A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

BACKGROUND: Purple curl leaf disease brings a significant threat to the development of agave industry, the underlying mechanism of disease-resistant Agave sisalana. hybrid 11648 (A. H11648R) is still unknown. RESULTS: To excavate the crucial disease-resistant genes against purple curl leaf disease, we performed an RNA-seq analysis for A.H11648R and A.H11648 during different stages of purple curl leaf disease. The DEGs (differentially expressed genes) were mainly enriched in linolenic acid metabolism, starch and sucrose mechanism, phenylpropanoid biosynthesis, hypersensitive response (HR) and systemic acquired resistance. Further analysis suggested that eight candidate genes (4'OMT2, ACLY, NCS1, GTE10, SMO2, FLS2, SQE1 and RCOM) identified by WGCNA (weighted gene co-expression network analysis) may mediate the resistance to agave purple curl disease by participating the biosynthesis of benzylisoquinoline alkaloids, steroid, sterols and flavonoids, and the regulation of plant innate immunity and systemic acquired resistance. After qPCR verification, we found that AsRCOM, coding a glycosyltransferase and relevant to the regulation of plant innate immunity and systemic acquired resistance, may be the most critical disease-resistant gene. Finally, the overexpression of AsRCOM gene in agave could significantly enhance the resistance to purple curl disease with abundant reactive oxygen species (ROS) accumulations. CONCLUSIONS: Integrative RNA-seq analysis found that HR may be an important pathway affecting the resistance to purple curl leaf disease in agave, and identified glycosyltransferase AsRCOM as the crucial gene that could significantly enhance the resistance to purple curl leaf disease in agave, with obvious ROS accumulations.

Integration of Metabolomics and Transcriptomics to Explore Dynamic Alterations in Fruit Color and Quality in 'Comte de Paris' Pineapples during Ripening Processes.

Pineapple color yellowing and quality promotion gradually manifest as pineapple fruit ripening progresses. To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid contents as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Integration analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, RNA-seq analysis showed that structural genes, such as FLS, FNS, F3H, DFR, ANR, and GST, in the flavonoid biosynthetic pathway were upregulated, whereas the COMT, CCR, and CAD genes involved in lignin metabolism were downregulated as fruit ripening progressed. APX as well as PPO, and ACO genes related to the organic acid accumulations were upregulated and downregulated, respectively. Importantly, a comprehensive regulatory network encompassing genes that contribute to the metabolism of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlie fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.

Genome-wide survey and expression analysis of the calcium-dependent protein kinase gene family in cassava.

Calcium-dependent protein kinases (CPKs) play important roles in regulating plant tolerance to abiotic stress and signal transduction; however, no data are currently available regarding the CPK family in cassava. Herein, we identified 27 CPK genes from cassava based on our previous genome sequencing data. Phylogenetic analysis showed that cassava CPKs could be clustered into three groups, which was further supported by gene structure and conserved protein motif analyses. Global expression analysis suggested that MeCPK genes showed distinct expression patterns in different tissues between wild subspecies and cultivated varieties, indicating their involvement in the functional diversity of different varieties. Transcriptomics, interaction networks, and co-expression assays revealed a broad transcriptional response of cassava CPKs and CPK-mediated networks to drought stress and their differential expression profiles in different varieties, implying their contribution to drought stress tolerance in cassava. Expression analysis of eight MeCPK genes suggested a comprehensive response to osmotic stress, salt, cold, abscisic acid, and H2O2, which indicated that cassava CPKs might be convergence points for different signaling pathways. This study provides a basis for crop improvements and understanding of abiotic stress responses and signal transduction mediated by CPKs in cassava.

Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana.

Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP) domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars.

Two maize homologs of mammalian proton-coupled folate transporter, ZmMFS_1-62 and ZmMFS_1-73, are essential to salt and drought tolerance.

Folates are essential to the maintenance of normal life activities in almost all organisms. Proton-coupled folate transporter (PCFT), belonging to the major facilitator superfamily, is one of the three major folate transporter types widely studied in mammals. However, information about plant PCFTs is limited. Here, a genome-wide identification of maize PCFTs was performed, and two PCFTs, ZmMFS_1-62 and ZmMFS_1-73, were functionally investigated. Both proteins contained the typical 12 transmembrane helixes with N- and C-termini located in the cytoplasm, and were localized in the plasma membrane. Molecular docking analysis indicated their binding activity with folates via hydrogen bonding. Interference with ZmMFS_1-62 and ZmMFS_1-73 in maize seedlings through virus-induced gene silencing disrupted folate homeostasis, mainly in the roots, and reduced tolerance to drought and salt stresses. Moreover, a molecular chaperone protein, ZmHSP20, was found to interact with ZmMFS_1-62 and ZmMFS_1-73, and interference with ZmHSP20 in maize seedlings also led to folate disruption and increased sensitivity to drought and salt stresses. Overall, this is the first report of functional identification of maize PCFTs, which play essential roles in salt and drought stress tolerance, thereby linking folate metabolism with abiotic stress responses in maize.

Low temperature storage alleviates internal browning of 'Comte de Paris' winter pineapple fruit by reducing phospholipid degradation, phosphatidic acid accumulation and membrane lipid peroxidation processes.

To uncover the mechanism underlying membrane lipid metabolism of low temperature induced internal browning tolerance in pineapple, membrane phospholipid alterations of harvested 'Comte de Paris' winter pineapple fruit stored at either 10 °C or 25 °C was investigated. Fruit stored at 10 °C developed low levels of internal browning as compared to fruit stored at 25 °C and was associated with high contents of phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, and phosphatidylethanolamine, and low levels of phosphatidic acid. Storage at 10 °C down-regulated the expression levels of phospholipase As. Fruit stored at 10 °C also exhibited high ratio of unsaturated fatty acid to saturated fatty acid and index of unsaturated fatty acid level. These findings suggest that maintenance phospholipid abundance, reduction in phosphatidic acid accumulation and membrane lipid peroxidation may have contributed to the enhanced internal browning tolerance in 'Comte de Paris' winter pineapple fruit at low temperature storage.

MaDREB1F confers cold and drought stress resistance through common regulation of hormone synthesis and protectant metabolite contents in banana.

Adverse environmental factors severely affect crop productivity. Improving crop resistance to multiple stressors is an important breeding goal. Although CBFs/DREB1s extensively participate in plant resistance to abiotic stress, the common mechanism underlying CBFs/DREB1s that mediate resistance to multiple stressors remains unclear. Here, we show the common mechanism for MaDREB1F conferring cold and drought stress resistance in banana. MaDREB1F encodes a dehydration-responsive element binding protein (DREB) transcription factor with nuclear localization and transcriptional activity. MaDREB1F expression is significantly induced after cold, osmotic, and salt treatments. MaDREB1F overexpression increases banana resistance to cold and drought stress by common modulation of the protectant metabolite levels of soluble sugar and proline, activating the antioxidant system, and promoting jasmonate and ethylene syntheses. Transcriptomic analysis shows that MaDREB1F activates or alleviates the repression of jasmonate and ethylene biosynthetic genes under cold and drought conditions. Moreover, MaDREB1F directly activates the promoter activities of MaAOC4 and MaACO20 for jasmonate and ethylene syntheses, respectively, under cold and drought conditions. MaDREB1F also targets the MaERF11 promoter to activate MaACO20 expression for ethylene synthesis under drought stress. Together, our findings offer new insight into the common mechanism underlying CBF/DREB1-mediated cold and drought stress resistance, which has substantial implications for engineering cold- and drought-tolerant crops.

The class III peroxidase gene family is involved in ascorbic acid induced delay of internal browning in pineapple.

Excessive production of reactive oxygen species (ROS) leads to potential toxicity in an organism. Class III peroxidases (PRXs) play an important role in maintaining ROS homeostasis in plants. Internal browning (IB) limits industrial development of pineapple, which is the third most important fruit trade in the world. IB is mainly caused by ROS, and the mechanism underlying IB is still unknown from the perspective of ROS. Here, we soaked pineapples in ascorbic acid after harvest and before storage to decrease excessive ROS and polyphenol oxidase (PPO) activity, ultimately restraining the spread and deterioration of IB. Using phylogenetic analysis; we identified 78 pineapple PRX genes (AcPRXs) and divided them into five subgroups. Gene structure analysis indicated that the exon numbers ranged from 2 to 14, and conserved motif analysis verified that all of the AcPRXs identified here have standard peroxidase domains. Analysis of duplication events suggested that tandem and segmental duplication events may have played equal and important roles in expanding the AcPRX family. Comprehensive transcriptomic analysis uncovered that AcPRXs may play an important role in negatively regulating the occurrence of IB. In summary, we found that ROS scavenging delayed IB occurrence. The results of characterized AcPRX family revealed that AcPRXs family responded to growth and development, and negatively regulated to IB occurrence in storage stage. This research provides potential target genes for future in-depth analysis of the molecular mechanisms underlying IB and contributes to develop IB-resistant pineapple varieties.

Novel Insight into the Relationship between Metabolic Profile and Fatty Acid Accumulation Altering Cellular Lipid Content in Pineapple Fruits at Different Stages of Maturity.

Pineapple fruits are usually harvested at different stages of maturity, based on consumer demands. The stage of maturity significantly affects the storage tolerance due to alterations in the cellular lipid homeostasis in the fruits. The characteristic abundance of metabolites and fatty acids (FAs) can provide vital information giving insight into the cellular lipid changes that occur during the ripening process in the fruits. Here, liquid chromatography-tandem mass spectrometry, largely based on the analysis of widely targeted metabolomics, was applied to evaluate the differences in the metabolites among the pineapple at three different stages of maturity namely, pineapples at the young fruit (YF), mature fruit (MF), and fully mature fruit (FMF) stages. In this study, 466 metabolites were annotated and identified. Among these, 59 lipids, including the glyceride esters, fatty acids and conjugates, and lysophospholipids (LPLs) were characterized. Notably, the LPLs were down-regulated in their relative abundance in the MF compared with the YF, and subsequently they remained almost stable in the FMF stage. The FA profiling results revealed the presence of certain unsaturated fatty acids (UFAs); besides, the total monounsaturated fatty acid (MUFA) to saturated fatty acid (SFA) ratio, as well as the polyunsaturated fatty acids (PUFA) to SFA ratio, showed noticeable decrease during the ripening process. The differential accumulation patterns of the LPLs, MUFAs, PUFAs, and SFAs imply that the lipid degradation and peroxidation take place in the pineapple fruits from the YF to MF and YF to FMF stages, respectively. The present study provides new insights into the alterations in the cellular lipid metabolism underlying the metabolite profiles and accumulation of FAs in pineapple fruits during ripening.

An aquaporin gene MaPIP2-7 is involved in tolerance to drought, cold and salt stresses in transgenic banana (Musa acuminata L.).

Aquaporins (AQPs) transport water and other small molecules; however, their precise role in abiotic stress responses is not fully understood. In this study, we cloned and characterized the PIP2 group AQP gene, MaPIP2-7, in banana. MaPIP2-7 expression was upregulated after osmotic (mannitol), cold, and salt treatments. Overexpression of MaPIP2-7 in banana improved tolerance to multiple stresses such as drought, cold, and salt. MaPIP2-7 transgenic plants showed lower levels of malondialdehyde (MDA) and ion leakage (IL), but higher contents of chlorophyll, proline, soluble sugar, and abscisic acid (ABA) compared with wild type (WT) plants under stress and recovery conditions. Additionally, MaPIP2-7 overexpression decreased cellular contents of Na+ and K+ under salt and recovery conditions, and produced an elevated K+/Na+ ratio under recovery conditions. Finally, ABA biosynthetic and responsive genes exhibited higher expression levels in transgenic lines relative to WT under stress conditions. Taken together, our results demonstrate that MaPIP2-7 confers tolerance to drought, cold, and salt stresses by maintaining osmotic balance, reducing membrane injury, and improving ABA levels.

TaPP2C1, a Group F2 Protein Phosphatase 2C Gene, Confers Resistance to Salt Stress in Transgenic Tobacco.

Group A protein phosphatases 2Cs (PP2Cs) are essential components of abscisic acid (ABA) signaling in Arabidopsis; however, the function of group F2 subfamily PP2Cs is currently less known. In this study, TaPP2C1 which belongs to group F2 was isolated and characterized from wheat. Expression of the TaPP2C1-GFP fusion protein suggested its ubiquitous localization within a cell. TaPP2C1 expression was downregulated by abscisic acid (ABA) and NaCl treatments, but upregulated by H2O2 treatment. Overexpression of TaPP2C1 in tobacco resulted in reduced ABA sensitivity and increased salt resistance of transgenic seedlings. Additionally, physiological analyses showed that improved resistance to salt stress conferred by TaPP2C1 is due to the reduced reactive oxygen species (ROS) accumulation, the improved antioxidant system, and the increased transcription of genes in the ABA-independent pathway. Finally, transgenic tobacco showed increased resistance to oxidative stress by maintaining a more effective antioxidant system. Taken together, these results demonstrated that TaPP2C1 negatively regulates ABA signaling, but positively regulates salt resistance. TaPP2C1 confers salt resistance through activating the antioxidant system and ABA-independent gene transcription process.

The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress.

Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 ARF genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and Arabidopsis suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from Arabidopsis. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in MaARF genes ranged from 5 to 21, suggesting large variation amongst banana ARF genes. The comprehensive expression profiles of MaARF genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MaARF genes for further functional assays in planta. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of MaARF gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes.

Genome-wide gene phylogeny of CIPK family in cassava and expression analysis of partial drought-induced genes.

Cassava is an important food and potential biofuel crop that is tolerant to multiple abiotic stressors. The mechanisms underlying these tolerances are currently less known. CBL-interacting protein kinases (CIPKs) have been shown to play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to abiotic stress. However, no data is currently available about the CPK family in cassava. In this study, a total of 25 CIPK genes were identified from cassava genome based on our previous genome sequencing data. Phylogenetic analysis suggested that 25 MeCIPKs could be classified into four subfamilies, which was supported by exon-intron organizations and the architectures of conserved protein motifs. Transcriptomic analysis of a wild subspecies and two cultivated varieties showed that most MeCIPKs had different expression patterns between wild subspecies and cultivatars in different tissues or in response to drought stress. Some orthologous genes involved in CIPK interaction networks were identified between Arabidopsis and cassava. The interaction networks and co-expression patterns of these orthologous genes revealed that the crucial pathways controlled by CIPK networks may be involved in the differential response to drought stress in different accessions of cassava. Nine MeCIPK genes were selected to investigate their transcriptional response to various stimuli and the results showed the comprehensive response of the tested MeCIPK genes to osmotic, salt, cold, oxidative stressors, and ABA signaling. The identification and expression analysis of CIPK family suggested that CIPK genes are important components of development and multiple signal transduction pathways in cassava. The findings of this study will help lay a foundation for the functional characterization of the CIPK gene family and provide an improved understanding of abiotic stress responses and signaling transduction in cassava.

Genome-Wide Identification and Expression Analysis of the NAC Transcription Factor Family in Cassava.

NAC [no apical meristem (NAM), Arabidopsis transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins is one of the largest groups of plant specific transcription factors and plays a crucial role in plant growth, development, and adaption to the environment. Currently, no information is known about the NAC family in cassava. In this study, 96 NAC genes (MeNACs) were identified from the cassava genome. Phylogenetic analysis of the NACs from cassava and Arabidopsis showed that MeNAC proteins can be clustered into 16 subgroups. Gene structure analysis found that the number of introns of MeNAC genes varied from 0 to 5, with the majority of MeNAC genes containing two introns, indicating a small gene structure diversity of cassava NAC genes. Conserved motif analysis revealed that all of the identified MeNACs had the conserved NAC domain and/or NAM domain. Global expression analysis suggested that MeNAC genes exhibited different expression profiles in different tissues between wild subspecies and cultivated varieties, indicating their involvement in the functional diversity of different accessions. Transcriptome analysis demonstrated that MeNACs had a widely transcriptional response to drought stress and that they had differential expression profiles in different accessions, implying their contribution to drought stress resistance in cassava. Finally, the expression of twelve MeNAC genes was analyzed under osmotic, salt, cold, ABA, and H2O2 treatments, indicating that cassava NACs may represent convergence points of different signaling pathways. Taken together, this work found some excellent tissue-specific and abiotic stress-responsive candidate MeNAC genes, which would provide a solid foundation for functional investigation of the NAC family, crop improvement and improved understanding of signal transduction in plants. These data bring new insight on the complexity of the transcriptional control of MeNAC genes and support the hypothesis that NACs play an important role in plant growth, development, and adaption of environment.