fruit size, cell number and the transport of heavy metals such as cadmium or zinc. In tomatoes, FW2.2 is a PLAC8 motif-containing gene that negatively controls fruit size by regulating cell division and expansion in the carpel ovary during fruit development. However, despite FW2.2, other FWL (FW2.2-Like) genes in tomatoes have not been investigated. In this study, we identified the 21 SlFWL genes, including FW2.2, examined their expression profiles under various abiotic adversity-related conditions. The SlFWL gene structures and motif compositions are conserved, indicating that tomato SlFWL genes may have similar roles. Cis-acting element analysis revealed that the SlFWL genes may participate in light and abiotic stress responses, and they also interacted with a variety of phytohormone-responsive proteins and plant development elements. Phylogenetic analyses were performed on five additional plant species, including Arabidopsis, pepper, soybean, rice and maize, these genes were classified into five subfamilies. Based on the results of collinearity analyses, the SlFWL genes have a tighter homologous evolutionary relationship with soybean, and these orthologous FWL gene pairs might have the common ancestor. Expression profiling of SlFWL genes show that they were all responsive to abiotic stresses, each subgroup of genes exhibited a different expression trend. Our findings provide a strong foundation for investigating the function and abiotic stress responses of the SlFWL family genes.

DREB1 and DREB2 Genes in Garlic (Allium sativum L.): Genome-Wide Identification, Characterization, and Stress Response

Dehydration-responsive element-binding (DREB) transcription factors (TFs) of the A1 and A2 subfamilies involved in plant stress responses have not yet been reported in Allium species. In this study, we used bioinformatics and comparative transcriptomics to identify and characterize DREB A1 and A2 genes redundant in garlic (Allium sativum L.) and analyze their expression in A. sativum cultivars differing in the sensitivity to cold and Fusarium infection. Eight A1 (AsaDREB1.1-1.8) and eight A2 (AsaDREB2.1-2.8) genes were identified. AsaDREB1.1-1.8 genes located in tandem on chromosome 1 had similar expression patterns, suggesting functional redundancy. AsaDREB2.1-2.8 were scattered on different chromosomes and had organ- and genotype-specific expressions. AsaDREB1 and AsaDREB2 promoters contained 7 and 9 hormone- and stress-responsive cis-regulatory elements, respectively, and 13 sites associated with TF binding and plant development. In both Fusarium-resistant and -sensitive cultivars, fungal infection upregulated the AsaDREB1.1-1.5, 1.8, 2.2, 2.6, and 2.8 genes and downregulated AsaDREB2.5, but the magnitude of response depended on the infection susceptibility of the cultivar. Cold exposure strongly upregulated the AsaDREB1 genes, but downregulated most AsaDREB2 genes. Our results provide the foundation for further functional analysis of the DREB TFs in Allium crops and could contribute to the breeding of stress-tolerant varieties.

Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat

Crop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog diversity, intra-varietal diversity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional diversity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous diversity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat.

Unraveling the genomic reorganization of polygalacturonase-inhibiting proteins in chickpea

Polygalacturonase-inhibiting proteins (PGIPs) are cell wall proteins that inhibit pathogen polygalacturonases (PGs). PGIPs, like other defense-related proteins, contain extracellular leucine-rich repeats (eLRRs), which are required for pathogen PG recognition. The importance of these PGIPs in plant defense has been well documented. This study focuses on chickpea (Cicer arietinum) PGIPs (CaPGIPs) owing to the limited information available on this important crop. This study identified two novel CaPGIPs (CaPGIP3 and CaPGIP4) and computationally characterized all four CaPGIPs in the gene family, including the previously reported CaPGIP1 and CaPGIP2. The findings suggest that CaPGIP1, CaPGIP3, and CaPGIP4 proteins possess N-terminal signal peptides, ten LRRs, theoretical molecular mass, and isoelectric points comparable to other legume PGIPs. Phylogenetic analysis and multiple sequence alignment revealed that the CaPGIP1, CaPGIP3, and CaPGIP4 amino acid sequences are similar to the other PGIPs reported in legumes. In addition, several cis-acting elements that are typical of pathogen response, tissue-specific activity, hormone response, and abiotic stress-related are present in the promoters of CaPGIP1, CaPGIP3, and CaPGIP4 genes. Localization experiments showed that CaPGIP1, CaPGIP3, and CaPGIP4 are located in the cell wall or membrane. Transcript levels of CaPGIP1, CaPGIP3, and CaPGIP4 genes analyzed at untreated conditions show varied expression patterns analogous to other defense-related gene families. Interestingly, CaPGIP2 lacked a signal peptide, more than half of the LRRs, and other characteristics of a typical PGIP and subcellular localization indicated it is not located in the cell wall or membrane. The study's findings demonstrate CaPGIP1, CaPGIP3, and CaPGIP4's similarity to other legume PGIPs and suggest they might possess the potential to combat chickpea pathogens.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Genome-Wide Analysis of Proline-Rich Extensin-Like Receptor Kinases (PERKs) Gene Family Reveals Their Roles in Plant Development and Stress Conditions in Oryza sativa L

Proline-rich extensin-like receptor kinases (PERKs) play a crucial role in a wide range of biological processes in plants. In model plants like Arabidopsis, the PERK gene family has been well investigated. Conversely, no information available on the PERK gene family and their biological functions largely remained unknown in rice. This study analyzed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, Gene ontology (GO) annotation and protein-protein interaction of OsPERK gene family members using various bioinformatics tools based on the whole-genome data of O. sativa. Thus, in this work, 8 PERK genes in rice were identified, and their roles in plant development, growth, and response to various stresses were studied. A phylogenetic study revealed that OsPERKs are grouped into seven classes. Chromosomal mapping also displayed that 8 PERK genes were unevenly distributed on 12 chromosomes. Further, the prediction of subcellular localization indicated that OsPERKs were mainly located at the endomembrane system. Gene structure analysis of OsPERKs has shown a distinctive evolutionary path. In addition, synteny analysis exhibited the 40 orthologous gene pairs in Arabidopsis thaliana, Triticum aestivum, Hordeum vulgare and Medicago truncatula. Furthermore, Ka to Ks proportion shows that most OsPERK genes experienced resilient purifying selection during evolutionary processes. The OsPERK promoters contained several cis-acting regulatory, which are crucial for plant development processes, phytohormone signaling, stress, and defense response. Moreover, the expression pattern of OsPERK family members showed differential expression patterns in different tissues and various stress conditions. Taken together, these results provide clear messages for a better understanding the roles of OsPERK genes in various development stages, tissues, and multifactorial stress as well as enriched the related research of OsPERK family members in rice.

Genome-Wide Identification and Expression Analysis of the Dof Transcription Factor in Annual Alfalfa Medicago polymorpha

The Dof transcription factor is a plant-specific transcription gene family that plays various biological functions in plant development and stress response. However, no relevant research has been conducted on Medicago polymorpha. Here, 36 MpDof genes were identified in the M. polymorpha genome and further divided into 10 groups based on the comparative phylogenetic analysis. The essential information of MpDof genes, such as chromosomal localization, gene structure, conserved motifs, and selective pressures were systematically analyzed. All 36 MpDof genes were predicted to contain more cis-acting elements related to hormone response. MpDof24 and MpDof25 were predicted to interact with MpDof11 and MpDof26 to involve in the photoperiod blooms process. The MpDof genes showed a diverse expression pattern in different tissues. Notably, MpDof29 and MpDof31 were specifically expressed in the large pod and root, respectively, suggesting their crucial role in the pod and root development. qRT-PCR analysis indicated that the expression levels of MpDof10, MpDof25, MpDof26, and MpDof29 were obviously up-regulated under drought, salt, and cold stress. Collectively, genome-wide identification, evolutionary, and expression analysis of the Dof transcription gene family in M. polymorpha will provide new information to further understand and utilize the function of these Dof genes in Medicago plants.

Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes

Cicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.

Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.)

The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit for further understanding their underlying evolutionary mechanism in plants. Using internal correspondence analysis (ICA), we reveal a significant difference in synonymous codon usage between SEGs and multiple-exon genes (MEGs) in rice. But the effect is weak, accounting for only 2.61% of the total codon usage variability. SEGs and MEGs contain remarkably different base compositions, and are under clearly differential selective constraints, with the former having higher GC content, and evolving relatively faster during evolution. In the group of SEGs, the variability in synonymous codon usage among genes is partially due to the variations in GC content, gene function, and gene expression level, which accounts for 22.03%, 5.99%, and 3.32% of the total codon usage variability, respectively. Therefore, mutational bias and natural selection should work on affecting the synonymous codon usage of SEGs in rice. These findings may deepen our knowledge for the mechanisms of origination, differentiation and regulation of SEGs in plants.

Trends in the evolution of intronless genes in Poaceae

Intronless genes (IGs), which are a feature of prokaryotes, are a fascinating group of genes that are also present in eukaryotes. In the current study, a comparison of Poaceae genomes revealed that the origin of IGs may have involved ancient intronic splicing, reverse transcription, and retrotranspositions. Additionally, IGs exhibit the typical features of rapid evolution, including recent duplications, variable copy numbers, low divergence between paralogs, and high non-synonymous to synonymous substitution ratios. By tracing IG families along the phylogenetic tree, we determined that the evolutionary dynamics of IGs differed among Poaceae subfamilies. IG families developed rapidly before the divergence of Pooideae and Oryzoideae and expanded slowly after the divergence. In contrast, they emerged gradually and consistently in the Chloridoideae and Panicoideae clades during evolution. Furthermore, IGs are expressed at low levels. Under relaxed selection pressure, retrotranspositions, intron loss, and gene duplications and conversions may promote the evolution of IGs. The comprehensive characterization of IGs is critical for in-depth studies on intron functions and evolution as well as for assessing the importance of introns in eukaryotes.

Decipher the molecular evolution and expression patterns of Cupin family genes in oilseed rape

Cupin proteins are involved in plant growth and development as well as in response to various stresses. Here, a total of 173 Cupin genes were identified in Brassica napus, and their molecular evolution and expression patterns were analyzed. These genes were classified into ten groups. Motif and exon-intron structure indicated a high degree of conservation within each group during evolution. BnaCupins were distributed on 19 chromosomes and their expansion is mainly contributed by whole-genome duplication (WGD) and segmental duplication events. BnaCupins have undergone severe purifying selection during a long evolutionary process. Meanwhile, some positive selection sites were identified. Expression patterns and cis-element analysis indicated that BnaCupins play significant roles in plant growth and stress responses. In addition, the expression levels of some BnCupins were significantly altered when treated with different conditions (cold, salt, drought, IAA, ABA, and 6-BA). Some BnaCupin interacting proteins, such as glycosyl hydrolase5 (GHs5), carbohydrate kinase (CHKs), ATP-dependent 6-phosphofructokinase (ATP-PFK), S-adenosylmethionine synthase (S-MAT), and aldolase class II (ALD II), were identified by the protein-protein interaction network. It will contribute to enriching our knowledge of the Cupin gene family in B. napus and provide a basis for further studies of their functions.

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis

Reactive oxygen species (ROS) are constant by-products of aerobic life. In excess, ROS lead to cytotoxic protein aggregates, which are a hallmark of ageing in animals and linked to age-related pathologies in humans. Acylamino acid-releasing enzymes (AARE) are bifunctional serine proteases, acting on oxidized proteins. AARE are found in all domains of life, albeit under different names, such as acylpeptide hydrolase (APEH/ACPH), acylaminoacyl peptidase (AAP), or oxidized protein hydrolase (OPH). In humans, AARE malfunction is associated with age-related pathologies, while their function in plants is less clear. Here, we provide a detailed analysis of AARE genes in the plant lineage and an in-depth analysis of AARE localization and function in the moss Physcomitrella and the angiosperm Arabidopsis. AARE loss-of-function mutants have not been described for any organism so far. We generated and analysed such mutants and describe a connection between AARE function, aggregation of oxidized proteins and plant ageing, including accelerated developmental progression and reduced life span. Our findings complement similar findings in animals and humans, and suggest a unified concept of ageing may exist in different life forms.

Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under Drought and Salt Stresses in Sweet Potato [Ipomoea batatas (L.) Lam]

The domain of unknown function 668 (DUF668) is a gene family that plays a vital role in responses to adversity coercion stresses in plant. However, the function of the DUF668 gene family is not fully understood in sweet potato. In this study, bioinformatics methods were used to analyze the number, physicochemical properties, evolution, structure, and promoter cis-acting elements of the IbDUF668 family genes, and RNA-seq and qRT-PCR were performed to detect gene expression and their regulation under hormonal and abiotic stress. A total of 14 IbDUF668 proteins were identified in sweet potato, distributed on nine chromosomes. By phylogenetic analysis, IbDUF668 proteins can be divided into two subfamilies. Transcriptome expression profiling revealed that many genes from DUF668 in sweet potato showed specificity and differential expression under cold, heat, drought, salt and hormones (ABA, GA3 and IAA). Four genes (IbDUF668-6, 7, 11 and 13) of sweet potato were significantly upregulated by qRT-PCR under ABA, drought and NaCl stress. Results suggest that the DUF668 gene family is involved in drought and salt tolerance in sweet potato, and it will further provide the basic information of DUF668 gene mechanisms in plants.

The revealing of a novel lipid transfer protein lineage in green algae

BACKGROUND

Non-specific lipid transfer proteins (nsLTPs) are a group of small and basic proteins that can bind and transfer various lipid molecules to the apoplastic space. A typical nsLTP carries a conserved architecture termed eight-cysteine motif (8CM), a scaffold of loop-linked helices folding into a hydrophobic cavity for lipids binding. Encoded by a multigene family, nsLTPs are widely distributed in terrestrial plants from bryophytes to angiosperms with dozens of gene members in a single species. Although the nsLTPs in the most primitive plants such as Marchantia already reach 14 members and are divergent enough to form separate groups, so far none have been identified in any species of green algae.

RESULTS

By using a refined searching strategy, we identified putative nsLTP genes in more than ten species of green algae as one or two genes per haploid genome but not in red and brown algae. The analyses show that the algal nsLTPs carry unique characteristics, including the extended 8CM spacing, larger molecular mass, lower pI value and multiple introns in a gene, which suggests that they could be a novel nsLTP lineage. Moreover, the results of further investigation on the two Chlamydomonas nsLTPs using transcript and protein assays demonstrated their late zygotic stage expression patterns and the canonical nsLTP properties were also verified, such as the fatty acids binding and proteinase resistance activities.

CONCLUSIONS

In conclusion, a novel nsLTP lineage is identified in green algae, which carries some unique sequences and molecular features that are distinguishable from those in land plants. Combined with the results of further examinations of the Chlamydomonas nsLTPs in vitro, possible roles of the algal nsLTPs are also suggested. This study not only reveals the existence of the nsLTPs in green algae but also contributes to facilitating future studies on this enigmatic protein family.