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

Genome-wide identification and expression analysis of the ADH gene family in Artemisia annua L. under UV-B stress

ADHs are key genes that catalyze the interconversion between alcohols and aldehydes, which play crucial roles in plant adaptation to a range of abiotic stresses. However, the characterization and evolutionary pathways of ADH genes in the antimalarial plant Artemisia annua are still unclear. This study identified 49 ADH genes in A. annua and conducted a detailed analysis of their structural features, conserved motifs, and duplication types, revealing that tandem and dispersed duplications are the primary mechanisms of gene expansion. Evolutionary analysis of ADH genes between A. annua (AanADH) and A. argyi (AarADH) revealed dynamic changes, with 35 genes identified deriving from their most recent common ancestor in both species. ADH1, crucial for artemisinin production, had two copies in both species, expanding via dispersed duplication in A. annua but whole-genome duplication in A. argyi. CREs and WGCNA analysis suggested that AanADH genes may be regulated by UV-B stress. Following short-term UV-B treatment, 16 DEGs were identified, including ADH1 (AanADH6 and AanADH7), and these genes were significantly downregulated after two hours treatment (UV2h) and upregulated after four hours treatment (UV4h). The expression changes of these genes were further confirmed by GO enrichment analysis and qRT-PCR experiments. Overall, this study comprehensively characterized the ADH gene family in A. annua and systematically identified AanADH genes that were responsive to UV-B stress, providing a foundation for further research on their roles in abiotic stress responses.

Genome-wide identification of alcohol dehydrogenase (ADH) gene family in oilseed rape (Brassica napus L.) and BnADH36 functional verification under salt stress

BACKGROUND

Alcohol dehydrogenase (ADH) is an enzyme that binds to zinc, facilitating the interconversion of ethanol and acetaldehyde or other corresponding alcohols/aldehydes in the pathway of ethanol fermentation. It plays a pivotal role in responding to environmental stress. However, the response of the ADH family to abiotic stress remains unknown in rapeseed.

RESULT

In this study, we conducted a comprehensive genome-wide investigation of the ADH family in rapeseed, encompassing analysis of their gene structure, replication patterns, conserved motifs, cis-acting elements, and response to stress. A total of 47 ADH genes were identified within the rapeseed genome. Through phylogenetic analysis, BnADHs were classified into four distinct clades (I, II, IV, V). Prediction of protein domains revealed that all BnADH members possessed a GroES-like (ADH_N) domain and a zinc-bound (ADH_zinc_N) domain. Analysis of promoter sequences demonstrated that BnADHs contained numerous cis-acting elements associated with hormone and stress responses, indicating their widespread involvement in various biological regulatory processes. Expression profiling under different concentrations of salt stress treatments (0%, 0.4%, 0.8%, 1.0% NaCl) further highlighted the significant role played by the BnADH family in abiotic stress response mechanisms. Overexpression of BnADH36 in rapeseed significantly improved the salt tolerance of rapeseed.

CONCLUSION

The features of the BnADH family in rapeseed was comprehensively characterized in this study, which could provide reference to the research of BnADHs in abiotic stress response.

Alcohol dehydrogenases regulated by a MYB44 transcription factor underlie Lauraceae citral biosynthesis

Lineage-specific terpenoids have arisen throughout the evolution of land plants and are believed to play a role in interactions between plants and the environment. Species-specific gene clusters in plants have provided insight on the evolution of secondary metabolism. Lauraceae is an ecologically important plant family whose members are also of considerable economic value given their monoterpene contents. However, the gene cluster responsible for the biosynthesis of monoterpenes remains yet to be elucidated. Here, a Lauraceae-specific citral biosynthetic gene cluster (CGC) was identified and investigated using a multifaceted approach that combined phylogenetic, collinearity, and biochemical analyses. The CGC comprises MYB44 as a regulator and 2 alcohol dehydrogenases (ADHs) as modifying enzymes, which derived from species-specific tandem and proximal duplication events. Activity and substrate divergence of the ADHs has resulted in the fruit of mountain pepper (Litsea cubeba), a core Lauraceae species, consisting of more than 80% citral. In addition, MYB44 negatively regulates citral biosynthesis by directly binding to the promoters of the ADH-encoding genes. The aggregation of citral biosynthetic pathways suggests that they may form the basis of important characteristics that enhance adaptability. The findings of this study provide insights into the evolution of and the regulatory mechanisms involved in plant terpene biosynthesis.

Genome-wide identification and expression analysis of the ADH gene family under diverse stresses in tobacco (Nicotiana tabacum L.)

BACKGROUND

Alcohol dehydrogenases (ADHs) are the crucial enzymes that can convert ethanol into acetaldehyde. In tobacco, members of ADH gene family are involved in various stresses tolerance reactions, lipid metabolism and pathways related to plant development. It will be of great application significance to analyze the ADH gene family and expression profile under various stresses in tobacco.

RESULTS

A total of 53 ADH genes were identified in tobacco (Nicotiana tabacum L.) genome and were grouped into 6 subfamilies based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were highly conserved among the NtADH genes, especially the members within the same subfamily. A total of 5 gene pairs of tandem duplication, and 3 gene pairs of segmental duplication were identified based on the analysis of gene duplication events. Cis-regulatory elements of the NtADH promoters participated in cell development, plant hormones, environmental stress, and light responsiveness. The analysis of expression profile showed that NtADH genes were widely expressed in topping stress and leaf senescence. However, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 13 NtADH genes displayed their differential expression pattern in response to the bacterial pathogen Ralstonia solanacearum L.

INFECTION

Metabolomics analysis revealed that NtADH genes were primarily associated with carbohydrate metabolism, and moreover, four NtADH genes (NtADH20/24/48/51) were notably involved in the pathway of alpha-linolenic acid metabolism which related to the up-regulation of 9-hydroxy-12-oxo-10(E), 15(Z)-octadecadienoic acid and 9-hydroxy-12-oxo-15(Z)-octadecenoic acid.

CONCLUSION

The genome-wide identification, evolutionary analysis, expression profiling, and exploration of related metabolites and metabolic pathways associated with NtADH genes have yielded valuable insights into the roles of these genes in response to various stresses. Our results could provide a basis for functional analysis of NtADH gene family under stressful conditions.

Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses

Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.

Genome-wide identification and characterization of ADH gene family and the expression under different abiotic stresses in tomato (Solanum lycopersicum L.)

The SlADH gene plays a key role in environmental stress response. However, limited studies exist regarding the tomato SlADH gene. In this study, we identified 35 SlADH genes in tomato by genome-wide identification. Among the 12 chromosomes of tomato, SlADH gene is distributed on 10 chromosomes, among which the 7th and 10th chromosomes have no family members, while the 11th chromosome has the most members with 8 family members. Members of this gene family are characterized by long coding sequences, few amino acids, and introns that make up a large proportion of the genetic structure of most members of this family. Moreover, the molecular weight of the proteins of the family members was similar, and the basic proteins were mostly, and the overall distribution was relatively close to neutral (pI = 7). This may indicate that proteins in this family have a more conserved function. In addition, a total of four classes of cis-acting elements were detected in all 35 SlADH promoter regions, most of which were associated with biotic and abiotic stresses. The results indicate that SlADH gene had a certain response to cold stress, salt stress, ABA treatment and PEG stress. This study provides a new candidate gene for improving tomato stress resistance.

Transcriptome and Metabolomics Integrated Analysis Reveals MdMYB94 Associated with Esters Biosynthesis in Apple (Malus × domestica)

Volatile esters are major aromas contributing to the organoleptic quality of apple fruit. However, the molecular mechanisms underlying the regulation of volatile ester biosynthesis in apple remain elusive. This study investigated the volatile profiles and transcriptomes of 'Qinguan' (QG) apple fruit during development and/or postharvest storage. Although the constitution of volatiles varied widely between the peel and flesh, the volatile profiles of the peel and flesh of ripening QG fruit were dominated by volatile esters. WGCNA results suggested that 19 genes belonging to ester biosynthesis pathways and 11 hub transcription factor genes potentially participated in the biosynthesis and regulation of esters. To figure out key regulators of ester biosynthesis, correlation network analysis, dual-luciferase assays, and yeast one-hybrid assay were conducted and suggested that MdMYB94 trans-activated the MdAAT2 promoter and participated in the regulation of ester biosynthesis. This study provides a framework for understanding ester biosynthesis and regulation in apple.

Identifying the “Dangshan” Physiological Disease of Pear Woolliness Response via Feature-Level Fusion of Near-Infrared Spectroscopy and Visual RGB Image

The “Dangshan” pear woolliness response is a physiological disease that causes large losses for fruit farmers and nutrient inadequacies.The cause of this disease is predominantly a shortage of boron and calcium in the pear and water loss from the pear. This paper used the fusion of near-infrared Spectroscopy (NIRS) and Computer Vision Technology (CVS) to detect the woolliness response disease of “Dangshan” pears. This paper employs the merging of NIRS features and image features for the detection of “Dangshan” pear woolliness response disease. Near-infrared Spectroscopy (NIRS) reflects information on organic matter containing hydrogen groups and other components in various biochemical structures in the sample under test, and Computer Vision Technology (CVS) captures image information on the disease. This study compares the results of different fusion models. Compared with other strategies, the fusion model combining spectral features and image features had better performance. These fusion models have better model effects than single-feature models, and the effects of these models may vary according to different image depth features selected for fusion modeling. Therefore, the model results of fusion modeling using different image depth features are further compared. The results show that the deeper the depth model in this study, the better the fusion modeling effect of the extracted image features and spectral features. The combination of the MLP classification model and the Xception convolutional neural classification network fused with the NIR spectral features and image features extracted, respectively, was the best combination, with accuracy (0.972), precision (0.974), recall (0.972), and F1 (0.972) of this model being the highest compared to the other models. This article illustrates that the accuracy of the “Dangshan” pear woolliness response disease may be considerably enhanced using the fusion of near-infrared spectra and image-based neural network features. It also provides a theoretical basis for the nondestructive detection of several techniques of spectra and pictures.

ADH Gene Cloning and Identification of Flooding-Responsive Genes in Taxodium distichum (L.) Rich

As a flooding-tolerant tree species, Taxodium distichum has been utilized in afforestation projects and proven to have important value in flooding areas. Alcohol dehydrogenase (ADH), which participates in ethanol fermentation, is essential for tolerance to the anaerobic conditions caused by flooding. In a comprehensive analysis of the ADH gene family in T. distichum, TdADHs were cloned on the basis of whole-genome sequencing, and then bioinformatic analysis, subcellular localization, and gene expression level analysis under flooding were conducted. The results show that the putative protein sequences of 15 cloned genes contained seven TdADHs and eight TdADH-like genes (one Class III ADH included) that were divided into five clades. All the sequences had an ADH_N domain, and except for TdADH-likeE2, all the other genes had an ADH_zinc_N domain. Moreover, the TdADHs in clades A, B, C, and D had a similar motif composition. Additionally, the number of TdADH amino acids ranged from 277 to 403, with an average of 370.13. Subcellular localization showed that, except for TdADH-likeD3, which was not expressed in the nucleus, the other genes were predominantly expressed in both the nucleus and cytosol. TdADH-likeC2 was significantly upregulated in all three organs (roots, stems, and leaves), and TdADHA3 was also highly upregulated under 24 h flooding treatment; the two genes might play key roles in ethanol fermentation and flooding tolerance. These findings offer a comprehensive understanding of TdADHs and could provide a foundation for the molecular breeding of T. distichum and current research on the molecular mechanisms driving flooding tolerance.

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry

The R2R3-MYB is a large gene family involved in various plant functions, including carotenoid biosynthesis. However, this gene family lacks a comprehensive analysis in wolfberry (Lycium barbarum L.) and other Solanaceae species. The recent sequencing of the wolfberry genome provides an opportunity for investigating the organization and evolutionary characteristics of R2R3-MYB genes in wolfberry and other Solanaceae species. A total of 610 R2R3-MYB genes were identified in five Solanaceae species, including 137 in wolfberry. The LbaR2R3-MYB genes were grouped into 31 subgroups based on phylogenetic analysis, conserved gene structures, and motif composition. Five groups only of Solanaceae R2R3-MYB genes were functionally divergent during evolution. Dispersed and whole duplication events are critical for expanding the R2R3-MYB gene family. There were 287 orthologous gene pairs between wolfberry and the other four selected Solanaceae species. RNA-seq analysis identified the expression level of LbaR2R3-MYB differential gene expression (DEGs) and carotenoid biosynthesis genes (CBGs) in fruit development stages. The highly expressed LbaR2R3-MYB genes are co-expressed with CBGs during fruit development. A quantitative Real-Time (qRT)-PCR verified seven selected candidate genes. Thus, Lba11g0183 and Lba02g01219 are candidate genes regulating carotenoid biosynthesis in wolfberry. This study elucidates the evolution and function of R2R3-MYB genes in wolfberry and the four Solanaceae species.

Genome-Wide Identification and Comparative Analysis of the ASR Gene Family in the Rosaceae and Expression Analysis of PbrASRs During Fruit Development

The members of the Abscisic Acid (ABA) Stress and Ripening gene family (ASR) encode a class of plant-specific proteins with ABA/WDS domains that play important roles in fruit ripening, abiotic stress tolerance and biotic stress resistance in plants. The ASR gene family has been widely investigated in the monocotyledons and dicotyledons. Although the genome sequence is already available for eight fruit species of the Rosaceae, there is far less information about the evolutionary characteristics and the function of the ASR genes in the Rosaceae than in other plant families. Twenty-seven ASR genes were identified from species in the Rosaceae and divided into four subfamilies (I, II, III, and IV) on the basis of structural characteristics and phylogenetic analysis. Purifying selection was the primary force for ASR family gene evolution in eight Rosaceae species. qPCR experiments showed that the expression pattern of PbrASR genes from Pyrus bretschneideri was organ-specific, being mainly expressed in flower, fruit, leaf, and root. During fruit development, the mRNA abundance levels of different PbrASR genes were either down- or up-regulated, and were also induced by exogenous ABA. Furthermore, subcellular localization results showed that PbrASR proteins were mainly located in the nucleus and cytoplasm. These results provide a theoretical foundation for investigation of the evolution, expression, and functions of the ASR gene family in commercial fruit species of the Rosaceae family.

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".

Genome‑wide characterization of the Gα subunit gene family in Rosaceae and expression analysis of PbrGPAs under heat stress

The Gα subunit is an important component of the heterotrimeric G-protein complex and an integral component of several signal transduction pathways. It plays crucial roles in the diverse processes of plant growth and development, including the response to abiotic stress, regulation of root development, involvement in stomatal movement, and participation in hormone responses, which have been well investigated in many species. However, no comprehensive analysis has identified and explored the evolution, expression pattern characteristics and heat stress response of the Gα subunit genes in Rosaceae. In this study, 52 Gα subunit genes were identified in eight Rosaceae species; these genes were divided into three subfamilies (I, II, and III) based on their phylogenetic, conserved motif, and structural characteristics. Whole genome and dispersed duplication events were found to have contributed significantly to the expansion of the Gα subunit gene family, and purifying selection to have played a key role in the evolution of Gα subunit genes. An expression analysis identified some PbrGPA genes that were highly expressed in leaf, root, and fruit, and exhibited diverse spatiotemporal expression models in pear. Under abiotic stress conditions, the mRNA transcript levels of PbrGPA genes were up-regulated in response to high temperature treatment in leaves. Furthermore, three Gα subunit genes were shown to be located in the plasma membrane and nucleus in pear. In conclusion, the study of the Gα subunit gene family will help us to better understand its evolutionary history and expression patterns, while facilitating further investigations into the function of the Gα subunit gene in response to heat stress.

Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

BACKGROUND

Heterotrimeric G-proteins, composed of Gα, Gβ and Gγ subunits, are important signal transmitters, mediating the cellular response to multiple stimuli in animals and plants. The Gγ subunit is an essential component of the G-protein, providing appropriate functional specificity to the heterotrimer complex and has been well studied in many species. However, the evolutionary history, expression pattern and functional characteristics of Gγ subunits has not been explored in the Rosaceae, representing many important fruit crops.

RESULTS

In this study, 35 Gγ subunit genes were identified from the eight species belonging to the Rosaceae family. Based on the structural gene characteristics, conserved protein motifs and phylogenetic analysis of the Gγ subunit genes, the genes were classified into three clades. Purifying selection was shown to play an important role in the evolution of Gγ subunit genes, while a recent whole-genome duplication event was the principal force determining the expansion of the Gγ subunit gene family in the subfamily Maloideae. Gγ subunit genes exhibited diverse spatiotemporal expression patterns in Chinese white pear, including fruit, root, ovary and bud, and under abiotic stress conditions, the relative expression of Gγ subunit genes were up-regulated or down-regulated. In addition, seven of the Gγ subunit proteins in pear were located on the plasma membrane, in the cytoplasm or nucleus.

CONCLUSION

Overall, this study of the Gγ subunit gene family in eight Rosaceae species provided useful information to better understand the evolution and expression of these genes and facilitated further exploration of their functions in these important crop plants.

Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum)

Background

Alcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear.

Methods

A total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication.

Results

The organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding.