F-box genes: Genome-wide expansion, evolution and their contribution to pollen growth in pear (Pyrus bretschneideri)

Comprehensive genomic analysis of CiPawPYL-PP2C-SnRK family genes in pecan (Carya illinoinensis) and functional characterization of CiPawSnRK2.1 under salt stress responses

Abscisic acid (ABA) is a pivotal regulator of plant growth, development, and responses to environmental stresses. The ABA signaling pathway involves three key components: ABA receptors known as PYLs, PP2Cs, and SnRK2s, which are conserved across higher plants. This study comprehensively investigated the PYL-PP2C-SnRK gene family in pecan, identifying 14 PYL genes, 97 PP2C genes, and 44 SnRK genes, which were categorized into subgroups through phylogenetic and sequence structure analysis. Whole-genome duplication (WGD) and dispersed duplication (DSD) were identified as major drivers of family expansion, and purifying selection was the primary evolutionary force. Tissue-specific expression analysis suggested diverse functions in different pecan tissues. qRT-PCR validation confirmed the involvement of CiPawPYLs, CiPawPP2CAs, and CiPawSnRK2s in salt stress response. Subcellular localization analysis revealed CiPawPP2C1 in the nucleus and CiPawPYL1 and CiPawSnRK2.1 in both the nucleus and the plasma membrane. In addition, VIGS indicated that CiPawSnRK2.1-silenced pecan seedling leaves display significantly reduced salt tolerance. Y2H and LCI assays verified that CiPawPP2C3 can interact with CiPawPYL5, CiPawPYL8, and CiPawSnRK2.1. This study characterizes the role of CiPawSnRK2.1 in salt stress and lays the groundwork for exploring the CiPawPYL-PP2C-SnRK module, highlighting the need to investigate the roles of other components in the pecan ABA signaling pathway.

Deciphering the mechanism of E3 ubiquitin ligases in plant responses to abiotic and biotic stresses and perspectives on PROTACs for crop resistance

With global climate change, it is essential to find strategies to make crops more resistant to different stresses and guarantee food security worldwide. E3 ubiquitin ligases are critical regulatory elements that are gaining importance due to their role in selecting proteins for degradation in the ubiquitin-proteasome proteolysis pathway. The role of E3 Ub ligases has been demonstrated in numerous cellular processes in plants responding to biotic and abiotic stresses. E3 Ub ligases are considered a class of proteins that are difficult to control by conventional inhibitors, as they lack a standard active site with pocket, and their biological activity is mainly due to protein-protein interactions with transient conformational changes. Proteolysis-targeted chimeras (PROTACs) are a new class of heterobifunctional molecules that have emerged in recent years as relevant alternatives for incurable human diseases like cancer because they can target recalcitrant proteins for destruction. PROTACs interact with the ubiquitin-proteasome system, principally the E3 Ub ligase in the cell, and facilitate proteasome turnover of the proteins of interest. PROTAC strategies harness the essential functions of E3 Ub ligases for proteasomal degradation of proteins involved in dysfunction. This review examines critical advances in E3 Ub ligase research in plant responses to biotic and abiotic stresses. It highlights how PROTACs can be applied to target proteins involved in plant stress response to mitigate pathogenic agents and environmental adversities.

The Identification and Analysis of the Self-Incompatibility Pollen Determinant Factor SLF in Lycium barbarum

Self-incompatibility is a widespread genetic mechanism found in flowering plants. It plays a crucial role in preventing inbreeding and promoting outcrossing. The genes that control self-incompatibility in plants are typically determined by the S-locus female determinant factor and the S-locus male determinant factor. In the Solanaceae family, the male determinant factor is often the SLF gene. In this research, we cloned and analyzed 13 S2-LbSLF genes from the L. barbarum genome, which are located on chromosome 2 and close to the physical location of the S-locus female determinant factor S-RNase, covering a region of approximately 90.4 Mb. The amino acid sequence identity of the 13 S2-LbSLFs is 58.46%, and they all possess relatively conserved motifs and typical F-box domains, without introns. A co-linearity analysis revealed that there are no tandemly repeated genes in the S2-LbSLF genes, and that there are two pairs of co-linear genes between S2-LbSLF and the tomato, which also belongs to the Solanaceae family. A phylogenetic analysis indicates that the S2-LbSLF members can be divided into six groups, and it was found that the 13 S2-LbSLFs are clustered with the SLF genes of tobacco and Petunia inflata to varying degrees, potentially serving as pollen determinant factors regulating self-incompatibility in L. barbarum. The results for the gene expression patterns suggest that S2-LbSLF is only expressed in pollen tissue. The results of the yeast two-hybrid assay showed that the C-terminal region of S2-LbSLFs lacking the F-box domain can interact with S-RNase. This study provides theoretical data for further investigation into the functions of S2-LbSLF members, particularly for the identification of pollen determinant factors regulating self-incompatibility in L. barbarum.

The Identification and Expression Analysis of the Liriodendron chinense F-Box Gene Family

The F-box gene family is one of the largest gene families in plants, and it plays a crucial role in regulating plant development, reproduction, cellular protein degradation, and response to biotic and abiotic stresses. Despite their significance, a comprehensive analysis of the F-box gene family in Liriodendron chinense and other magnoliaceae species has not been reported. In this study, we report for the first time the identification of 144 full-length F-box genes in L. chinense. Based on specific domains and phylogenetic analyses, these genes were divided into 10 distinct subfamilies. We further analyzed their gene structure, conserved domain and chromosome distribution, genome-wide replication events, and collinearity. Additionally, based on GO analysis, we found that F-box genes exhibit functional specificity, with a significant proportion of them being involved in protein binding (GO:0005515), suggesting that F-box genes may play an important role in gene regulation in L. chinense. Transcriptome data and q-PCR results also showed that F-box genes are involved in the development of multiple tissues in L. chinense, regulate the somatic embryogenesis of Liriodendron hybrids, and play a pivotal role in abiotic stress. Altogether, these findings provide a foundation for understanding the biological function of F-box genes in L. chinense and other plant species.

Exploring the role of FBXL fbxl gene family in Soybean: Implications for plant height and seed size regulation

F-box proteins constitute a significant family in eukaryotes and, as a component of the Skp1p-cullin-F-box complex, are considered critical for cellular protein degradation and other biological processes in plants. Despite their importance, the functions of F-box proteins, particularly those with C-terminal leucine-rich repeat (LRR) domains, remain largely unknown in plants. Therefore, the present study conducted genome-wide identification and in silico characterization of F-BOX proteins with C-terminal LRR domains in soybean (Glycine max L.) (GmFBXLs). A total of 45 GmFBXLs were identified. The phylogenetic analysis showed that GmFBXLs could be subdivided into ten subgroups and exhibited a close relationship with those from Arabidopsis thaliana, Cicer aretineum, and Medicago trunculata. It was observed that most cis-regulatory elements in the promoter regions of GmFBXLs are involved in hormone signalling, stress responses, and developmental stages. In silico transcriptome data illustrated diverse expression patterns of the identified GmFBXLs across various tissues, such as shoot apical meristem, flower, green pods, leaves, nodules, and roots. Overexpressing (OE) GmFBXL12 in Tianlong No.1 cultivar resulted in a significant difference in seed size, number of pods, and number of seeds per plant, indicated a potential increase in yield compared to wild type. This study offers valuable perspectives into the role of FBXLs in soybean, serving as a foundation for future research. Additionally, the identified OE lines represent valuable genetic resources for enhancing seed-related traits in soybean.

VDR promotes testosterone synthesis in mouse Leydig cells via regulation of cholesterol side chain cleavage cytochrome P450 (Cyp11a1) expression

BACKGROUND

The vitamin D receptor (VDR) mediates the pleiotropic biological actions that include osteoporosis, immune responses and androgen synthesis.VDR is widely expressed in testis cells such as Leydig cells, Sertoli cells, and sperm. The levels of steroids are critical for sexual development. In the early stage of steroidogenesis, cholesterol is converted to pregnenolone (precursor of most steroid hormones) by cholesterol side-chain lyase (CYP11A1), which eventually synthesizes the male hormone testosterone.

OBJECTIVE

This study aims to reveal how VDR regulates CYP11A1 expression and affects testosterone synthesis in murine Leydig cells.

METHODS

The levels of VDR, CYP11A1 were determined by quantitative real-time polymerase chain reaction (RT-qPCR) or western blot. Targeted relationship between VDR and Cyp11a1 was evaluated by dual-luciferase reporter assay. The levels of testosterone concentrations in cell culture media serum by enzyme-linked immunosorbent assay (ELISA).

RESULTS

Phylogenetic and motif analysis showed that the Cyp11a1 family had sequence loss, which may have special biological functions during evolution. The results of promoter prediction showed that vitamin D response element (VDRE) existed in the upstream promoter region of murine Cyp11a1. Dual-luciferase assay confirmed that VDR could bind candidate VDREs in upstream region of Cyp11a1, and enhance gene expression. Tissue distribution and localizatio analysis showed that Cyp11a1 was mainly expressed in testis, and dominantly existed in murine Leydig cells. Furthermore, over-expression VDR and CYP11A1 significantly increased testosterone synthesis in mice Leydig cells.

CONCLUSIONS

Active vitamin D3 (VD3) and Vdr interference treatment showed that VD3/VDR had a positive regulatory effect on Cyp11a1 expression and testosterone secretion. VDR promotes testosterone synthesis in male mice by up-regulating Cyp11a1 expression, which played an important role for male reproduction.

Genome-wide identification and characterization of ABA receptor pyrabactin resistance 1-like protein (PYL) family in oat

Abscisic acid (ABA) is a phytohormone that plays an important role in plant growth and development. Meanwhile, ABA also plays a key role in the plant response to abiotic stressors such as drought and high salinity. The pyrabactin resistance 1-like (PYR/PYL) protein family of ABA receptors is involved in the initial step of ABA signal transduction. However, no systematic studies of the PYL family in "Avena sativa, a genus Avena in the grass family Poaceae," have been conducted to date. Thus, in this study, we performed a genome-wide screening to identify PYL genes in oat and characterized their responses to drought stress. A total of 12 AsPYL genes distributed on nine chromosomes were identified. The phylogenetic analysis divided these AsPYLs into three subfamilies, based on structural and functional similarities. Gene and motif structure analysis of AsPYLs revealed that members of each subfamily share similar gene and motif structure. Segmental duplication appears to be the driving force for the expansion of PYLs, Furthermore, stress-responsive AsPYLs were detected through RNA-seq analysis. The qRT-PCR analysis of 10 AsPYL genes under drought, salt, and ABA stress revealed that AsPYL genes play an important role in stress response. These data provide a reference for further studies on the oat PYL gene family and its function.

Role of F-box E3-ubiquitin ligases in plant development and stress responses

KEY MESSAGE

F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.

Identification of F-box gene family in Brassica oleracea and expression analysis in response to low-temperature stress

Unfavorable climatic conditions, such as low temperatures, often hinder the growth and production of crops worldwide. The F-box protein-encoding gene family performs an essential role in plant stress resistance. However, a comprehensive analysis of the F-box gene family in cabbage (Brassica oleracea var capitata L.) has not been reported yet. In this study, genome-wide characterization of F-box proteins in cabbage yielded 303 BoFBX genes and 224 BoFBX genes unevenly distributed on 9 chromosomes of cabbage. Phylogenetic analysis of 303 BoFBX genes was classified into nine distinct subfamily groups (GI-GIX). Analysis of the gene structure of BoFBX genes indicated that most genes within the same clade are highly conserved. In addition, tissue-specific expression analysis revealed that six F-box genes in cabbage showed the highest expression in rosette leaves, followed by roots and stems and the lowest expression was observed in the BoFBX156 gene. In contrast, the expression of the other five genes, BoFBX100, BoFBX117, BoFBX136, BoFBX137 and BoFBX213 was observed to be upregulated in response to low-temperature stress. Moreover, we found that the expression level of the BoFBX gene in the cold-tolerant cultivar "ZG" was higher than that in cold-sensitive "YC" with the extension of stress duration, while expression levels of each gene in "ZG" were higher than "YC" at 24 h. Knowledge of the various functions provided by BoFBXs genes and their expression patterns provides a firm theoretical foundation for explaining the functions of BoFBXs, thereby contributing to the molecular breeding process of cabbage.

The involvement of Ein3-binding F-box protein PbrEBF3 in regulating ethylene signaling during Cuiguan pear fruit ripening

Ein3-binding F-box (EBF) proteins have been determined to modulate ethylene response processes by regulating EIN3/EIL protein degradation in Arabidopsis and tomato. However, the function of pear PbrEBFs in ethylene-dependent responses during fruit ripening remains unclear. In this study, PbrEBF1, PbrEBF2, and PbrEBF3 display contrasting expression patterns in response to ethylene and 1-MCP treatment. PbrEBF3 displayed potential fruit ripening-associated function in a transient expression experiment. Yeast two-hybrid (Y2H) and Firefly luciferase complementation imaging (LCI) assays indicated that PbrEBF3 interacts with PbrEIL1, PbrEIL2, and PbrEIL3 proteins. In turn, the transcription of PbrEBF3 is directly regulated by PbrEILs via a feedback loop. PbrEILs trigger a transcriptional cascade of PbrERF24 and finally affect ethylene synthesis. Overall, PbrEBF3 plays a central role in pear fruit ripening through mediation of the ethylene signaling pathway.

Genome-Wide Analysis of the FBA Subfamily of the Poplar F-Box Gene Family and Its Role under Drought Stress

F-box proteins are important components of eukaryotic SCF E3 ubiquitin ligase complexes, which specifically determine protein substrate proteasomal degradation during plant growth and development, as well as biotic and abiotic stress. It has been found that the FBA (F-box associated) protein family is one of the largest subgroups of the widely prevalent F-box family and plays significant roles in plant development and stress response. However, the FBA gene family in poplar has not been systematically studied to date. In this study, a total of 337 F-box candidate genes were discovered based on the fourth-generation genome resequencing of P. trichocarpa. The domain analysis and classification of candidate genes revealed that 74 of these candidate genes belong to the FBA protein family. The poplar F-box genes have undergone multiple gene replication events, particularly in the FBA subfamily, and their evolution can be attributed to genome-wide duplication (WGD) and tandem duplication (TD). In addition, we investigated the P. trichocarpa FBA subfamily using the PlantGenIE database and quantitative real-time PCR (qRT-PCR); the results showed that they are expressed in the cambium, phloem and mature tissues, but rarely expressed in young leaves and flowers. Moreover, they are also widely involved in the drought stress response. At last, we selected and cloned PtrFBA60 for physiological function analysis and found that it played an important role in coping with drought stress. Taken together, the family analysis of FBA genes in P. trichocarpa provides a new opportunity for the identification of P. trichocarpa candidate FBA genes and elucidation of their functions in growth, development and stress response, thus demonstrating their utility in the improvement of P. trichocarpa.

The complete chloroplast genome of Crataegus scabrifolia (Franch.) Rehd (Rosaceae), a medicinal and edible plant in Southwest China

Crataegus scabrifolia (Franch.) Rehd is a medicinal and edible plant in Southwest China. The chloroplast genome of C. scabrifolia was analyzed by high-throughput sequencing technology, and its genetic relationship to related species was discussed. The chloroplast genome is 159,637 bp long, with two inverted repeat (IR) regions (26,384 bp each) that separate a large single-copy (LSC) region (87,730 bp) and a small single-copy (SSC) region (19,139 bp). A total of 127 genes were annotated, including 83 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. The phylogenetic tree shows that C. hupehensis is closely related to C. scabrifolia with strong bootstrap support.

Genome-Wide Analysis and Characterization of Eggplant F-Box Gene Superfamily: Gene Evolution and Expression Analysis under Stress

F-box genes play an important role in plant growth and resistance to abiotic and biotic stresses. To date, systematic analysis of F-box genes and functional annotation in eggplant (Solanum melongena) is still limited. Here, we identified 389 F-box candidate genes in eggplant. The domain study of F-box candidate genes showed that the F-box domain is conserved, whereas the C-terminal domain is diverse. There are 376 SmFBX candidate genes distributed on 12 chromosomes. A collinearity analysis within the eggplant genome suggested that tandem duplication is the dominant form of F-box gene replication in eggplant. The collinearity analysis between eggplant and the three other species (Arabidopsis thaliana, rice and tomato) provides insight into the evolutionary characteristics of F-box candidate genes. In addition, we analyzed the expression of SmFBX candidate genes in different tissues under high temperature and bacterial wilt stress. The results identified several F-box candidate genes that potentially participate in eggplant heat tolerance and bacterial wilt resistance. Moreover, the yeast two-hybrid assay showed that several representative F-box candidate proteins interacted with representative Skp1 proteins. Overexpression of SmFBX131 and SmFBX230 in tobacco increased resistance to bacterial wilt. Overall, these results provide critical insights into the functional analysis of the F-box gene superfamily in eggplant and provide potentially valuable targets for heat and bacterial resistance.

Genome-Wide Identification and Expression Patterns of the F-box Family in Poplar under Salt Stress

The F-box family exists in a wide variety of plants and plays an extremely important role in plant growth, development and stress responses. However, systematic studies of F-box family have not been reported in populus trichocarpa. In the present study, 245 PtrFBX proteins in total were identified, and a phylogenetic tree was constructed on the basis of their C-terminal conserved domains, which was divided into 16 groups (A–P). F-box proteins were located in 19 chromosomes and six scaffolds, and segmental duplication was main force for the evolution of the F-box family in poplar. Collinearity analysis was conducted between poplar and other species including Arabidopsis thaliana, Glycine max, Anemone vitifolia Buch, Oryza sativa and Zea mays, which indicated that poplar has a relatively close relationship with G. max. The promoter regions of PtrFBX genes mainly contain two kinds of cis-elements, including hormone-responsive elements and stress-related elements. Transcriptome analysis indicated that there were 82 differentially expressed PtrFBX genes (DEGs), among which 64 DEGs were in the roots, 17 in the leaves and 26 in the stems. In addition, a co-expression network analysis of four representative PtrFBX genes indicated that their co-expression gene sets were mainly involved in abiotic stress responses and complex physiological processes. Using bioinformatic methods, we explored the structure, evolution and expression pattern of F-box genes in poplar, which provided clues to the molecular function of F-box family members and the screening of salt-tolerant PtrFBX genes.

Phylogenetic and Transcriptional Analyses of the HSP20 Gene Family in Peach Revealed That PpHSP20-32 Is Involved in Plant Height and Heat Tolerance

The heat shock protein 20 (HSP20) proteins comprise an ancient, diverse, and crucial family of proteins that exists in all organisms. As a family, the HSP20s play an obvious role in thermotolerance, but little is known about their molecular functions in addition to heat acclimation. In this study, 42 PpHSP20 genes were detected in the peach genome and were randomly distributed onto the eight chromosomes. The primary modes of gene duplication of the PpHSP20s were dispersed gene duplication (DSD) and tandem duplication (TD). PpHSP20s in the same class shared similar motifs. Based on phylogenetic analysis of HSP20s in peach, Arabidopsis thaliana, Glycine max, and Oryza sativa, the PpHSP20s were classified into 11 subclasses, except for two unclassified PpHSP20s. cis-elements related to stress and hormone responses were detected in the promoter regions of most PpHSP20s. Gene expression analysis of 42 PpHSP20 genes revealed that the expression pattern of PpHSP20-32 was highly consistent with shoot length changes in the cultivar 'Zhongyoutao 14', which is a temperature-sensitive semi-dwarf. PpHSP20-32 was selected for further functional analysis. The plant heights of three transgenic Arabidopsis lines overexpressing PpHSP20-32 were significantly higher than WT, although there was no significant difference in the number of nodes. In addition, the seeds of three over-expressing lines of PpHSP20-32 treated with high temperature showed enhanced thermotolerance. These results provide a foundation for the functional characterization of PpHSP20 genes and their potential use in the growth and development of peach.

Soybean F-Box-Like Protein GmFBL144 Interacts With Small Heat Shock Protein and Negatively Regulates Plant Drought Stress Tolerance

The F-box gene family is one of the largest gene families in plants. These genes regulate plant growth and development, as well as biotic and abiotic stress responses, and they have been extensively researched. Drought stress is one of the major factors limiting the yield and quality of soybean. In this study, bioinformatics analysis of the soybean F-box gene family was performed, and the role of soybean F-box-like gene GmFBL144 in drought stress adaptation was characterized. We identified 507 F-box genes in the soybean genome database, which were classified into 11 subfamilies. The expression profiles showed that GmFBL144 was highly expressed in plant roots. Overexpression of GmFBL144 increased the sensitivity of transgenic Arabidopsis to drought stress. Under drought stress, the hydrogen peroxide (H₂O₂) and malonaldehyde (MDA) contents of transgenic Arabidopsis were higher than those of the wild type (WT) and empty vector control, and the chlorophyll content was lower than that of the control. Y2H and bimolecular fluorescence complementation (BiFC) assays showed that GmFBL144 can interact with GmsHSP. Furthermore, our results showed that GmFBL144 can form SCF ^FBL144 (E3 ubiquitin ligase) with GmSkp1 and GmCullin1. Altogether, these results indicate that the soybean F-box-like protein GmFBL144 may negatively regulate plant drought stress tolerance by interacting with sHSP. These findings provide a basis for molecular genetics and breeding of soybean.

Genome-wide identification and characterization of F-box family proteins in sweet potato and its expression analysis under abiotic stress

In this study, genome-wide characterization of F-box proteins in sweet potato yielded 243 IbFBX genes, unevenly distributed on the 15 chromosomes of sweet potato. Gene duplication analysis suggested segmental duplication as the principal factor influencing the expansive evolution of IbFBX genes in sweet potato. Phylogenetic analysis clustered F-box proteins in sweet potato, Arabidopsis, and rice into six clades (I-VI). Gene structure analysis of the IbFBX genes revealed that most of the genes within the same clade were highly conserved. Expression profiles of IbFBX family genes in 9 different tissues and under stress conditions revealed that the IbFBXs were highly upregulated or downregulated in response to salt and drought stress, suggesting their significant roles in abiotic stress response and adaptation. Knowledge of the diverse functions and expression patterns of IbFBXs presents a solid theoretical basis for annotating the functions of IbFBXs and further facilitate the molecular breeding of sweet potato.

Genome-wide identification and comparative analysis of the PYL gene family in eight Rosaceae species and expression analysis of seeds germination in pear

Abscisic acid (ABA) is a phytohormone that plays important roles in the regulation of plant growth, seed germination, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein, an ABA receptor, was involved in the initial step in ABA signal transduction. However, the evolutionary history and characteristics of PYL genes expression remain unclear in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. In this study, 67 PYL genes were identified in eight Rosaceae species, and have been classified into three subgroups based on specific motifs and phylogenetic analysis. Intriguingly, we observed that whole-genome duplication (WGD) and dispersed duplication (DSD) have a major contribution to PYL family expansion. Purifying selection was the major force in PYL genes evolution. Expression analysis finds that PYL genes may function in multiple pear tissues. qRT-PCR validation of 11 PbrPYL genes indicates their roles in seed germination and abiotic stress responses. Our study provides a basis for further elucidation of the function of PYL genes and analysis of their expansion, evolution and expression patterns, which helps to understand the molecular mechanism of pear response to seed germination and seedling abiotic stress.

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.

Genome-wide Identification and Evolution of the PP2C Gene Family in Eight Rosaceae Species and Expression Analysis Under Stress in Pyrus bretschneideri

Type 2C protein phosphatase (PP2C) plays an essential role in abscisic acid (ABA) signaling transduction processes. In the current study, we identify 719 putative PP2C genes in eight Rosaceae species, including 118 in Chinese white pear, 110 in European pear, 73 in Japanese apricot, 128 in apple, 74 in peach, 65 in strawberry, 78 in sweet cherry, and 73 in black raspberry. Further, the phylogenetic analysis categorized PbrPP2C genes of Chinese white pear into twelve subgroups based on the phylogenic analysis. We observed that whole-genome duplication (WGD) and dispersed gene duplication (DSD) have expanded the Rosaceae PP2C family despite simultaneous purifying selection. Expression analysis finds that PbrPP2C genes have organ-specific functions. QRT-PCR validation of nine PbrPP2C genes of subgroup A indicates a role in ABA-mediated response to abiotic stress. Finally, we find that five PbrPP2C genes of subgroup A function in the nucleus. In summary, our research suggests that the PP2C family functions to modulate ABA signals and responds to abiotic stress.

Genome-wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri)

The Multidrug and Toxic Compound Extrusion (MATE) protein belongs to a secondary transporter gene family, which plays a primary role in transporting many kinds of substrates such as organic compounds, secondary metabolites, and phytohormones. MATE protein members exist in both prokaryotes and eukaryotes. However, evolution and comprehensive analysis of the MATE genes has not been performed in Rosaceae species. In the present study, a total of 404 MATEs genes were identified from six Rosaceae genomes (Prunus avium, Pyrus bretschneideri, Prunus persica, Fragaria vesca, Prunus mume, and Malus domestica) and classified into eight main subfamilies (I-VII) based on structural and phylogenetic analysis. Microcollinearity analysis showed that whole-genome duplication events might play a vital role in the expansion of the MATE genes family. The Ka/Ks analysis, chromosomal localization, subcellular localization, and molecular characteristics (length, weight, and pI) were performed using various bioinformatics tools. Furthermore, different subfamilies have different introns-exons structures, cis-acting elements, and conserved motifs analysis, indicating functional divergence in the MATE family. Subsequently, RNA-seq analysis and real-time qRT-PCR were conducted during Chinese pear fruit development. Moreover, PbMATE genes were significantly expressed under hormonal treatments of MeJA (methyl jasmonate), SA (salicylic acid), and ABA (abscisic acid). Overall, our results provide helpful insights into the functions, expansion complexity, and evolutions of the MATE genes in Chinese pear and five Rosaceae species.

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

Regulation of Glycosylphosphatidylinositol-Anchored Protein (GPI-AP) Expression by F-Box/LRR-Repeat (FBXL) Protein in Wheat (Triticum aestivum L.)

F-box proteins are substrate recognition components of the Skp1-Cullin-F-box (SCF) complex, which performs many important biological functions including the degradation of numerous proteins via the ubiquitin–26S proteasome system. In this study, we isolated the gene encoding the F-box/LRR-repeat (FBXL) protein from wheat (Triticum aestivum L.) seedlings and validated that the TaFBXL protein is a component of the SCF complex. Yeast two-hybrid assays revealed that TaFBXL interacts with the wheat glycosylphosphatidylinositol-anchored protein (TaGPI-AP). The green fluorescent protein (GFP) fusion protein of TaFBXL was detected in the nucleus and plasma membrane, whereas that of TaGPI-AP was observed in the cytosol and probably also plasma membrane. yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays revealed that TaFBXL specifically interacts with TaGPI-AP in the nucleus and plasma membrane, and TaGPI-AP is targeted by TaFBXL for degradation via the 26S proteasome system. In addition, TaFBXL and TaGPI-AP showed antagonistic expression patterns upon treatment with indole-3-acetic acid (IAA), and the level of TaGPI-AP was higher in tobacco leaves treated with both MG132 (proteasome inhibitor) and IAA than in leaves treated with either MG132 or IAA. Taken together, our data suggest that TaFBXL regulates the TaGPI-AP protein level in response to exogenous auxin application.

Identification, evolutionary profiling, and expression analysis of F-box superfamily genes under phosphate deficiency in tomato

F-box genes are an integral component of the Skp1-cullin-F-box (SCF) complex in eukaryotes. These genes are primarily involved in determining substrate specificities during cellular proteolysis. Here we report that 410 members constitute the F-box superfamily in tomato. Based on the incidence of C-terminal domains, these genes fell into ten subfamilies, leucine-rich repeat domain-containing F-box members constituting the largest subfamily. The F-box genes are present on all 12 chromosomes with varying gene densities. Both segmental and tandem duplication events contribute significantly to their expansion in the tomato genome. The syntenic analysis revealed close relationships among F-box homologs within Solanaceae species genomes. Transcript profiling of F-box members identified several ripening-associated genes with altered expression in the ripening mutants. RNA-sequencing data analysis showed that phosphate (Pi) deficiency affected 55 F-box transcripts in the Pi-deficient seedlings compared to their control seedlings. The persistent up-regulation of eight members, including two phloem protein 2B (PP2-B) genes, PP2-B15, and MATERNAL EFFECT EMBRYO ARREST 66 (MEE66) homologs, at multiple time-points in the roots, shoot, and seedling, point towards their pivotal roles in Pi starvation response in tomato. The attenuation of such upregulation in sucrose absence revealed the necessity of this metabolite for robust activation of these genes in the Pi-deficient seedlings. Altogether, this study identifies novel F-box genes with potential roles in fruit ripening and Pi starvation response and unlocks new avenues for functional characterization of candidate genes in tomato and other related species.

Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)

F-box genes play an important role in the growth and development of plants, but there are few studies on its role in a plant's response to abiotic stresses. In order to further study the functions of F-box genes in tomato (Solanum lycopersicum, Sl), a total of 139 F-box genes were identified in the whole genome of tomato using bioinformatics methods, and the basic information, transcript structure, conserved motif, cis-elements, chromosomal location, gene evolution, phylogenetic relationship, expression patterns and the expression under cold stress, drought stress, jasmonic acid (JA) treatment and salicylic acid (SA) treatment were analyzed. The results showed that SlFBX genes were distributed on 12 chromosomes of tomato and were prone to TD (tandem duplication) at the ends of chromosomes. WGD (whole genome duplication), TD, PD (proximal duplication) and TRD (transposed duplication) modes seem play an important role in the expansion and evolution of tomato SlFBX genes. The most recent divergence occurred 1.3042 million years ago, between SlFBX89 and SlFBX103. The cis-elements in SlFBX genes' promoter regions were mainly responded to phytohormone and abiotic stress. Expression analysis based on transcriptome data and qRT-PCR (Real-time quantitative PCR) analysis of SlFBX genes showed that most SlFBX genes were differentially expressed under abiotic stress. SlFBX24 was significantly up-regulated at 12 h under cold stress. This study reported the SlFBX gene family of tomato for the first time, providing a theoretical basis for the detailed study of SlFBX genes in the future, especially the function of SlFBX genes under abiotic stress.

Genome-wide characterization of the hyperaccumulator Sedum alfredii F-box family under cadmium stress

The F-box genes, which form one of the largest gene families in plants, are vital for plant growth, development and stress response. However, F-box gene family in Sedum alfredii remains unknown. Comprehensive studies addressing their function responding to cadmium stress is still limited. In the present study, 193 members of the F-box gene (SaFbox) family were identified, which were classified into nine subfamilies. Most of the SaFboxs had highly conserved domain and motif. Various functionally related cis-elements involved in plant growth regulation, stress and hormone responses were located in the upstream regions of SaFbox genes. RNA-sequencing and co-expression network analysis revealed that the identified SaFbox genes would be involved in Cd stress. Expression analysis of 16 hub genes confirmed their transcription level in different tissues. Four hub genes (SaFbox40, SaFbox51, SaFbox136 and SaFbox170) were heterologously expressed in a Cd-sensitive yeast cell to assess their effects on Cd tolerance. The transgenic yeast cells carrying SaFbox40, SaFbox51, SaFbox136, or SaFbox170 were more sensitive and accumulated more cadmium under Cd stress than empty vector transformed control cells. Our results performed a comprehensive analysis of Fboxs in S. alfredii and identified their potential roles in Cd stress response.

Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum

The MYB family, one of the largest transcription factor (TF) families, plays an important role in plant growth, development, and stress response. Although genome-wide analysis of the MYB family has been performed in many species based on sequence similarity, predicting the potential functions of the MYB genes and classifying the regulators into specific metabolic pathways remains difficult. In this study, using a hidden Markov model search and co-expression regulatory network analysis, we demonstrated a process to screen and identify potential MYB TFs in the anthocyanin biosynthesis pathway of Gossypium hirsutum. As a result, we identified 617 and 784 MYB genes (812 in total) from the previously reported and recently released genomes, respectively. Using 126 structural genes involved in the anthocyanin biosynthesis pathway as targets for several co-expression network analyses, we sorted out 31 R2R3-MYB genes, which are potential regulators in the specific pathway. Phylogenetic and collinearity analyses indicated that 83.9% of the 31 MYB genes originated from whole genome duplication or polyploidization. In addition, we revealed relatively specific regulatory relationships between the MYB TFs and their target structural genes. Approximately, 71% of the MYBs could regulate only a single anthocyanin-related structural gene. Moreover, we found that the A- and D- subgenome homoeologs of MYB TFs in G. hirsutum rarely co-regulate the same target gene. The current study not only demonstrated an easy method to rapidly predict potential TFs in a specific metabolic pathway, but also enhanced our understanding of the evolution, gene characteristics, expression, and regulatory pattern of MYB TFs in G. hirsutum.

Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress

Background

The members of the sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family are specific serine/threonine protein kinases in plants that play important roles in stress signal transduction and adaptation. Because of their positive regulatory roles in response to adverse conditions, the genes encoding thes proteins are considered potential candidates for breeding of plants for disease resistance and genetic improvement. However, there is far less information about this kinase family, and the function of these genes has not been explored in Rosaceae.

Results

A genome-wide survey and analysis of the genes encoding members of the SnRK2 family were performed in pear (Pyrus bretschneideri) and seven other Rosaceae species. A total of 71 SnRK2 genes were identified from the eight Rosaceae species and classified into three subgroups based on phylogenetic analysis and structural characteristics. Purifying selection played a crucial role in the evolution of SnRK2 genes, and whole-genome duplication and dispersed duplication were the primary forces underlying the characteristics of the SnRK2 gene family in Rosaceae. Transcriptome data and qRT-PCR assay results revealed that the distribution of PbrSnRK2s was very extensive, including across the roots, leaves, pollen, styles, and flowers, although most of them were mainly expressed in leaves. In addition, under stress conditions, the transcript levels of some of the genes were upregulated in leaves in response to ABA treatment.

Conclusions

This study provides useful information and a theoretical introduction for the study of the evolution, expression, and functions of the SnRK2 gene family in plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07201-w.

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

Genome-wide identification and comparative analysis of the ADH gene family in Chinese white pear (Pyrus bretschneideri) and other Rosaceae species

Alcohol dehydrogenase (ADH) is essential to the formation of aromatic compounds in fruits. However, the evolutionary history and characteristics of ADH gene expression remain largely unclear in Rosaceae fruit species. In this study, 464 ADH genes were identified in eight Rosaceae fruit species, 68 of the genes were from pear and which were classified into four subgroups. Frequent single gene duplication events were found to have contributed to the formation of ADH gene clusters and the expansion of the ADH gene family in these eight Rosaceae species. Purifying selection was the major force in ADH gene evolution. The younger genes derived from tandem and proximal duplications had evolved faster than those derived from other types of duplication. RNA-Seq and qRT-PCR analysis revealed that the expression levels of three ADH genes were closely correlated with the content of aromatic compounds detected during fruit development.

Comparative analysis of the P-type ATPase gene family in seven Rosaceae species and an expression analysis in pear (Pyrus bretschneideri Rehd.)

P-type ATPases are integral membrane transporters that play important roles in transmembrane transport in plants. However, a comprehensive analysis of the P-type ATPase gene family has not been conducted in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. Here, we identified 419 P-type ATPase genes from seven Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, Prunus mume, Pyrus communis and Pyrus betulifolia). Structural and phylogenetic analyses revealed that P-type ATPase genes can be divided into five subfamilies. Different subfamilies have different conserved motifs and cis-acting elements, which may lead to functional divergence within one gene family. Dispersed duplication and whole-genome duplication may play critical roles in the expansion of the P-type ATPase family. Purifying selection was the primary force driving the evolution of P-type ATPase family genes. Based on the dynamic transcriptome analysis and transient transformation of Chinese white pear fruit, Pbr029767.1 in the P_3A subfamily were found to be associated with malate accumulation during pear fruit development. Using a co-expression network, we identified several transcription factors that may have regulatory relationships with the P-type ATPase gene family. Overall, this study lays a solid foundation for understanding the evolution and functions of P-type ATPase genes in Chinese white pear and six other Rosaceae species.

Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L

Background

F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects.

Results

In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction.

Conclusion

The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.

Genome-wide identification and transcriptome profiling reveal that E3 ubiquitin ligase genes relevant to ethylene, auxin and abscisic acid are differentially expressed in the fruits of melting flesh and stony hard peach varieties

Background

Ubiquitin ligases (E3) are the enzymes in the ubiquitin/26S proteasome pathway responsible for targeting proteins to the degradation pathway and play major roles in multiple biological activities. However, the E3 family and their functions are yet to be identified in the fruit of peach.

Results

In this study, genome-wide identification, classification and characterization of the E3 ligase genes within the genome of peach (Prunus persica) was carried out. In total, 765 E3 (PpE3) ligase genes were identified in the peach genome. The PpE3 ligase genes were divided into eight subfamilies according to the presence of known functional domains. The RBX subfamily was not detected in peach. The PpE3 ligase genes were not randomly distributed among the 8 chromosomes, with a greater concentration on the longer chromosomes. The primary mode of gene duplication of the PpE3 ligase genes was dispersed gene duplication (DSD). Four subgroups of the BTB subfamily never characterized before were newly identified in peach, namely BTBAND, BTBBL, BTBP and BTBAN. The expression patterns of the identified E3 ligase genes in two peach varieties that display different types of fruit softening (melting flesh, MF, and stony hard, SH) were analyzed at 4 different stages of ripening using Illumina technology. Among the 765 PpE3 ligase genes, 515 (67.3%) were expressed (FPKM > 1) in the fruit of either MF or SH during fruit ripening. In same-stage comparisons, 231 differentially expressed genes (DEGs) were identified between the two peach cultivars. The number of DEGs in each subfamily varied. Most DEGs were members of the BTB, F-box, U-box and RING subfamilies. PpE3 ligase genes predicted to be involved in ethylene, auxin, or ABA synthesis or signaling and DNA methylation were differentially regulated. Eight PpE3 ligase genes with possible roles in peach flesh texture and fruit ripening were discussed.

Conclusions

The results of this study provide useful information for further understanding the functional roles of the ubiquitin ligase genes in peach. The findings also provide the first clues that E3 ligase genes may function in the regulation of peach ripening.

Genome-Wide Identification and Transcriptional Expression of the METTL21C Gene Family in Chicken

The chicken is a common type of poultry that is economically important both for its medicinal and nutritional values. Previous studies have found that free-range chickens have more skeletal muscle mass. The methyltransferase-like 21C gene (METTL21C) plays an important role in muscle development; however, there have been few reports on the role of METTL21C in chickens. In this study, we performed a genome-wide identification of chicken METTL21C genes and analyzed their phylogeny, transcriptional expression profile, and real-time quantitative polymerase chain reaction (qPCR). We identified 10 GgMETTL21C genes from chickens, 11 from mice, and 32 from humans, and these genes were divided into six groups, which showed a large amount of variation among these three species. A total of 15 motifs were detected in METTL21C genes, and the intron phase of the gene structure showed that the METTL21C gene family was conservative in evolution. Further, both the transcript data and qPCR showed that a single gene’s (GgMETTL21C3) expression level increased with the muscle development of chickens, indicating that the METTL21C genes are involved in the development of chicken muscles. Our results provide some reference value for the subsequent study of the function of METTL21C.

Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

The common walnut (or Persian walnut), Juglans regia L., is an economically important temperate tree species valued for both its edible nut and high-quality wood. F-box gene family members are involved in plant development, which includes regulating plant development, reproduction, cellular protein degradation, response to biotic and abiotic stresses, and flowering. However, in common walnut (J. regia), there are no reports about the F-box gene family. Here, we report a genome-wide identification of J. regia F-box genes and analyze their phylogeny, duplication, microRNA, pathway, and transcriptional expression profile. In this study, 74 F-box genes were identified and clustered into three groups based on phylogenetic analysis and eight subfamilies based on special domains in common walnut. These common walnut F-box genes are distributed on 31 different pseudo-chromosomes. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and microRNA profiles showed that the F-box gene family might play a critical role in the flowering of common walnut. The expressions were significantly higher in female flowers and male flowers compared with leaf and hull tissues at a transcriptome level. The results revealed that the expressions of the F-box gene in female flowers were positively correlated with male flowers, but there was no correlation between any other tissue combinations in common walnut. Our results provided insight into the general characteristics of the F-box genes in common walnut.

Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot

The homeobox gene family, a large family represented by transcription factors, has been implicated in secondary growth, early embryo patterning, and hormone response pathways in plants. However, reports about the information and evolutionary history of the homeobox gene family in carrot are limited. In the present study, a total of 130 homeobox family genes were identified in the carrot genome. Specific codomain and phylogenetic analyses revealed that the genes were classified into 14 subgroups. Whole genome and proximal duplication participated in the homeobox gene family expansion in carrot. Purifying selection also contributed to the evolution of carrot homeobox genes. In Gene Ontology (GO) analysis, most members of the HD-ZIP III and IV subfamilies were found to have a lipid binding (GO:0008289) term. Most HD-ZIP III and IV genes also harbored a steroidogenic acute regulatory protein-related lipid transfer (START) domain. These results suggested that the HD-ZIP III and IV subfamilies might be related to lipid transfer. Transcriptome and quantitative real-time PCR (RT-qPCR) data indicated that members of the WOX and KNOX subfamilies were likely implicated in carrot root development. Our study provided a useful basis for further studies on the complexity and function of the homeobox gene family in carrot.