Genome-wide identification, expression profiling, and network analysis of AT-hook gene family in maize

Promoter of Cassava MeAHL31 Responds to Diverse Abiotic Stresses and Hormone Signals in Transgenic Arabidopsis

The AT-hook motif nuclear-localized (AHL) family is pivotal for the abiotic stress response in plants. However, the function of the cassava AHL genes has not been elucidated. Promoters, as important regulatory elements of gene expression, play a crucial role in stress resistance. In this study, the promoter of the cassava MeAHL31 gene was cloned. The MeAHL31 protein was localized to the cytoplasm and the nucleus. qRT-PCR analysis revealed that the MeAHL31 gene was expressed in almost all tissues tested, and the expression in tuber roots was 321.3 times higher than that in petioles. Promoter analysis showed that the MeAHL31 promoter contains drought, methyl jasmonate (MeJA), abscisic acid (ABA), and gibberellin (GA) cis-acting elements. Expression analysis indicated that the MeAHL31 gene is dramatically affected by treatments with salt, drought, MeJA, ABA, and GA3. Histochemical staining in the proMeAHL31-GUS transgenic Arabidopsis corroborated that the GUS staining was found in most tissues and organs, excluding seeds. Beta-glucuronidase (GUS) activity assays showed that the activities in the proMeAHL31-GUS transgenic Arabidopsis were enhanced by different concentrations of NaCl, mannitol (for simulating drought), and MeJA treatments. The integrated findings suggest that the MeAHL31 promoter responds to the abiotic stresses of salt and drought, and its activity is regulated by the MeJA hormone signal.

ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L

Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.

S, Sharma VK. Genome-wide dissection of AT-hook motif nuclear-localized gene family and their expression profiling for drought and salt stress in rice (Oryza sativa)

AT-hook motif nuclear localized (AHL) genes are functionally very less explored, but their nature is very diverse. In the present study, we identified 20 AHL genes in rice. Phylogenetic analyses and evolutionary classification of AHL genes showed that they are conserved in plants, but the number of genes is still expanding in different crops and regulating new biological functions. Gene structure analysis showed that OsAHLs are with and without intron types of genes, suggesting that AHL genes added intron during evolution for neofunctionalization. The cis analysis of OsAHL genes suggested its motif diversity. In order to understand the function, 19 transcriptomes were identified from various tissues and different developmental stages of rice, and they were divided into eight groups by different temporal and spatial expression. Through co-expression analysis, 11 OsAHLs and 13 novel genes with intricate networks that control many biological pathways in rice were identified. The interactions of OsAHL proteins showed that they co-regulate important processes including flowering, reproductive organ development, and photosynthesis activity. The functionality of all 20 genes of OsAHL for drought and salt stress in leaf tissues of two contrasting genotypes (IR64 and NL44) of rice was studied using qRT-PCR. The result clearly showed significant upregulation of OsAHL genes under drought and salt conditions over the control. The differential expression between IR64 and NL44 showed a significant upregulation of OsAHL genes in NL44 as compared to the IR64 genotype under drought and salt stress. Overall, the result indicates that AHL genes might be involved in mediating drought and salt-signaling transduction pathways. The drought- and salt-tolerant nature of NL44 was also confirmed by expression profiling.

Identification of tomato AHL gene families and functional analysis their roles in fruit development and abiotic stress response

The AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) transcription factors play important roles in regulating plant development and stress response. However, the AHL family genes have not been identified in tomato (Solanum lycopersicum) and their biological functions have not been elucidated. In this work, the gene families encoding AHLs were identified in tomato genome, and their physical and chemical characteristics, subcellular localization, gene expression profiles during fruit development and upon abiotic stimulus were investigated. Overall, a total of 18 AHL members were identified in tomato genome, phylogenetic analysis classified these SlAHL members into two clades, clade A (SlAHL1-8) and clade B (SlAHL9-18). Six clade A SlAHLs were detected to be subcellular localized in the nucleus. The transcripts of the representative clade A SlAHLs predominantly accumulated 10 days post anthesis (dpa) in tomato fruits, revealing an involvement of these SlAHLs in early fruit development. Furthermore, compared with clade B members, the transcripts of the clade A SlAHLs were more responsive to heat, drought, cold and salt stresses, suggesting that these SlAHLs may play major roles in response to abiotic stresses. Moreover, overexpression of SlAHL1 and SlAHL7 in Arabidopsis increased the sensitivity to ABA during seed germination and seedling stages. Overexpression of SlAHL1 inhibited seed germination while increased primary root elongation upon salt and drought stresses. Together, our work suggested that the clade A SlAHL genes may play an important role in response to abiotic stresses, which paving the way for future functional analysis of AHL genes in tomato and other Solanaceae species.

Genome-wide identification and analyses of the AHL gene family in rice (Oryza sativa)

AHL (AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED) family members play a critical role in stress resistance regulation by DNA-protein and protein-protein interactions in a number of plant biological processes. Using genomic data, an attempt was made to evaluate AHL genes in rice. Using a genome database, we performed in silico detection and characterization of AHL family genes in rice. The data of the gene were obtained from the Rice Genome Annotation Project (RGAP) database. The rice genome data were analyzed using bioinformatics software. The main objectives of the research are genome-wide recognition, expression, structural examination, phylogenetic analysis of AHL gene family, classification of AHL proteins into different classes based on motif and domain composition, analysis of promoter regions to identify stress and phytohormone-associated cis-elements, expression analysis of OsAHL genes in diverse tissues and stressful situations and understanding the roles of AHLs in controlling rice plant development. The genome-wide recognition, expression, and structural examination of the AHL gene family were undertaken in this research to evaluate the structural activities of AHLs in rice. From the Oryza sativa genome, 26 AHL genes have been identified. WoLF PSORT analysis predicted different subcellular localizations for these proteins, including nuclear, cytoplasmic, chloroplast, and endoplasmic reticulum. According to a phylogenetic study, rice AHLs resulted in two clades: Clade-A with no introns (excluding OsAHL15 and OsAHL21) and Clade-B with four introns. Depending on the AT-hook motif (s) (AHM) and PPC/DUF 296 domain composition, the AHL proteins are categorized into the following three classes: Type-I, Type-II, and Type-III, among Type-I AHLs constituting Clade-A, Type-II, and Type-III creating Clade-B. Type-I was the largest gene family, representing 57.69% of OsAHL genes. The exon-intron organization within clades of OsAHL genes was similar. Multiple sequence alignment identified 15 conserved motifs, including AT-hook motifs and the PPC domain, suggesting DNA-binding functionality. OsAHL genes were distributed across 12 chromosomes, with chromosome 2 and 8 harboring the highest number of genes. Gene duplication analysis revealed eight paralogous pairs, indicating evolutionary divergence between 13.32 and 35.59 million years ago. The emergence of OsAHL paralogous pairs was favored by purifying selection. Synteny analysis between rice and Arabidopsis demonstrated collinearity among AHL gene pairs, implying comparable structure and function in the two species. The role of stress- and phytohormone-associated cis-elements in the OsAHL genes was discovered by promoter analysis. OsAHL genes participated in various biological processes, with a prominent involvement in cellular and metabolic processes. They exhibited a significant enrichment in binding functions, including a substantial proportion of transcription regulators. OsAHL genes displayed diverse expression patterns in different tissues and under abiotic stress conditions. According to their expression patterns, the majority of OsAHLs of Clade-B were expressed mainly in the pistil indicating their roles in flower formation, while Clade-A OsAHLs had the minimal expression in pistil and highly expressed in embryos, indicating that the AHLs within each clade had the same expression patterns. Some OsAHL genes were also expressed in stressful situations, such as cold, salt, and drought. Protein interaction analysis revealed networks involving AHL proteins and other proteins, suggesting their participation in phytohormone responses, abiotic stress, and plant development. In this work, 26 OsAHL genes were found in the genome of rice. Rice OsAHLs were grouped into two phylogenetic groups. It is further divided into three types on the basis of the motif and domain composition. At various phases of development, the expression analysis of OsAHLs showed numerous variations in expression levels in diverse tissues and stress situations. Our findings shed light on the significant roles of AHLs in controlling rice plant development.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03666-0.

ClNAC100 Is a NAC Transcription Factor of Chinese Fir in Response to Phosphate Starvation

Phosphate (Pi) deficiency is one of the most limiting factors for Chinese fir growth and production. Moreover, continuous cultivation of Chinese fir for multiple generations led to the reduction of soil nutrients, which hindered the yield of Chinese fir in southern China. Although NAC (NAM, ATAF, and CUC) transcription factors (TFs) play critical roles in plant development and abiotic stress resistance, it is still unclear how they regulate the response of Chinese fir to phosphate (Pi) starvation. Based on Pi-deficient transcriptome data of Chinses fir root, we identified a NAC transcription factor with increased expression under Pi deficiency, which was obtained by PCR and named ClNAC100. RT-qPCR confirmed that the expression of ClNAC100 in the root of Chinese fir was induced by phosphate deficiency and showed a dynamic change with time. It was positively regulated by ABA and negatively regulated by JA, and ClNAC100 was highly expressed in the roots and leaves of Chinese fir. Transcriptional activation assay confirmed that ClNAC100 was a transcriptional activator. The promoter of ClNAC100 was obtained by genome walking, which was predicted to contain a large number of stress, hormone, and growth-related cis-elements. Tobacco infection was used to verify the activity of the promoter, and the core promoter was located between -1519 bp and -589 bp. We identified 18 proteins bound to the ClNAC100 promoter and 5 ClNAC100 interacting proteins by yeast one-hybrid and yeast two-hybrid, respectively. We speculated that AHL and TIFY family transcription factors, calmodulin, and E3 ubiquitin ligase in these proteins might be important phosphorus-related proteins. These results provide a basis for the further study of the regulatory mechanism and pathways of ClNAC100 under Pi starvation.

Systematical Characterization of the AT-Hook Gene Family in Juglans regia L. and the Functional Analysis of the JrAHL2 in Flower Induction and Hypocotyl Elongation

AT-hook motif nuclear localization (AHL) proteins play essential roles in various plant biological processes. Yet, a comprehensive understanding of AHL transcription factors in walnut (Juglans regia L.) is missing. In this study, 37 AHL gene family members were first identified in the walnut genome. Based on the evolutionary analysis, JrAHL genes were grouped into two clades, and their expansion may occur due to segmental duplication. The stress-responsive nature and driving of developmental activities of JrAHL genes were revealed by cis-acting elements and transcriptomic data, respectively. Tissue-specific expression analysis showed that JrAHLs had a profound transcription in flower and shoot tip, JrAHL2 in particular. Subcellular localization showed that JrAHL2 is anchored to the nucleus. Overexpression of JrAHL2 in Arabidopsis adversely affected hypocotyl elongation and delayed flowering. Our study, for the first time, presented a detailed analysis of JrAHL genes in walnut and provided theoretical knowledge for future genetic breeding programs.

AT-Hook Transcription Factors Show Functions in Liriodendron chinense under Drought Stress and Somatic Embryogenesis

AT-hook motif nuclear localized (AHL) is a transcription factor that can directly induce plant somatic embryogenesis without adding exogenous hormones. One of its functional domains, the AT-hook motif, has a chromatin-modifying function and participates in various cellular processes, including DNA replication and repair and gene transcription leading to cell growth. Liriodendron chinense (Hemsl.) Sargent is an important ornamental and timber tree in China. However, its low drought-resistant ability further leads to a low natural growth rate of its population. Based on bioinformatics analysis, this study identified a total of 21 LcAHLs in L. chinense. To explore the expression pattern of the AHL gene family under drought and somatic embryogenesis, we performed a systematic analysis including basic characteristics, gene structure, chromosome localization, replication event, cis-acting elements and phylogenetic analyses. According to the phylogenetic tree, the 21 LcAHL genes are divided into three separate clades (Clade I, II, and III). Cis-acting element analysis indicated the involvement of the LcAHL genes in drought, cold, light, and auxin regulation. In the generated drought stress transcriptome, a total of eight LcAHL genes showed increased expression levels, with their expression peaking at 3 h and leveling off after 1 d. Nearly all LcAHL genes were highly expressed in the process of somatic embryogenesis. In this study, we performed a genome-wide analysis of the LcAHL gene family and found that LcAHLs take part in resistance to drought stress and the development of somatic embryos. These findings will provide an important theoretical basis for understanding of the LcAHL gene function.

Redox homeostasis at SAM: a new role of HINT protein

ScHINT1 was identified at sugarcane SAM using subtractive libraries. Here, by bioinformatic tools, two-hybrid approach, and biochemical assays, we proposed that its role might be associated to control redox homeostasis. Such control is important for plant development and flowering transition, and this is ensured with some protein partners such as PAL and SBT that interact with ScHINT1. The shoot apical meristem transition from vegetative to reproductive is a crucial step for plants. In sugarcane (Saccharum spp.), this process is not well known, and it has an important impact on production due to field reduction. In view of this, ScHINT1 (Sugarcane HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN) was identified previously by subtractive cDNA libraries using Shoot Apical Meristem (SAM) by our group. This protein is a member of the HIT superfamily that was composed of hydrolase with an AMP site ligation. To better understand the role of ScHINT1 in sugarcane flowering, here its function in SAM was characterized using different approaches such as bioinformatics, two-hybrid assays, transgenic plants, and biochemical assays. ScHINT1 was conserved in plants, and it was grouped into four clades (HINT1, HINT2, HINT3, and HINT4). The 3D model proposed that ScHINT1 might be active as it was able to ligate to AMP subtract. Moreover, the two-hybrid approach identified two protein interactions: subtilase and phenylalanine ammonia-lyase. The evolutionary tree highlighted the relationships that each sequence has with specific subfamilies and different proteins. The 3D models constructed reveal structure conservation when compared with other PDB-related crystals, which indicates probable functional activity for the sugarcane models assessed. The interactome analysis showed a connection to different proteins that have antioxidative functions in apical meristems. Lastly, the transgenic plants with 35S::ScHINT1_AS (anti-sense orientation) produced more flowers than wild-type or 35S::ScHINT1_S (sense). Alpha-tocopherol and antioxidant enzymes measurement showed that their levels were higher in 35S::ScHINT_S plants than in 35S::ScHINT1_AS or wild-type plants. These results proposed that ScHINT1 might have an important role with other proteins in orchestrating this complex network for plant development and flowering.

AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins of ancient origin radiate new functions

AHL (AT-HOOK MOTIF NUCLEAR LOCALIZED) protein is an important transcription factor in plants that regulates a wide range of biological process. It is considered to have evolved from an independent PPC domain in prokaryotes to a complete protein in modern plants. AT-hook motif and PPC conserved domains are the main functional domains of AHL. Since the discovery of AHL, their evolution and function have been continuously studied. The AHL gene family has been identified in multiple species and the functions of several members of the gene family have been studied. Here, we summarize the evolution and structural characteristics of AHL genes, and emphasize their biological functions. This review will provide a basis for further functional study and crop breeding.

Ascorbate peroxidase 1 confers resistance to southern corn leaf blight in maize

Southern corn leaf blight (SCLB), caused by Bipolaris maydis, is one of the most devastating diseases affecting maize production. However, only one SLCB resistance gene, conferring partial resistance, is currently known, underscoring the importance of isolating new SCLB resistance-related genes. Here, we performed a comparative proteomic analysis and identified 258 proteins showing differential abundance during the maize response to B. maydis. These proteins included an ascorbate peroxidase (Zea mays ascorbate peroxidase 1 (ZmAPX1)) encoded by a gene located within the mapping interval of a previously identified quantitative trait locus associated with SCLB resistance. ZmAPX1 overexpression resulted in lower H₂ O₂ accumulation and enhanced resistance against B. maydis. Jasmonic acid (JA) contents and transcript levels for JA biosynthesis and responsive genes increased in ZmAPX1-overexpressing plants infected with B. maydis, whereas Zmapx1 mutants showed the opposite effects. We further determined that low levels of H₂ O₂ are accompanied by an accumulation of JA that enhances SCLB resistance. These results demonstrate that ZmAPX1 positively regulates SCLB resistance by decreasing H₂ O₂ accumulation and activating the JA-mediated defense signaling pathway. This study identified ZmAPX1 as a potentially useful gene for increasing SCLB resistance. Furthermore, the generated data may be relevant for clarifying the functions of plant APXs.

Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize

Amino acid transporters (AATs) are essential membrane proteins that transfer amino acids across cells. They are necessary for plant growth and development. The lysine histidine transporter (LHT) gene family in maize (Zea mays) has not yet been characterized. According to sequence composition and phylogenetic placement, this study found 15 LHT genes in the maize genome. The ZmLHT genes are scattered across the plasma membrane. The study also analyzed the evolutionary relationships, gene structures, conserved motifs, 3D protein structure, a transmembrane domain, and gene expression of the 15 LHT genes in maize. Comprehensive analyses of ZmLHT gene expression profiles revealed distinct expression patterns in maize LHT genes in various tissues. This study's extensive data will serve as a foundation for future ZmLHT gene family research. This study might make easier to understand how LHT genes work in maize and other crops.

AHLs' life in plants: Especially their potential roles in responding to Fusarium wilt and repressing the seed oil accumulation

Members of the AT-hook motif nuclear localized (AHL) family contain diverse but poorly understood biological functions. We identified 371 AHLs in 20 land plants, varying from the early diverging lycophyte Selagineila moellendorfi to a variety of higher plants. The AHLs were divided into two clades (Clade-A and Clade-B) with three different types (Type-I, Type-II, and Type-III AHLs). The divergence between Clade-A and Clade-B likely occurred before the separation of S. moellendorfi from the vascular plant lineages. Members of the AHLs family expanded with the specific whole-genome duplication (WGD)/segmental duplication in some genomes, such as Hevea brasiliensis. The ortholog (Vf00G1914/Amo018442) exhibited opposite expression patterns between two Vernicia species (V. fordii and V. montana), indicating that it was implicated in resistance to Fusarium wilt disease. The expression of Vf09G2138 exhibited a negative correlation with lipid biosynthesis in V. fordii seeds during different stages of development, suggesting that this gene might repress the seed oil accumulation. The core AT-hook motif and PPC domain were responsible for guiding the localization of AHL in the nucleus. This study helps us to understand the evolution of AHLs in multiple plants, further highlight their functions during V. fordii seed development and response to Fusarium wilt disease.

Genome-wide identification and evolution of WNK kinases in Bambusoideae and transcriptional profiling during abiotic stress in Phyllostachys edulis

With-no-lysine (WNK) kinases play vital roles in abiotic stress response, circadian rhythms, and regulation of flowering time in rice, Arabidopsis, and Glycine max. However, there are no previous reports of WNKs in the Bambusoideae, although genome sequences are available for diploid, tetraploid, and hexaploid bamboo species. In the present study, we identified 41 WNK genes in five bamboo species and analysed gene evolution, phylogenetic relationship, physical and chemical properties, cis-elements, and conserved motifs. We predicted the structure of PeWNK proteins of moso bamboo and determined the exposed, buried, structural and functional amino acids. Real-time qPCR analysis revealed that PeWNK5, PeWNK7, PeWNK8, and PeWNK11 genes are involved in circadian rhythms. Analysis of gene expression of different organs at different developmental stages revealed that PeWNK genes are tissue-specific. Analysis of various abiotic stress transcriptome data (drought, salt, SA, and ABA) revealed significant gene expression levels in all PeWNKs except PeWNK11. In particular, PeWNK8 and PeWNK9 were significantly down- and up-regulated, respectively, after abiotic stress treatment. A co-expression network of PeWNK genes also showed that PeWNK2, PeWNK4, PeWNK7, and PeWNK8 were co-expressed with transcriptional regulators related to abiotic stress. In conclusion, our study identified the PeWNKs of moso bamboo involved in circadian rhythms and abiotic stress response. In addition, this study serves as a guide for future functional genomic studies of the WNK genes of the Bambusoideae.

Genome-wide identification studies - A primer to explore new genes in plant species

Genome data have accumulated rapidly in recent years, doubling roughly after every 6 months due to the influx of next-generation sequencing technologies. A plethora of plant genomes are available in comprehensive public databases. This easy access to data provides an opportunity to explore genome datasets and recruit new genes in various plant species not possible a decade ago. In the past few years, many gene families have been published using these public datasets. These genome-wide studies identify and characterize gene members, gene structures, evolutionary relationships, expression patterns, protein interactions and gene ontologies, and predict putative gene functions using various computational tools. Such studies provide meaningful information and an initial framework for further functional elucidation. This review provides a concise layout of approaches used in these gene family studies and demonstrates an outline for employing various plant genome datasets in future studies.

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

BACKGROUND

SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes.

RESULTS

We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs.

CONCLUSION

This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations

The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single- nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Surprisingly, only 110 (1.56%) SNPs under selection were common in both populations, while the majority (98.4%) were unique to each population. This result indicated that high and low RPR phenotypes are produced by biologically distinct mechanisms. Remarkably, regions harboring lignin and polysaccharide genes were preferentially selected in high and low RPR populations, respectively. The preferential selection was manifested as higher lignification and increased saccharification of the high and low RPR stalks, respectively. The evolution of distinct gene classes according to the direction of selection was unexpected in the context of parallel evolution and demonstrated that selection for a trait, albeit in different directions, does not necessarily act on the same genes. Tricin, a grass-specific monolignol that initiates the incorporation of lignin in the cell walls, emerged as a key determinant of RPR. Integration of selection mapping and transcriptomic analyses with published genetic studies of RPR identified several candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, ZmEXPA2, ZmIAA41 and hk5. These findings provide a foundation for an enhanced understanding of RPR and the improvement of stalk lodging resistance.

Characteristics of the AT-Hook Motif Containing Nuclear Localized (AHL) Genes in Carrot Provides Insight into Their Role in Plant Growth and Storage Root Development

The AT-hook motif containing nuclear localized (AHL) gene family, controlling various developmental processes, is conserved in land plants. They comprise Plant and Prokaryote Conserved (PPC) domain and one or two AT-hook motifs. DcAHLc1 has been proposed as a candidate gene governing the formation of the carrot storage root. We identified and in-silico characterized carrot AHL proteins, performed phylogenetic analyses, investigated their expression profiles and constructed gene coexpression networks. We found 47 AHL genes in carrot and grouped them into two clades, A and B, comprising 29 and 18 genes, respectively. Within Clade-A, we distinguished three subclades, one of them grouping noncanonical AHLs differing in their structure (two PPC domains) and/or cellular localization (not nucleus). Coexpression network analysis attributed AHLs expressed in carrot roots into four of the 72 clusters, some of them showing a large number of interactions. Determination of expression profiles of AHL genes in various tissues and samples provided basis to hypothesize on their possible roles in the development of the carrot storage root. We identified a group of rapidly evolving noncanonical AHLs, possibly differing functionally from typical AHLs, as suggested by their expression profiles and their predicted cellular localization. We pointed at several AHLs likely involved in the development of the carrot storage root.

Genome-wide identification and expression analysis of the AT-hook Motif Nuclear Localized gene family in soybean

BACKGROUND

Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean.

RESULTS

To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean.

CONCLUSION

Sixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.

Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa

The AT-hook motif nuclear-localized (AHL) family is a plant transcription factor family, which plays an important role in growth and development and stress responses. We identified and analyzed 37 AHL genes in poplar (Populus trichocarpa). Phylogenetic analysis classified the PtrAHL members into three subfamilies based on their conserved domain. All PtrAHL paralogous pairs evolved under purifying selection. The promoter analysis revealed the presence of stress-related and phytohormone-related cis-elements of the PtrAHL genes. Our analysis of the tissue-specific expression pattern of PtrAHL genes indicated their significance in tissue and organ development. Network-based prediction suggested that PtrAHL genes may interact with histone deacetylases (HDAC) and participate in the development of organs, such as roots. Drought negatively impacts plant growth and development. ABA is produced under osmotic stress condition, and it takes an important part in the stress response and tolerance of plants. Real-time quantitative PCR (qRT-PCR) showed that PtrAHL genes were induced by drought stress and ABA treatment. These insights into the expression of PtrAHL genes under stress provide a basis for PtrAHL gene functional analysis. Our study will help develop new breeding strategies to improve drought tolerance in poplar.

Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress

Dirigent (DIR) proteins are induced under various stress conditions and involved in sterio- and regio-selective coupling of monolignol. A striking lack of information about dirigent genes in cucurbitaceae plants underscores the importance of functional characterization. In this study, 112 DIR genes were identified in six species, and 61 genes from major cultivated species were analyzed. DIRs were analyzed using various bioinformatics tools and complemented by expression profiling. Phylogenetic analysis segregated the putative DIRs into six distinctively known subgroups. Chromosomal mapping revealed uneven distribution of genes, whereas synteny analysis exhibited that duplication events occurred during gene evolution. Gene structure analysis suggested the gain of introns during gene diversification. Gene ontology (GO) enrichment analysis indicates the participation of proteins in lignification and pathogen resistance activities. We also determined their organ-specific expression levels in three species revealing preferential expression in root and leaves. Furthermore, the number of CmDIR (CmDIR1, 6, 7 and 12) and ClDIR (ClDIR2, 5, 8, 9 and 17) genes exhibited higher expression in resistant cultivars after powdery mildew (PM) inoculation. In summary, based on the expression and in-silico analysis, we propose a role of DIRs in disease resistance mechanisms.

Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus

AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.

Transcriptomic and network analyses reveal distinct nitrate responses in light and dark in rice leaves (Oryza sativa Indica var. Panvel1)

Nitrate (N) response is modulated by light, but not understood from a genome-wide perspective. Comparative transcriptomic analyses of nitrate response in light-grown and etiolated rice leaves revealed 303 and 249 differentially expressed genes (DEGs) respectively. A majority of them were exclusive to light (270) or dark (216) condition, whereas 33 DEGs were common. The latter may constitute response to N signaling regardless of light. Functional annotation and pathway enrichment analyses of the DEGs showed that nitrate primarily modulates conserved N signaling and metabolism in light, whereas oxidation–reduction processes, pentose-phosphate shunt, starch-, sucrose- and glycerolipid-metabolisms in the dark. Differential N-regulation of these pathways by light could be attributed to the involvement of distinctive sets of transporters, transcription factors, enriched cis-acting motifs in the promoters of DEGs as well as differential modulation of N-responsive transcriptional regulatory networks in light and dark. Sub-clustering of DEGs-associated protein–protein interaction network constructed using experimentally validated interactors revealed that nitrate regulates a molecular complex consisting of nitrite reductase, ferredoxin-NADP reductase and ferredoxin. This complex is associated with flowering time, revealing a meeting point for N-regulation of N-response and N-use efficiency. Together, our results provide novel insights into distinct pathways of N-signaling in light and dark conditions.

Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)

BACKGROUND

Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton.

RESULTS

To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the specific WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules.

CONCLUSION

In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three types based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.