Ectopic expression of VpALDH2B4, a novel aldehyde dehydrogenase gene from Chinese wild grapevine (Vitis pseudoreticulata), enhances resistance to mildew pathogens and salt stress in Arabidopsis

Genome-Wide Identification and Expression Analysis of the Melon Aldehyde Dehydrogenase (ALDH) Gene Family in Response to Abiotic and Biotic Stresses

Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragmental duplications within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon's ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue- or stage-specific. We analyzed the ALDH gene's expression patterns under six stress types, namely salt, cold, waterlogged, powdery mildew, Fusarium wilt, and gummy stem blight. The results showed differential expression of CmALDH2C4 and CmALDH11A3 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR (quantitative reverse transcription PCR) analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Comparative evaluation of physiological and molecular responses of blackcurrant varieties to powdery mildew infection

The black currant (Ribes nigrum L.), a member of the Saxifragaceae family's Ribes genus, has gained consumer and grower acceptance due to its high nutritional value and economic potential. However, powdery mildew, the primary leaf disease affecting black currants, significantly impacts growers and the industry. Developing varieties highly resistant to powdery mildew is currently considered the most scientifically sound solution. However, the black currant's physiological and disease resistance mechanisms post-infection by powdery mildew remain understudied, thereby impeding further breeding efforts. Therefore, this study aimed to elucidate the pathogenesis of powdery mildew in various susceptible varieties, post-infection physiological changes, and molecular mechanisms related to powdery mildew. This was achieved through phenotypic observation, physiological data analysis, transcriptomic analysis, and qRT-PCR-mediated gene expression analysis.

Genome-wide identification and expression analysis of the ALDH gene family and functional analysis of PaALDH17 in Prunus avium

ALDH (Aldehyde dehydrogenase), as an enzyme that encodes the dehydroxidization of aldehydes into corresponding carboxylic acids, played an important role inregulating gene expression in response to many kinds of biotic and abiotic stress, including saline-alkali stress. Saline-alkali stress was a common stress that seriously affected plant growth and productivity. Saline-alkali soil contained the characteristics of high salinity and high pH value, which could cause comprehensive damage such as osmotic stress, ion toxicity, high pH, and HCO3-/CO32- stress. In our study, 18 PaALDH genes were identified in sweet cherry genome, and their gene structures, phylogenetic analysis, chromosome localization, and promoter cis-acting elements were analyzed. Quantitative real-time PCR confirmed that PaALDH17 exhibited the highest expression compared to other members under saline-alkali stress. Subsequently, it was isolated from Prunus avium, and transgenic A. thaliana was successfully obtained. Compared with wild type, transgenic PaALDH17 plants grew better under saline-alkali stress and showed higher chlorophyll content, Superoxide dismutase (SOD), Peroxidase (POD) and Catalase (CAT) enzyme activities, which indicated that they had strong resistance to stress. These results indicated that PaALDH17 improved the resistance of sweet cherries to saline-alkali stress, which in turn improved quality and yields.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01444-7.

Comprehensive analysis of the aldehyde dehydrogenase gene family in Phaseolus vulgaris L. and their response to saline-alkali stress

Background

Aldehyde dehydrogenase (ALDH) scavenges toxic aldehyde molecules by catalyzing the oxidation of aldehydes to carboxylic acids. Although ALDH gene family members in various plants have been extensively studied and were found to regulate plant response to abiotic stress, reports on ALDH genes in the common bean (Phaseolus vulgaris L.) are limited. In this study, we aimed to investigate the effects of neutral (NS) and basic alkaline (AS) stresses on growth, physiological and biochemical indices, and ALDH activity, ALDH gene expression of common bean. In addition, We used bioinformatics techniques to analyze the physical and chemical properties, phylogenetic relationships, gene replication, collinearity, cis-acting elements, gene structure, motifs, and protein structural characteristics of PvALDH family members.

Results

We found that both NS and AS stresses weakened the photosynthetic performance of the leaves, induced oxidative stress, inhibited common bean growth, and enhanced the antioxidative system to scavenge reactive oxygen species. Furthermore, we our findings revealed that ALDH in the common bean actively responds to NS or AS stress by inducing the expression of PvALDH genes. In addition, using the established classification criteria and phylogenetic analysis, 27 PvALDHs were identified in the common bean genome, belonging to 10 ALDH families. The primary expansion mode of PvALDH genes was segmental duplication. Cis-acting elemental analysis showed that PvALDHs were associated with abiotic stress and phytohormonal responses. Gene expression analysis revealed that the PvALDH gene expression was tissue-specific. For instance, PvALDH3F1 and PvALDH3H1 were highly expressed in flower buds and flowers, respectively, whereas PvALDH3H2 and PvALDH2B4 were highly expressed in green mature pods and young pods, respectively. PvALDH22A1 and PvALDH11A2 were highly expressed in leaves and young trifoliates, respectively; PvALDH18B2 and PvALDH18B3 were highly expressed in stems and nodules, respectively; and PvALDH2C2 and PvALDH2C3 were highly expressed in the roots. PvALDHs expression in the roots responded positively to NS-AS stress, and PvALDH2C3, PvALDH5F1, and PvALDH10A1 were significantly (P < 0.05) upregulated in the roots.

Conclusion

These results indicate that AS stress causes higher levels of oxidative damage than NS stress, resulting in weaker photosynthetic performance and more significant inhibition of common bean growth. The influence of PvALDHs potentially modulates abiotic stress response, particularly in the context of saline-alkali stress. These findings establish a basis for future research into the potential roles of ALDHs in the common bean.

Advances in understanding grapevine downy mildew: From pathogen infection to disease management

Plasmopara viticola is geographically widespread in grapevine-growing regions. Grapevine downy mildew disease, caused by this biotrophic pathogen, leads to considerable yield losses in viticulture annually. Because of the great significance of grapevine production and wine quality, research on this disease has been widely performed since its emergence in the 19th century. Here, we review and discuss recent understanding of this pathogen from multiple aspects, including its infection cycle, disease symptoms, genome decoding, effector biology, and management and control strategies. We highlight the identification and characterization of effector proteins with their biological roles in host-pathogen interaction, with a focus on sustainable control methods against P. viticola, especially the use of biocontrol agents and environmentally friendly compounds.

PusALDH1 gene confers high levels of volatile aroma accumulation in both pear and tomato fruits

Aroma is an important commercial trait that determines fruit quality and has an important influence on the overall flavor of fruits. Plant ALDH genes have been implicated in diverse pathways and play crucial roles in physiological activities. In this study, via genome resequencing we identified one gene PusALDH1 (Pbr034873.1) related to aroma biosynthesis that can respond to the induction of methyl jasmonate. Transient transformation of pear fruits and heterologous stable transformation of tomato further confirmed the function of PusALDH1 in aroma accumulation. The content of ALDH precursor substance, benzaldehyde, was reduced in the overexpressing pear and tomato fruits, and the content of ALDH product, benzoic acid and benzoic acid derivatives, was increased in the pear fruits. Meanwhile, transgenic tomato fruits with PusALDH1 overexpression exhibited a greater area of yellow placenta, indicating that the gene may be related to the growth and development of the fruit. Taken together, PusALDH1 could act as a strong candidate gene in aroma synthesis.

Genome-wide characterization of aldehyde dehydrogenase gene family members in groundnut (Arachis hypogaea) and the analysis under saline-alkali stress

Groundnut or peanut (Arachis hypogaea) is a legume crop. Its seeds are rich in protein and oil. Aldehyde dehydrogenase (ALDH, EC: 1.2.1.3) is an important enzyme involved in detoxification of aldehyde and cellular reactive oxygen species, as well as in attenuation of lipid peroxidation-meditated cellular toxicity under stress conditions. However, few studies have been identified and analyzed about ALDH members in Arachis hypogaea. In the present study, 71 members of the ALDH superfamily (AhALDH) were identified using the reference genome obtained from the Phytozome database. A systematic analysis of the evolutionary relationship, motif, gene structure, cis-acting elements, collinearity, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and expression patterns was conducted to understand the structure and function of AhALDHs. AhALDHs exhibited tissue-specific expression, and quantitative real-time PCR identified significant differences in the expression levels of AhALDH members under saline-alkali stress. The results revealed that some AhALDHs members could be involved in response to abiotic stress. Our findings on AhALDHs provide insights for further study.

Transcriptomic Analysis Elaborates the Resistance Mechanism of Grapevine Rootstocks against Salt Stress

Grapes are subject to a wide range of climatic conditions during their life cycle, but the use of rootstocks can effectively ameliorate the effects of abiotic stress. However, the tolerance mechanism of different grape rootstock varieties varies under various stresses, and systematic research on this aspect is limited. On the basis of previous research, transcriptome sequencing was performed on three tolerant grape rootstock varieties (3309C, 520A, 1103P) and three intolerant grape rootstock varieties (5BB, 101-14, Beta). In total, 56,478,468 clean reads were obtained. One hundred and ten genes only existed in all combinations during P1 with a downregulated trend, and 178 genes existed only in P1 of tolerant grape rootstock varieties. Salt treatment firstly affected the photosynthesis of leaves, and tolerant varieties weakened or even eliminated this effect through their own mechanisms in the later stage. Tolerant varieties mobilized a large number of MFs during the P2 stage, such as hydrolase activity, carboxypeptidase activity, and dioxygenase activity. Carbon metabolism was significantly enriched in P1, while circadian rhythm and flavonoid biosynthesis were only enriched in tolerant varieties. In the intolerant varieties, photosynthesis-related pathways were always the most significantly enriched. There were large differences in the gene expression of the main signal pathways related to salt stress in different varieties. Salt stress affected the expression of genes related to plant abiotic stress, biotic stress, transcription factors, hormones, and secondary metabolism. Tolerant varieties mobilized more bHLH, WRKY, and MYB transcription factors to respond to salt stress than intolerant varieties. In the tolerant rootstocks, SOS was co-expressed. Among these, SOS1 and SOS2 were upregulated, and the SOS3 and SOS5 components were downregulated. The genes of heat shock proteins and the phenylalanine pathway were upregulated in the tolerant varieties. These findings outline a tolerance mechanism model for rootstocks for coping with osmotic stress, providing important information for improving the resistance of grapes under global climate change.

Aldehyde Dehydrogenase 2 as a Therapeutic Target in Oxidative Stress-Related Diseases: Post-Translational Modifications Deserve More Attention

Aldehyde dehydrogenase 2 (ALDH2) has both dehydrogenase and esterase activity; its dehydrogenase activity is closely related to the metabolism of aldehydes produced under oxidative stress (OS). In this review, we recapitulate the enzyme activity of ALDH2 in combination with its protein structure, summarize and show the main mechanisms of ALDH2 participating in metabolism of aldehydes in vivo as comprehensively as possible; we also integrate the key regulatory mechanisms of ALDH2 participating in a variety of physiological and pathological processes related to OS, including tissue and organ fibrosis, apoptosis, aging, and nerve injury-related diseases. On this basis, the regulatory effects and application prospects of activators, inhibitors, and protein post-translational modifications (PTMs, such as phosphorylation, acetylation, S-nitrosylation, nitration, ubiquitination, and glycosylation) on ALDH2 are discussed and prospected. Herein, we aimed to lay a foundation for further research into the mechanism of ALDH2 in oxidative stress-related disease and provide a basis for better use of the ALDH2 function in research and the clinic.

Multi-Omics-Based Identification and Functional Characterization of Gh_A06G1257 Proves Its Potential Role in Drought Stress Tolerance in Gossypium hirsutum

Cotton is one of the most important fiber crops globally. Despite this, various abiotic stresses, including drought, cause yield losses. We used transcriptome profiles to investigate the co-expression patterns of gene networks associated with drought stress tolerance. We identified three gene modules containing 3,567 genes highly associated with drought stress tolerance. Within these modules, we identified 13 hub genes based on intramodular significance, for further validation. The yellow module has five hub genes (Gh_A07G0563, Gh_D05G0221, Gh_A05G3716, Gh_D12G1438, and Gh_D05G0697), the brown module contains three hub genes belonging to the aldehyde dehydrogenase (ALDH) gene family (Gh_A06G1257, Gh_A06G1256, and Gh_D06G1578), and the pink module has five hub genes (Gh_A02G1616, Gh_D12G2599, Gh_D07G2232, Gh_A02G0527, and Gh_D07G0629). Based on RT-qPCR results, the Gh_A06G1257 gene has the highest expression under drought stress in different plant tissues and it might be the true candidate gene linked to drought stress tolerance in cotton. Silencing of Gh_A06G1257 in cotton leaves conferred significant sensitivity in response to drought stress treatments. Overexpression of Gh_A06G1257 in Arabidopsis also confirms its role in drought stress tolerance. L-valine, Glutaric acid, L-proline, L-Glutamic acid, and L-Tryptophan were found to be the most significant metabolites playing roles in drought stress tolerance. These findings add significantly to existing knowledge of drought stress tolerance mechanisms in cotton.

Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping

Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10^-06 to 4.80 × 10^-05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F_2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.

Differential responses of the scavenging systems for reactive oxygen species (ROS) and reactive carbonyl species (RCS) to UV-B irradiation in Arabidopsis thaliana and its high altitude perennial relative Arabis alpina

The present work aimed to compare antioxidant response and lipid peroxide detoxification capacity of an arctic-alpine species Arabis alpina to its close relative model species Arabidopsis thaliana under acute short duration (3 h and 6 h) UV-B stress (4.6 and 8.2 W/m²). After 3 and 6 h exposure to UV-B, A. alpina showed lower lipid peroxidation and H₂O₂ accumulation when compared to A. thaliana. Moreover, F_v/F_m value of A. thaliana dropped to 0.70, while A. alpina dropped to 0.75 indicating better protection of PSII in this species. For elucidation of the antioxidant response, activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POX), ascorbate peroxidase (APX), glutathione reductase (GR) and dehydroascorbate reductase (DHAR) were measured. SOD induction with 6 h of UV-B was more prominent in A. alpina. Also, A. alpina had higher chloroplastic FeSOD activity when compared to A. thaliana. APX activity was also significantly induced in A. alpina, while its activity decreased at 3 h or did not change at 6 h in A. thaliana. A. alpina was able to maintain constant CAT activity, but drastic decreases were observed in A. thaliana at both time points. Moreover, A. alpina was able to maintain or induce aldehyde dehydrogenase (ALDH), alkenal reductases (AERs) and glutathione-S-transferases (GST) activity, while an opposite trend was observed in A. thaliana. These findings indicate that A. alpina was able to maintain/induce its antioxidant defence and lipid peroxide detoxification conferring better protection against UV-B.

Aldehyde dehydrogenase plays crucial roles in response to lower temperature stress in Solanum tuberosum and Nicotiana benthamiana

The aim of this study is to elucidate the role of ALDH2B7a during the response to lower temperature in Solanum tuberosum. This gene was found to have altered intragenic DNA methylation status in our previous reports. A total of 18 orthologs of StALDH2B7a were identified in the S. tuberosum genome, which were then divided into 8 aldehyde dehydrogenase (ALDH) subfamilies. The methylation statuses of four intragenic cytosine sites in intron 5 and exon 6 of genomic StALDH2B7a were altered by lower temperature stress, resulting in changes in the expression of StALDH2B7a. Silencing of NbALDH2C4, a homolog of StALDH2B7a in Nicotiana benthamiana, resulted in plants which were sensitive to lower temperature and accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA). These data suggested that the expression of StALDH2B7a was upregulated by alteration of its intragenic cytosine methylation status during lower temperature stress, and additional StALDH2B7a enzymes scavenged excess aldehydes resulting from ROS in a response to cold stress in potato. Our study expands the understanding of the mechanisms involved in plant responses to lower temperature, and provides a new gene source to improve potato tolerance to cold stress in northern China, where lower temperature is one of the key limiting factors for crop production.

Recent advances in biotechnological studies on wild grapevines as valuable resistance sources for smart viticulture

Cultivated grapevines, Vitis vinifera subsp. sativa, are thought to have been domesticated from wild populations of Vitis vinifera subsp. sylvestris in Central Asia. V. vinifera subsp. sativa is one of the most economically important fruit crops worldwide. Since cultivated grapevines are susceptible to multiple biotic and abiotic soil factors, they also need to be grafted on resistant rootstocks that are mostly developed though hybridization between American wild grapevine species (V. berlandieri, V. riparia, and V. rupestris). Therefore, wild grapevine species are essential genetic materials for viticulture to face biotic and abiotic stresses in both cultivar and rootstock parts. Actually, viticulture faces several environmental constraints that are further intensified by climate change. Recently, several reports on biotic and abiotic stresses-response in wild grapevines revealed accessions tolerant to different constraints. The emergence of advanced techniques such as omics technologies, marker-assisted selection (MAS), and functional analysis tools allowed a more detailed characterization of resistance mechanisms in these wild grapevines and suggest a number of species (V. rotundifolia, V. rupestris, V. riparia, V. berlandieri and V. amurensis) have untapped potential for new resistance traits including disease resistance loci and key tolerance genes. The present review reports on the importance of different biotechnological tools in exploring and examining wild grapevines tolerance mechanisms that can be employed to promote elite cultivated grapevines under climate change conditions.

Emergent Ascomycetes in Viticulture: An Interdisciplinary Overview

The reduction of pesticide usage is a current imperative and the implementation of sustainable viticulture is an urgent necessity. A potential solution, which is being increasingly adopted, is offered by the use of grapevine cultivars resistant to its main pathogenic threats. This, however, has contributed to changes in defense strategies resulting in the occurrence of secondary diseases, which were previously controlled. Concomitantly, the ongoing climate crisis is contributing to destabilizing the increasingly dynamic viticultural context. In this review, we explore the available knowledge on three Ascomycetes which are considered emergent and causal agents of powdery mildew, black rot and anthracnose. We also aim to provide a survey on methods for phenotyping disease symptoms in fields, greenhouse and lab conditions, and for disease control underlying the insurgence of pathogen resistance to fungicide. Thus, we discuss fungal genetic variability, highlighting the usage and development of molecular markers and barcoding, coupled with genome sequencing. Moreover, we extensively report on the current knowledge available on grapevine-ascomycete interactions, as well as the mechanisms developed by the host to counteract the attack. Indeed, to better understand these resistance mechanisms, it is relevant to identify pathogen effectors which are involved in the infection process and how grapevine resistance genes function and impact the downstream cascade. Dealing with such a wealth of information on both pathogens and the host, the horizon is now represented by multidisciplinary approaches, combining traditional and innovative methods of cultivation. This will support the translation from theory to practice, in an attempt to understand biology very deeply and manage the spread of these Ascomycetes.

Genome-wide characterization of ALDH Superfamily in Brassica rapa and enhancement of stress tolerance in heterologous hosts by BrALDH7B2 expression

Aldehyde dehydrogenase (ALDH) carries out oxidation of toxic aldehydes using NAD⁺/NADP⁺ as cofactors. In the present study, we performed a genome-wide identification and expression analysis of genes in the ALDH gene family in Brassica rapa. A total of 23 ALDH genes in the superfamily have been identified according to the classification of ALDH Gene Nomenclature Committee (AGNC). They were distributed unevenly across all 10 chromosomes. All the 23 Brassica rapa ALDH (BrALDH) genes exhibited varied expression patterns during treatments with abiotic stress inducers and hormonal treatments. The relative expression profiles of ALDH genes in B. rapa showed that they are predominantly expressed in leaves and stem suggesting their function in the vegetative tissues. BrALDH7B2 showed a strong response to abiotic stress and hormonal treatments as compared to other ALDH genes; therefore, it was overexpressed in heterologous hosts, E. coli and yeast to study its possible function under abiotic stress conditions. Over-expression of BrALDH7B2 in heterologous systems, E. coli and yeast cells conferred significant tolerance to abiotic stress treatments. Results from this work demonstrate that BrALDH genes are a promising and untapped genetic resource for crop improvement and could be deployed further in the development of drought and salinity tolerance in B. rapa and other economically important crops.

Transcriptome and proteome analyses of the molecular mechanisms associated with coix seed nutritional quality in the process of breeding

In present study, the content of main nutrients in wild coix seed were significantly higher than cultivated coix seed. Transcriptome and proteome were combined to provide new insight of the molecular mechanisms linked to nutritional quality of wild coix seed and cultivated coix seed by RNA sequencing and isobaric tags for relative and absolute quantification techniques. A total of 20,039 genes and 471 proteins exhibited differential expression level in cultivated coix seed when compared with wild coix seed. These genes and proteins revealed that the pathway of flavonoids biosynthesis, starch and sucrose metabolism, lipid metabolism and amino acid metabolism were linked to nutritional quality of coix seed. Our results provided transcriptomics and proteomics information with respect to the molecular mechanisms of nutritional changes of coix seed, identified key genes and proteins that associated with the metabolism and accumulation of nutrients, and helped clarify the mechanisms of nutrient differences.

Ectopic expression of FvWRKY42, a WRKY transcription factor from the diploid woodland strawberry (Fragaria vesca), enhances resistance to powdery mildew, improves osmotic stress resistance, and increases abscisic acid sensitivity in Arabidopsis

WRKY transcription factors play a critical role in biotic and abiotic stress responses in plants, but very few WRKYs have been reported in strawberry plants. Here, a multiple stress-inducible gene, FvWRKY42, was isolated from the wild diploid woodland strawberry (accession Heilongjiang-3). FvWRKY42 expression was induced by treatment with powdery mildew, salt, drought, salicylic acid (SA), methyl jasmonate (MeJA), abscisic acid (ABA), and ethylene. The protein interaction network analysis showed that the FvWRKY42 protein interacts with various stress-related proteins. Overexpression of FvWRKY42 in Arabidopsis resulted in cell death, sporulation, slow hypha growth, and enhanced resistance to powdery mildew that was concomitant with increased expression of PR1 genes in Arabidopsis. Overexpression also led to enhanced salt and drought stress tolerance, increased primary root length and germination rate, decreased water loss rate, reduced relative electrolyte leakage, and malondialdehyde accumulation, and upregulation of superoxide dismutase and catalase activity. Additionally, FvWRKY42-overexpressing Arabidopsis plants showed increased ABA sensitivity during seed germination and seedling growth, increased stomatal closure after ABA and drought treatment, and altered expression of ABA-responsive genes. Collectively, our data demonstrate that FvWRKY42 may play an important role in powdery mildew infection and the regulation of salt and drought stress responses in plants.

Overexpression of VpEIFP1, a novel F-box/Kelch-repeat protein from wild Chinese Vitis pseudoreticulata, confers higher tolerance to powdery mildew by inducing thioredoxin z proteolysis

An F-box protein (VpEIFP1) induced by Erysiphe necator was isolated from Vitis pseudoreticulata, a wild Chinese grapevine species naturally resistant to powdery mildew (PM). It contains an F-box domain and two Kelch-repeat motifs. Expression profiles indicate the VpEIFP1 is strongly induced at both transcriptional and translational levels by PM infection. A subcellular localisation assay showed that VpEIFP1 is predominantly located in the nucleus and cytoplasm. Overexpression of VpEIFP1 accelerated the accumulation of hydrogen peroxide (H₂O₂) and up-regulated the expressions of ICS2, NPR1 and PR1 involved in defence responses, resulting in suppression of PM germination and growth. As an F-box protein, VpEIFP1 interacts with thioredoxin z (VpTrxz) in the yeast-two-hybrid (Y2H) assay and in the bimolecular fluorescence complementation (BiFC) assay. Decreased amounts of VpTrxz protein in transgenic grapevine leaves overexpressing VpEIFP1 were restored by proteasome inhibitor MG132, implying that VpEIFP1 mediated VpTrxz for degradation through the SCF^VpEIFP1 (Skp1-Cullin-F-box) E3 ubiquitin ligase complex. The RNA interference line of VpTrxz showed increased H₂O₂ accumulation following PM inoculation. We propose VpEIFP1 positively modulates the grapevine defence response to PM by inducing the degradation of VpTrxz via the ubiquitin/26S proteasome system.

Genome-wide characterization and expression analysis of the aldehyde dehydrogenase (ALDH) gene superfamily under abiotic stresses in cotton

In plants, aldehyde dehydrogenases (ALDHs) function as 'aldehyde scavengers' by removing reactive aldehydes and thus play important roles in stress responses. To date, 30 ALDHs have been identified in Gossypium raimondii, whereas ALDHs have not been studied in Gossypium arboreum or in tetraploid cotton. In this study, we identified 30, 59 and 59 aldehyde dehydrogenase (ALDH) genes from G. arboreum, G. hirsutum and G. barbadense, respectively. Gene structure analysis revealed that members of the same family exhibit similar exon-intron structures and structural domains, and all members of the ALDH18 family possess a distinct AA-kinase domain. Synteny analysis showed that segmental and tandem duplications have played an important role in the expansion and evolution of ALDHs in cotton. Phylogenetic and synteny analysis between G. arboreum and G. raimondii demonstrated that all GaALDHs and GrALDHs are orthologous and that most GaALDHs are located in syntenic blocks corresponding to those of G. raimondii, implying that these genes appeared before the divergence of G. arboreum and G. raimondii and that no expansion of the ALDH superfamily has occurred in these two cotton species. Quantitative real-time PCR analysis revealed that the majority of GaALDHs and GhALDHs are up-regulated under conditions of high salinity and drought, indicating that these genes may be stress responsive. The findings of this study, based on genome-wide identification of ALDHs in Gossypium and analysis of their evolution and expression, provide a foundation for further analysis of ALDHs and suggest potential target genes for improving stress resistance in cotton.

Physcomitrella Patens Dehydrins (PpDHNA and PpDHNC) Confer Salinity and Drought Tolerance to Transgenic Arabidopsis Plants

Dehydrins (DHNs) as a member of late-embryogenesis-abundant (LEA) proteins are involved in plant abiotic stress tolerance. Two dehydrins PpDHNA and PpDHNC were previously characterized from the moss Physcomitrella patens, which has been suggested to be an ideal model plant to study stress tolerance due to its adaptability to extreme environment. In this study, functions of these two genes were analyzed by heterologous expressions in Arabidopsis. Phenotype analysis revealed that overexpressing PpDHN dehydrin lines had stronger stress resistance than wild type and empty-vector control lines. These stress tolerance mainly due to the up-regulation of stress-related genes expression and mitigation to oxidative damage. The transgenic plants showed strong scavenging ability of reactive oxygen species(ROS), which was attributed to the enhancing of the content of antioxidant enzymes like superoxide dismutase (SOD) and catalase (CAT). Further analysis showed that the contents of chlorophyll and proline tended to be the appropriate level (close to non-stress environment) and the malondialdehyde (MDA) were repressed in these transgenic plants after exposure to stress. All these results suggest the PpDHNA and PpDHNC played a crucial role in response to drought and salt stress.

Active Sites of Reduced Epidermal Fluorescence1 (REF1) Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots

Plant aldehyde dehydrogenases (ALDHs) play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.

Transcriptome Analysis of an Anthracnose-Resistant Tea Plant Cultivar Reveals Genes Associated with Resistance to Colletotrichum camelliae

Tea plant breeding is a topic of great economic importance. However, disease remains a major cause of yield and quality losses. In this study, an anthracnose-resistant cultivar, ZC108, was developed. An infection assay revealed different responses to Colletotrichum sp. infection between ZC108 and its parent cultivar LJ43. ZC108 had greater resistance than LJ43 to Colletotrichum camelliae. Additionally, ZC108 exhibited earlier sprouting in the spring, as well as different leaf shape and plant architecture. Microarray data revealed that the genes that are differentially expressed between LJ43 and ZC108 mapped to secondary metabolism-related pathways, including phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways. In addition, genes involved in plant hormone biosynthesis and signaling as well as plant-pathogen interaction pathways were also changed. Quantitative real-time PCR was used to examine the expression of 27 selected genes in infected and uninfected tea plant leaves. Genes encoding a MADS-box transcription factor, NBS-LRR disease-resistance protein, and phenylpropanoid metabolism pathway components (CAD, CCR, POD, beta-glucosidase, ALDH and PAL) were among those differentially expressed in ZC108.

Genome-wide Identification and Expression Analysis of the CDPK Gene Family in Grape, Vitis spp

BACKGROUND

Calcium-dependent protein kinases (CDPKs) play vital roles in plant growth and development, biotic and abiotic stress responses, and hormone signaling. Little is known about the CDPK gene family in grapevine.

RESULTS

In this study, we performed a genome-wide analysis of the 12X grape genome (Vitis vinifera) and identified nineteen CDPK genes. Comparison of the structures of grape CDPK genes allowed us to examine their functional conservation and differentiation. Segmentally duplicated grape CDPK genes showed high structural conservation and contributed to gene family expansion. Additional comparisons between grape and Arabidopsis thaliana demonstrated that several grape CDPK genes occured in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of grapevine and Arabidopsis. Phylogenetic analysis divided the grape CDPK genes into four groups. Furthermore, we examined the expression of the corresponding nineteen homologous CDPK genes in the Chinese wild grape (Vitis pseudoreticulata) under various conditions, including biotic stress, abiotic stress, and hormone treatments. The expression profiles derived from reverse transcription and quantitative PCR suggested that a large number of VpCDPKs responded to various stimuli on the transcriptional level, indicating their versatile roles in the responses to biotic and abiotic stresses. Moreover, we examined the subcellular localization of VpCDPKs by transiently expressing six VpCDPK-GFP fusion proteins in Arabidopsis mesophyll protoplasts; this revealed high variability consistent with potential functional differences.

CONCLUSIONS

Taken as a whole, our data provide significant insights into the evolution and function of grape CDPKs and a framework for future investigation of grape CDPK genes.

Current understanding of grapevine defense mechanisms against the biotrophic fungus (Erysiphe necator), the causal agent of powdery mildew disease

The most economically important disease of cultivated grapevines worldwide is powdery mildew (PM) caused by the ascomycete fungus Erysiphe necator. The majority of grapevine cultivars used for wine, table grape, and dried fruit production are derived from the Eurasian grape species Vitis vinifera because of its superior aroma and flavor characteristics. However, this species has little genetic resistance against E. necator meaning that grape production is highly dependent on the frequent use of fungicides. The integration of effective genetic resistance into cultivated grapevines would lead to significant financial and environmental benefits and represents a major challenge for viticultural industries and researchers worldwide. This review will outline the strategies being used to increase our understanding of the molecular basis of V. vinifera susceptibility to this fungal pathogen. It will summarize our current knowledge of different resistance loci/genes that have evolved in wild grapevine species to restrict PM infection and assess the potential application of these defense genes in the generation of PM-resistant grapevine germplasm. Finally, it addresses future research priorities which will be important in the rapid identification, evaluation, and deployment of new PM resistance genes which are capable of conferring effective and durable resistance in the vineyard.

Role and structural characterization of plant aldehyde dehydrogenases from family 2 and family 7

Aldehyde dehydrogenases (ALDHs) are responsible for oxidation of biogenic aldehyde intermediates as well as for cell detoxification of aldehydes generated during lipid peroxidation. So far, 13 ALDH families have been described in plants. In the present study, we provide a detailed biochemical characterization of plant ALDH2 and ALDH7 families by analysing maize and pea ALDH7 (ZmALDH7 and PsALDH7) and four maize cytosolic ALDH(cALDH)2 isoforms RF2C, RF2D, RF2E and RF2F [the first maize ALDH2 was discovered as a fertility restorer (RF2A)]. We report the crystal structures of ZmALDH7, RF2C and RF2F at high resolution. The ZmALDH7 structure shows that the three conserved residues Glu(120), Arg(300) and Thr(302) in the ALDH7 family are located in the substrate-binding site and are specific to this family. Our kinetic analysis demonstrates that α-aminoadipic semialdehyde, a lysine catabolism intermediate, is the preferred substrate for plant ALDH7. In contrast, aromatic aldehydes including benzaldehyde, anisaldehyde, cinnamaldehyde, coniferaldehyde and sinapaldehyde are the best substrates for cALDH2. In line with these results, the crystal structures of RF2C and RF2F reveal that their substrate-binding sites are similar and are formed by an aromatic cluster mainly composed of phenylalanine residues and several nonpolar residues. Gene expression studies indicate that the RF2C gene, which is strongly expressed in all organs, appears essential, suggesting that the crucial role of the enzyme would certainly be linked to the cell wall formation using aldehydes from phenylpropanoid pathway as substrates. Finally, plant ALDH7 may significantly contribute to osmoprotection because it oxidizes several aminoaldehydes leading to products known as osmolytes.

Plant aldo-keto reductases (AKRs) as multi-tasking soldiers involved in diverse plant metabolic processes and stress defense: A structure-function update

The aldo-keto reductase (AKR) superfamily comprises of a large number of primarily monomeric protein members, which reduce a broad spectrum of substrates ranging from simple sugars to potentially toxic aldehydes. Plant AKRs can be broadly categorized into four important functional groups, which highlight their roles in diverse plant metabolic reactions including reactive aldehyde detoxification, biosynthesis of osmolytes, secondary metabolism and membrane transport. Further, multiple overlapping functional aspects of plant AKRs including biotic and abiotic stress defense, production of commercially important secondary metabolites, iron acquisition from soil, plant-microbe interactions etc. are discussed as subcategories within respective major groups. Owing to the broad substrate specificity and multiple stress tolerance of the well-characterized AKR4C9 from Arabidopsis thaliana, protein sequences of all the homologues of AKR4C9 (A9-like proteins) from forty different plant species (Phytozome database) were analyzed. The analysis revealed that all A9-like proteins possess strictly conserved key catalytic residues (D-47, Y-52 and K-81) and belong to the pfam00248 and cl00470 AKR superfamilies. Based on structural homology of the three flexible loops of AKR4C9 (Loop A, B and C) responsible for broad substrate specificity, A9-like proteins found in Brassica rapa, Phaseolus vulgaris, Cucumis sativus, Populus trichocarpa and Solanum lycopersicum were predicted to have a similar range of substrate specificity. Thus, plant AKRs can be considered as potential breeding targets for developing stress tolerant varieties in the future. The present review provides a consolidated update on the current research status of plant AKRs with an emphasis on important functional aspects as well as their potential future prospects and an insight into the overall structure-function relationships of A9-like proteins.

Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes

BACKGROUND

Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.

RESULTS

We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.

CONCLUSION

The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

Transcriptome of Erysiphe necator-infected Vitis pseudoreticulata leaves provides insight into grapevine resistance to powdery mildew

Powdery mildew (PM), which is caused by the pathogen Erysiphe necator (Schw.) Burr., is the single most damaging disease of cultivated grapes (Vitis vinifera) worldwide. However, little is known about the transcriptional response of grapes to infection with PM. RNA-seq analysis was used for deep sequencing of the leaf transcriptome to study PM resistance in Chinese wild grapes (V. pseudoreticulata Baihe 35-1) to better understand the interaction between host and pathogen. Greater than 100 million (M) 90-nt cDNA reads were sequenced from a cDNA library derived from PM-infected leaves. Among the sequences obtained, 6541 genes were differentially expressed (DEG) and were annotated with Gene Ontology terms and by pathway enrichment. The significant categories that were identified included the following: defense, salicylic acid (SA) and jasmonic acid (JA) responses; systemic acquired resistance (SAR); hypersensitive response; plant-pathogen interaction; flavonoid biosynthesis; and plant hormone signal transduction. Various putative secretory proteins were identified, indicating potential defense responses to PM infection. In all, 318 putative R-genes and 183 putative secreted proteins were identified, including the defense-related R-genes BAK1, MRH1 and MLO3 and the defense-related secreted proteins GLP and PR5. The expression patterns of 16 genes were further illuminated by RT-qPCR. The present study identified several candidate genes and pathways that may contribute to PM resistance in grapes and illustrated that RNA-seq is a powerful tool for studying gene expression. The RT-qPCR results reveal that effective resistance responses of grapes to PM include enhancement of JA and SAR responses and accumulation of phytoalexins.

Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily of Gossypium raimondii

BACKGROUND

Aldehyde dehydrogenases (ALDHs) are members of the NAD(P)(+)-dependent protein superfamily which catalyzes aliphatic and aromatic aldehyde oxidation to non-toxic carboxylic acids. ALDH genes may offer promise for improving plant adaptation to environmental stress. Recently, elucidated genome sequences of Gossypium raimondii provide a foundation for systematic identification and analysis of ALDH genes. To date, this has been accomplished for many plant species except G. raimondii.

RESULTS

In this study, thirty unique ALDH sequences that code for 10 ALDH families were identified in the G. raimondii genome. Phylogenetic analysis revealed that ALDHs were split into six clades in G. raimondii, and ALDH proteins from the same families were clustered together. Phylogenetic relationships of ALDHs from 11 plant species suggest that ALDHs in G. raimondii shared the highest protein homology with ALDHs from poplar. Members within ALDH families possessed homologous exon-intron structures. Chromosomal distribution of ALDH did not occur evenly in the G. raimondii genome and many ALDH genes were involved in the syntenic region as documented by identification of physical locations among single chromosomes. In addition, syntenic analysis revealed that homologues of many G. raimondii ALDHs appeared in corresponding Arabidopsis and poplar syntenic blocks, indicating that these genes arose prior to G. raimondii, Arabidopsis and poplar speciation. Finally, based on gene expression analysis of microarray and RNA-seq, we can speculate that some G. raimondii ALDH genes might respond to drought or waterlogging stresses.

CONCLUSION

Genome-wide identification and analysis of the evolution and expression of ALDH genes in G. raimondii laid a foundation for studying this gene superfamily and offers new insights into the evolution history and speculated roles in Gossypium. These data can be used to inform functional genomic studies and molecular breeding in cotton.

Characteristics and expression patterns of the aldehyde dehydrogenase (ALDH) gene superfamily of foxtail millet (Setaria italica L.)

Recent genomic sequencing of the foxtail millet, an abiotic, stress-tolerant crop, has provided a great opportunity for novel gene discovery and functional analysis of this popularly-grown grass. However, few stress-mediated gene families have been studied. Aldehyde dehydrogenases (ALDHs) comprise a gene superfamily encoding NAD (P) +-dependent enzymes that play the role of "aldehyde scavengers", which indirectly detoxify cellular ROS and reduce the effect of lipid peroxidation meditated cellular toxicity under various environmental stresses. In the current paper, we identified a total of 20 ALDH genes in the foxtail millet genome using a homology search and a phylogenetic analysis and grouped them into ten distinct families based on their amino acid sequence identity. Furthermore, evolutionary analysis of foxtail millet reveals that both tandem and segmental duplication contributed significantly to the expansion of its ALDH genes. The exon-intron structures of members of the same family in foxtail millet or the orthologous genes in rice display highly diverse distributions of their exonic and intronic regions. Also, synteny analysis shows that the majority of foxtail millet and rice ALDH gene homologs exist in the syntenic blocks between the two, implying that these ALDH genes arose before the divergence of cereals. Semi-quantitative and real-time quantitative PCR data reveals that a few SiALDH genes are expressed in an organ-specific manner and that the expression of a number of foxtail millet ALDH genes, such as, SiALDH7B1, SiALDH12A1 and SiALDH18B2 are up-regulated by osmotic stress, cold, H2O2, and phytohormone abscisic acid (ABA). Furthermore, the transformation of SiALDH2B2, SiALDH10A2, SiALDH5F1, SiALDH22A1, and SiALDH3E2 into Escherichia coli (E.coli) was able to improve their salt tolerance. Taken together, our results show that genome-wide identification characteristics and expression analyses provide unique opportunities for assessing the functional roles of foxtail millet ALDH genes in stress responses.

The Chinese wild grapevine (Vitis pseudoreticulata) E3 ubiquitin ligase Erysiphe necator-induced RING finger protein 1 (EIRP1) activates plant defense responses by inducing proteolysis of the VpWRKY11 transcription factor

Ubiquitin-mediated regulation responds rapidly to specific stimuli; this rapidity is particularly important for defense responses to pathogen attack. Here, we investigated the role of the E3 ubiquitin ligase Erysiphe necator-induced RING finger protein 1 (EIRP1) in the defense response of Chinese wild grapevine Vitis pseudoreticulata. The regulatory function of E3 ubiquitin ligase EIRP1 was investigated using molecular, genetic and biochemical approaches. EIRP1 encodes a C3HC4-type Really Interesting New Gene (RING) finger protein that harbors E3 ligase activity. This activity requires the conserved RING domain, and VpWRKY11 also interacts with EIRP1 through the RING domain. VpWRKY11 localizes to the nucleus and activates W-box-dependent transcription in planta. EIRP1 targeted VpWRKY11 in vivo, resulting in VpWRKY11 degradation. The expression of EIRP1 and VpWRKY11 responds rapidly to powdery mildew in Vitis pseudoreticulata grapevine; also, overexpression of EIRP1 in Arabidopsis confers enhanced resistance to the pathogens Golovinomyces cichoracearum and Pseudomonas syringae pv tomato DC3000. Our data suggest that the EIRP1 E3 ligase positively regulates plant disease resistance by mediating proteolysis of the negative regulator VpWRKY11 via degradation by the 26S proteasome.

Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus × domestica Borkh.)

Aldehyde dehydrogenases (ALDHs) represent a protein superfamily encoding NAD(P)(+)-dependent enzymes that oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes. In plants, they are involved in many biological processes and play a role in the response to environmental stress. In this study, a total of 39 ALDH genes from ten families were identified in the apple (Malus × domestica Borkh.) genome. Synteny analysis of the apple ALDH (MdALDH) genes indicated that segmental and tandem duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of these gene families in apple. Moreover, synteny analysis between apple and Arabidopsis demonstrated that several MdALDH genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes appeared before the divergence of lineages that led to apple and Arabidopsis. In addition, phylogenetic analysis, as well as comparisons of exon-intron and protein structures, provided further insight into both their evolutionary relationships and their putative functions. Tissue-specific expression analysis of the MdALDH genes demonstrated diverse spatiotemporal expression patterns, while their expression profiles under abiotic stress and various hormone treatments indicated that many MdALDH genes were responsive to high salinity and drought, as well as different plant hormones. This genome-wide identification, as well as characterization of evolutionary relationships and expression profiles, of the apple MdALDH genes will not only be useful for the further analysis of ALDH genes and their roles in stress response, but may also aid in the future improvement of apple stress tolerance.

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD(+)- or NADP(+)-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as 'aldehyde scavengers' by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried out genome-wide identification of ALDH genes in a number of plant species-including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.

Aldehyde dehydrogenase protein superfamily in maize

Maize (Zea mays ssp. mays L.) is an important model organism for fundamental research in the agro-biotechnology field. Aldehydes were generated in response to a suite of environmental stresses that perturb metabolism including salinity, dehydration, desiccation, and cold and heat shock. Many biologically important aldehydes are metabolized by the superfamily of NAD(P)(+)-dependent aldehyde dehydrogenases. Here, starting from the database of Z. mays, we identified 28 aldehyde dehydrogenase (ALDH) genes and 48 transcripts by the in silico cloning method using the ALDH-conserved domain amino acid sequence of Arabidopsis and rice as a probe. Phylogenetic analysis shows that all 28 members of the ALDH gene families were classified to ten distinct subfamilies. Microarray data and quantitative real-time PCR analysis reveal that ZmALDH9, ZmALDH13, and ZmALDH17 genes involve the function of drought stress, acid tolerance, and pathogens infection. These results suggested that these three ZmALDH genes might be potentially useful in maize genetic improvement.