Genome-wide analysis of the light-harvesting chlorophyll a/b-binding gene family in apple (Malus domestica) and functional characterization of MdLhcb4.3, which confers tolerance to drought and osmotic stress

Transcriptome analysis reveals the key role of overdominant expression of photosynthetic and respiration-related genes in the formation of tobacco(Nicotiana tabacum L.) biomass heterosis

BACKGROUND

Leaves are the nutritional and economic organs of tobacco, and their biomass directly affects tobacco yield and the economic benefits of farmers. In the early stage, our research found that tobacco hybrids have more leaves and larger leaf areas, but the performance and formation reasons of biomass heterosis are not yet clear.

RESULTS

This study selected 5 parents with significant differences in tobacco biomass and paired them with hybrid varieties. It was found that tobacco hybrid varieties have a common biomass heterosis, and 45 days after transplantation is the key period for the formation of tobacco biomass heterosis; By analyzing the biomass heterosis of hybrids, Va116×GDH94 and its parents were selected for transcriptome analysis. 76.69% of the differentially expressed genes between Va116×GDH94 and its parents showed overdominant expression pattern, and these overdominant expression genes were significantly enriched in the biological processes of photosynthesis and TCA cycle; During the process of photosynthesis, the overdominant up-regulation of genes such as Lhc, Psa, and rbcl promotes the progress of photosynthesis, thereby increasing the accumulation of tobacco biomass; During the respiratory process, genes such as MDH, ACO, and OGDH are overedominantly down-regulated, inhibiting the TCA cycle and reducing substrate consumption in hybrid offspring; The photosynthetic characteristics of the hybrid and its parents were measured, and the net photosynthetic capacity of the hybrid was significantly higher than that of the parents.

CONCLUSION

These results indicate that the overdominant expression effect of differentially expressed genes in Va116×GDH94 and its parents plays a crucial role in the formation of tobacco biomass heterosis. The overdominant expression of genes related to photosynthesis and respiration enhances the photosynthetic ability of Va116×GDH94, reduces respiratory consumption, promotes the increase of biomass, and exhibits obvious heterosis.

Double roles of light-harvesting chlorophyll a/b binding protein TaLhc2 in wheat stress tolerance and photosynthesis

Light-harvesting chlorophyll a/b binding proteins are encoded by nucleus genes and widely involve in capturing light energy, transferring energy, and responding to various stresses. However, their roles in wheat photosynthesis and stress tolerance are largely unknown. Here, Triticum aestivumlight-harvesting chlorophyll a/b binding protein TaLhc2 was identified. It showed subcellular localization in chloroplast, contained light responsive cis-elements, and highly expressed in green tissues and down-regulated by multiple stresses. TaLhc2 promoted the colonization of hemi-biotrophic pathogen; further analysis showed that TaLhc2 strengthened BAX-induced cell death, enhanced the ROS accumulation, and up-regulated pathogenesis-related genes; those results suggested that TaLhc2 has adverse influence on host immunity and function as a susceptible gene, thus host decreased its expression when faced with pathogen infection. RT-qPCR results showed that TaLhc2 was down-regulated by drought and salt stresses, while TaLhc2 improved the ROS accumulation under the two stresses, suggesting TaLhc2 may participate in wheat responding to abiotic stress. Additionally, TaLhc2 can increase the content of total chlorophyll and carotenoid by 1.3 % and 2.9 %, increase the net photosynthetic rate by 18 %, thus promote plant photosynthesis. Conclusively, we preliminarily deciphered the function of TaLhc2 in biotic/abiotic stresses and photosynthesis, which laid foundation for its usage in wheat breeding.

The light-harvesting chlorophyll a/b-binding proteins of photosystem II family members are responsible for temperature sensitivity and leaf color phenotype in albino tea plant

INTRODUCTION

Light-harvesting chlorophyll a/b-binding (LHCB) protein complexes of photosystem II are integral to the formation of thylakoid structure and the photosynthetic process. They play an important role in photoprotection, a crucial process in leaf development under low-temperature stress. Nonetheless, potential key genes directly related to low-temperature response and albino phenotype have not been precisely identified in tea plant. Moreover, there are no studies simultaneously investigating multiple albino tea cultivars with different temperature sensitivity.

OBJECTIVES

The study aimed to clarify the basic characteristics of CsLHCB gene family members, and identify critical CsLHCB genes potentially influential in leaf color phenotypic variation and low-temperature stress response by contrasting green and albino tea cultivars. Concurrently, exploring the differential expression of the CsLHCB gene family across diverse temperature-sensitive albino tea cultivars.

METHODS

We identified 20 putative CsLHCB genes according to phylogenetic analysis. Evolutionary relationships, gene duplication, chromosomal localization, and structures were analyzed by TBtools; the physiological and biochemical characteristics were analyzed by protein analysis websites; the differences in coding sequences and protein accumulation in green and albino tea cultivars, gene expression with maturity were tested by molecular biology technology; and protein interaction was analyzed in the STRING database.

RESULTS

All genes were categorized into seven groups, mapping onto 7 chromosomes, including three tandem and one segmental duplications. They all own a conserved chlorophyll A/B binding protein domain. The expression of CsLHCB genes was tissue-specific, predominantly in leaves. CsLHCB5 may play a key role in the process of leaf maturation and senescence. In contrast to CsLHCB5, CsLHCB1.1, CsLHCB2, and CsLHCB3.2 were highly conserved in amino acid sequence between green and albino tea cultivars. In albino tea cultivars, unlike in green cultivars, the expression of CsLHCB1.1, CsLHCB1.2, and CsLHCB2 was down-regulated under low-temperature stress. The accumulation of CsLHCB1 and CsLHCB5 proteins was lower in albino tea cultivars. Greater accumulation of CsLHCB2 protein was detected in RX1 and RX2 compared to other albino cultivars.

CONCLUSIONS

CsLHCB1.1, CsLHCB1.2, and CsLHCB2 played a role in the response to low-temperature stress. The amino acid sequence site mutation of CsLHCB5 would distinguish the green and albino tea cultivars. The less accumulation of CsLHCB1 and CsLHCB5 had a potential influence on albino leaves. Albino cultivars more sensitive to temperature exhibited lower CsLHCB gene expression. CsLHCB2 may serve as an indicator of temperature sensitivity differences in albino tea cultivars. This study could provide a reference for further studies of the functions of the CsLHCB family and contribute to research on the mechanism of the albino in tea plant.

PoWRKY71 is involved in Paeonia ostii resistance to drought stress by directly regulating light-harvesting chlorophyll a/b-binding 151 gene

Although the functions of WRKY transcription factors in drought resistance are well known, their regulatory mechanisms in response to drought by stabilising photosynthesis remain unclear. Here, a differentially expressed PoWRKY71 gene that was highly expressed in drought-treated Paeonia ostii leaves was identified through transcriptome analysis. PoWRKY71 positively responded to drought stress with significantly enhanced expression patterns and overexpressing PoWRKY71 in tobacco greatly improved plant tolerance to drought stress, whereas silencing PoWRKY71 in P. ostii resulted in a drought-intolerant phenotype. Furthermore, lower chlorophyll contents, photosynthesis, and inhibited expression of photosynthesis-related light-harvesting chlorophyll a/b-binding 151 (CAB151) gene were found in PoWRKY71-silenced P. ostii. Meanwhile, a homologous system indicated that drought treatment increased PoCAB151 promoter activity. Interactive assays revealed that PoWRKY71 directly bound on the W-box element of PoCAB151 promoter and activated its transcription. In addition, PoCAB151 overexpressing plants demonstrated increased drought tolerance, together with significantly higher chlorophyll contents and photosynthesis, whereas these indices were dramatically lower in PoCAB151-silenced P. ostii. The above results indicated that PoWRKY71 activated the expression of PoCAB151, thus stabilising photosynthesis via regulating chloroplast homeostasis and chlorophyll content in P. ostii under drought stress. This study reveals a novel drought-resistance mechanism in plants and provides a feasible strategy for improving plant drought resistance via stabilising photosynthesis.

Comparative genomics analysis provide insights into evolution and stress responses of Lhcb genes in Rosaceae fruit crops

BACKGROUND

Light-harvesting chlorophyll a/b b evelopment of higher plants and in response to abiotic stress. Previous works has demonstrated that that Lhcb genes were involved in the phytochrome regulation and responded to the different light and temperature conditions in Poaceae (such as maize). However, the evolution and functions of Lhcb genes remains poorly characterized in important Rosaceae species.

RESULTS

In this investigation, we conducted a genome-wide analysis and identified a total of 212 Lhcb genes across nine Rosaceae species. Specifically, we found 23 Lhcb genes in Fragaria vesca, 20 in Prunus armeniaca, 33 in Malus domestica 'Gala', 21 in Prunus persica, 33 in Rosa chinensis, 29 in Pyrus bretschneideri, 18 in Rubus occidentalis, 20 in Prunus mume, and 15 in Prunus salicina. Phylogenetic analysis revealed that the Lhcb gene family could be classified into seven major subfamilies, with members of each subfamily sharing similar conserved motifs. And, the functions of each subfamily was predicted based on the previous reports from other species. The Lhcb proteins were highly conserved within their respective subfamilies, suggesting similar functions. Interestingly, we observed similar peaks in Ks values (0.1-0.2) for Lhcb genes in apple and pear, indicating a recent whole genome duplication event (about 30 to 45 million years ago). Additionally, a few Lhcb genes underwent tandem duplication and were located across all chromosomes of nine species of Rosaceae. Furthermore, the analysis of the cis-acting elements in the 2000 bp promoter region upstream of the pear Lhcb gene revealed four main categories: light response correlation, stress response correlation, hormone response correlation, and plant growth. Quantitative expression analysis demonstrated that Lhcb genes exhibited tissue-specific expression patterns and responded differently to low-temperature stress in Rosaceae species.

CONCLUSIONS

These findings shed light on the evolution and phylogeny of Lhcb genes in Rosaceae and highlight the critical role of Lhcb in pear's response to low temperatures. The results obtained provide valuable insights for further investigations into the functions of Lhcb genes in Rosaceae, and these functional genes will be used for further fruit tree breeding and improvement to cope with the current climate changes.

Identification of the Light-Harvesting Chlorophyll a/b Binding Protein Gene Family in Peach (Prunus persica L.) and Their Expression under Drought Stress

In higher plants, light-harvesting chlorophyll a/b binding (Lhc) proteins play a vital role in photosynthetic processes and are widely involved in the regulation of plant growth, development, and response to abiotic stress. However, the Lhc gene family has not been well identified in peaches (Prunus persica L.). In this study, 19 PpLhc genes were identified in the peach genome database, which were unevenly distributed on all chromosomes. Phylogenetic analysis demonstrated that PpLhc proteins could be divided into three major subfamilies, each of whose members had different exon-intron structures but shared similar conserved motifs. A total of 17 different kinds of cis-regulatory elements were identified in the promoter regions of all PpLhc genes, which could be classified into three categories: plant growth and development, stress response, and phytohormone response. In addition, transcriptomic data analysis and RT-qPCR results revealed that the expression profiles of some PpLhc genes changed under drought treatment, suggesting the crucial roles of Lhc genes in the regulation of plant tolerance to drought stress. Taken together, these findings will provide valuable information for future functional studies of PpLhc genes, especially in response to drought stress.

A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress

The main factor leading to a decrease in crop productivity is abiotic stresses, particularly drought. Plants with C4 and CAM photosynthesis are better adapted to drought-prone areas than C3 plants. Therefore, it is beneficial to compare the stress response of plants with different photosynthetic pathways. Since most crops are C3 and C4 plants, this study focused on conducting an RNA-seq meta-analysis to investigate and compare how C3 and C4 plants respond to drought stress at the gene expression level in their leaves. Additionally, the accuracy of the meta-analysis results was confirmed with RT-qPCR. Based on the functional enrichment and network analysis, hub genes related to ribosomal proteins and photosynthesis were found to play a potential role in stress response. Moreover, our findings suggest that the low abundant amino acid degradation pathway, possibly through providing ATP source for the TCA cycle, in both groups of plants and the activation of the OPPP pathway in C4 plants, through providing the electron source required by this plant, can help to improve drought stress tolerance.

Genome-wide analysis and identification of light-harvesting chlorophyll a/b binding (LHC) gene family and BSMV-VIGS silencing TaLHC86 reduced salt tolerance in wheat

The discovery and identification of gene families by using wide-genome and public databases is an effective way to gain initial insight into gene function, which also is one of the current hot spots of research. Chlorophyll ab-binding proteins (LHC) are important for photosynthesis and widely involved in plant adversity stress. However, the study in wheat has not been reported. In this study, we identified 127 TaLHC members from common wheat which were unevenly distributed on all chromosomes except 3B and 3D. All members divided into three subfamilies, LHC a, LHC b and the LHC t which was only discovered in wheat. All of them had maximum expression in leaves and contained multiple light-responsive cis-acting element, which were evidence of the extensive involvement of LHC families in photosynthesis. In addition, we also analyzed their collinear relationship, targeting relationship with miRNA and their responses under different stresses. Based on these analyses, it was found that TaLHC86 was an excellent candidate gene for stress resistance. The full-length ORF of TaLHC86 was 792 bp and was localized on the chloroplasts. The salt tolerance of wheat was reduced when BSMV-VIGS silenced TaLHC86, and the photosynthetic rate and electron transport were also seriously affected. This study made a comprehensive analysis of the TaLHC family and found that TaLHC86 was a good gene for salt tolerance.

Analysis of Lhc family genes reveals development regulation and diurnal fluctuation expression patterns in Cyperus esculentus, a Cyperaceae plant

Sixteen Lhc genes representing 13 phylogenetic groups were identified from the full-length transcriptome of tigernut, exhibiting development regulation and diurnal fluctuation expression patterns in leaves. Nuclear encoded light-harvesting chlorophyll a/b-binding (Lhc) proteins play indispensable roles in oxygenic photosynthesis. In this study, we present the first transcriptome-based characterization of Lhc family genes in tigernut (Cyperus esculentus L.), a Cyperaceae C₄ plant producing oil in underground tubers. A number of 16 Lhc genes representing 13 phylogenetic groups identified from the full-length tigernut transcriptome are equal to that found in both Carex littledalei (another Cyperaceae plant) and papaya, slightly more than 15 members present in both rice and jatropha, but relatively less than 18, 20, and 21 members present in sorghum, cassava, and Arabidopsis, respectively. Nevertheless, nearly one-vs-one orthologous relationship was observed in most groups, though some of them are no longer located in syntenic blocks and species-specific expansion was frequently found in Lhcb1. Comparative genomics analysis revealed that the loss of two groups (i.e., Lhca2 and Lhca5) in C. littledalei is species-specific, sometime after the split with tigernut, and the expansion of Lhcb1 was mainly contributed by tandem duplication as observed in most species. Interestingly, a transposed duplication, which appears to be shared by monocots, was also identified in Lhcb1. Further transcriptome profiling revealed a predominant expression pattern of most CeLhc family genes in photosynthetic tissues and enhanced transcription during leaf maturation, reflecting their key roles in light absorption. Moreover, qRT-PCR analysis revealed an apparent diurnal fluctuation expression pattern of 11 dominant CeLhc genes. These findings not only highlight species-specific evolution of Lhc genes in the Cyperaceae family as well as the monocot lineage, but also provide valuable information for further functional analysis and genetic improvement in tigernut.

Identification of PLATZ genes in Malus and expression characteristics of MdPLATZs in response to drought and ABA stresses

Plant AT-rich sequences and zinc-binding proteins (PLATZ) play crucial roles in response to environmental stresses. Nevertheless, PLATZ gene family has not been systemically studied in Rosaceae species, such as in apple, pear, peach, or strawberry. In this study, a total of 134 PLATZ proteins were identified from nine Rosaceae genomes and were classified into seven phylogenetic groups. Subsequently, the chromosomal localization, duplication, and collinearity relationship for apple PLATZ genes were investigated, and segmental duplication is a major driving-force in the expansion of PLATZ in Malus. Expression profiles analysis showed that PLATZs had distinct expression patterns in different tissues, and multiple genes were significantly changed after drought and ABA treatments. Furthermore, the co-expression network combined with RNA-seq data showed that PLATZ might be involved in drought stress by regulating ABA signaling pathway. In summary, this study is the first in-depth and systematic identification of PLATZ gene family in Rosaceae species, especially for apple, and provided specific PLATZ gene resource for further functional research in response to abiotic stress.

Exogenous Dopamine and MdTyDC Overexpression Enhance Apple Resistance to Fusarium solani

Fusarium solani, one of the main pathogenic fungi involved in apple replant disease (ARD), is a serious threat to apple growth and development. Dopamine and tyrosine decarboxylase (TyDC), a key enzyme in the dopamine synthesis pathway, have been reported to play an active role in plant responses to biotic and abiotic stresses, but little is known about the functions of dopamine and Malus domestica TyDC (MdTyDC) in the interaction between F. solani and apple roots. In this study, seedlings treated with exogenous dopamine and apple plants overexpressing MdTyDC were inoculated with F. solani; both treatments reduced the root system damage caused by F. solani. After inoculation with F. solani, exogenous dopamine increased dopamine content in the seedlings; alleviated the inhibition of biomass accumulation; increased root metabolic activity, photosynthetic efficiency, and antioxidant enzyme activities; reduced reactive oxygen species accumulation; and upregulated the expression of genes encoding chitinase, β-1,3-glucanase, and pathogenesis-related proteins. Similar results were observed in MdTyDC-overexpressing apple plants. In addition, the overexpression of MdTyDC increased tyramine content and the deposition of cell wall-bound amines in roots. Overall, our results reveal that exogenous dopamine and overexpression of MdTyDC enhance apple resistance to F. solani, which is an important application for the prevention of ARD.

Transcriptomic and splicing changes underlying tomato responses to combined water and nutrient stress

Tomato is a horticultural crop of high economic and nutritional value. Suboptimal environmental conditions, such as limited water and nutrient availability, cause severe yield reductions. Thus, selection of genotypes requiring lower inputs is a goal for the tomato breeding sector. We screened 10 tomato varieties exposed to water deficit, low nitrate or a combination of both. Biometric, physiological and molecular analyses revealed different stress responses among genotypes, identifying T270 as severely affected, and T250 as tolerant to the stresses applied. Investigation of transcriptome changes caused by combined stress in roots and leaves of these two genotypes yielded a low number of differentially expressed genes (DEGs) in T250 compared to T270, suggesting that T250 tailors changes in gene expression to efficiently respond to combined stress. By contrast, the susceptible tomato activated approximately one thousand and two thousand genes in leaves and roots respectively, indicating a more generalized stress response in this genotype. In particular, developmental and stress-related genes were differentially expressed, such as hormone responsive factors and transcription factors. Analysis of differential alternative splicing (DAS) events showed that combined stress greatly affects the splicing landscape in both genotypes, highlighting the important role of AS in stress response mechanisms. In particular, several stress and growth-related genes as well as transcription and splicing factors were differentially spliced in both tissues. Taken together, these results reveal important insights into the transcriptional and post-transcriptional mechanisms regulating tomato adaptation to growth under reduced water and nitrogen inputs.

The mechanism of bud dehyperhydricity by the method of 'starvation drying combined with AgNO3' in Lycium ruthenicum

Micropropagation is very important for rapid clonal propagation and scientific research of woody plants. However, the micropropagated materials usually show hyperhydricity, which seriously hinders application of the micropropagation. Lycium ruthenicum is an important species of eco-economic forests. Herein, treatment of 'starvation and drying combined with 30 μM AgNO3' (SDCAg+) removed serious hyperhydricity of L. ruthenicum buds regenerated from its green-inflorescence-explants, and then gene expression, metabolites of various phytohormones, chloroplasts, chlorophyll (Chl) and total soluble proteins of the hyperhydric and dehyperhydric leaves were compared and analyzed. The results suggested that the SDCAg+ treatment might remove hyperhydricity of L. ruthenicum through: reducing water uptake; increasing water loss; up-regulating the expression of chloroplast-ribosomal-protein genes from nuclear genome; down-regulating the expression of cytoplasmic-ribosomal-protein genes; up-regulating the synthesis of the total soluble proteins; restoring the lamellar structure of chloroplast grana and matrix; improving Chl synthesis and reducing Chl metabolism; increasing expression of light-harvesting Chl protein complex genes and content of Chla and b; up-regulating both photosynthesis and starch and sucrose metabolism KEGG pathways; up-regulating abscisic acid, salicylic acid and their signaling; down-regulating cytokinin, jasmonic acid, jasmonoyl-l-isoleucine and their signaling. Also, the above events interact to form a regulatory network of dehyperhydricity by SDCAg+ treatment. Overall, the study indicated key genes/pathways and physiological/subcellular changes involved in dehyperhydricity and then established a dehyperhydric mechanism model of L. ruthenicum. This not only proposed clues for preventing or removing hyperhydricity but also laid foundations for molecular breeding of L. ruthenicum and other species.

Genome-Wide Identification of the LHC Gene Family in Kiwifruit and Regulatory Role of AcLhcb3.1/3.2 for Chlorophyll a Content

Light-harvesting chlorophyll a/b-binding (LHC) protein is a superfamily that plays a vital role in photosynthesis. However, the reported knowledge of LHCs in kiwifruit is inadequate and poorly understood. In this study, we identified 42 and 45 LHC genes in Actinidia chinensis (Ac) and A. eriantha (Ae) genomes. Phylogenetic analysis showed that the kiwifruit LHCs of both species were grouped into four subfamilies (Lhc, Lil, PsbS, and FCII). Expression profiles and qRT-PCR results revealed expression levels of LHC genes closely related to the light, temperature fluctuations, color changes during fruit ripening, and kiwifruit responses to Pseudomonas syringae pv. actinidiae (Psa). Subcellular localization analysis showed that AcLhcb1.5/3.1/3.2 were localized in the chloroplast while transient overexpression of AcLhcb3.1/3.2 in tobacco leaves confirmed a significantly increased content of chlorophyll a. Our findings provide evidence of the characters and evolution patterns of kiwifruit LHCs genes in kiwifruit and verify the AcLhcb3.1/3.2 genes controlling the chlorophyll a content.

Identification and expression analysis of chlorophyll a/b binding protein gene family in grape (Vitis vinifera)

In higher plants, light capture of chlorophyll a/b binding protein (Lhc) plays a crucial role in the plant's response to adverse environment. So far, the family has not been systematically identified in grapes. In this study, 20 VvLhcs were identified in the grape genome, which were distributed in 13 of 19 grape chromosomes and divided into 7 developing branches. The results of gene duplication analysis showed that 6 VvLhcs formed fragment duplication events, while there was no tandem duplication in VvLhcs. Exon-intron structure analysis showed that they had a wide number of exons. Protein conserved motif analysis showed that VvLhcs contained more similar motif structures in the same phylogenetic branch. The cis-acting elements in the VvLhcs promoter region mainly respond to light, plant hormones and abiotic stresses. In addition, qRT-PCR results showed that different proportions of salt stress and red-blue light affected the expression of VvLhcs and the expression patterns of genes in different grape varieties were different. The results for further study on different grape varieties in different combinations of red and blue light of the Lhc provide a theoretical basis.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01204-5.

The role of hydrogen water in delaying ripening of banana fruit during postharvest storage

Experiments were conducted to identify the role of hydrogen water (HW) in banana fruit ripening. Banana fruit soaked with 0.8 ppm HW showed longer ripening than control fruit. HW treatment significantly reduced ethylene production and respiratory rate, and inhibited the expressions of ethylene synthesis- and signaling-related genes. Similarly, HW treatment inhibited the down-regulation of chlorophylls binding proteins and delayed the increase of chromaticity a*, b* and L* in banana peel. Furthermore, HW-treated peel exhibited lower expressions of cell wall degradation-related genes and higher levels of fruit firmness, pectin, hemicellulose and lignin. In addition, HW-treated pulp exhibited higher levels of starch, lower level of total soluble solids (TSS) and lower expression of flavor-related genes. Microstructural observation further confirmed that HW treatment delayed the degradations of starch and cell walls. Those results indicated that HW treatment delayed banana ripening via the role of ethylene in relation to degreening, flavor and softening.

Genome-Wide Analysis of the Apple CBL Family Reveals That Mdcbl10.1 Functions Positively in Modulating Apple Salt Tolerance

Abiotic stresses are increasingly harmful to crop yield and quality. Calcium and its signaling pathway play an important role in modulating plant stress tolerance. As specific Ca²⁺ sensors, calcineurin B-like (CBL) proteins play vital roles in plant stress response and calcium signaling. The CBL family has been identified in many plant species; however, the characterization of the CBL family and the functional study of apple MdCBL proteins in salt response have yet to be conducted in apple. In this study, 11 MdCBL genes were identified from the apple genome. The coding sequences of these MdCBL genes were cloned, and the gene structure and conserved motifs were analyzed in detail. The phylogenetic analysis indicated that these MdCBL proteins could be divided into four groups. The functional identification in Na⁺-sensitive yeast mutant showed that the overexpression of seven MdCBL genes could confer enhanced salt stress resistance in transgenic yeast. The function of MdCBL10.1 in regulating salt tolerance was also verified in cisgenic apple calli and apple plants. These results provided valuable insights for future research examining the function and mechanism of CBL proteins in regulating apple salt tolerance.

The genome of a thorny species: comparative genomic analysis among South and North American Cactaceae

The first South American cactus nuclear genome assembly associated with comparative genomic analyses provides insights into nuclear and plastid genomic features, such as size, transposable elements, and metabolic processes related to cactus development. Here, we assembled the partial genome, plastome, and transcriptome of Cereus fernambucensis (Cereeae, Cactaceae), a representative species of the South American core Cactoideae. We accessed other genomes and transcriptomes available for cactus species to compare the heterozygosity level, genome size, transposable elements, orthologous genes, and plastome structure. These estimates were obtained from the literature or using the same pipeline adopted for C. fermabucensis. In addition to the C. fernambucensis plastome, we also performed de novo plastome assembly of Pachycereus pringlei, Stenocereus thurberi, and Pereskia humboldtii based on the sequences available in public databases. We estimated a genome size of ~ 1.58 Gb for C. fernambucensis, the largest genome among the compared species. The genome heterozygosity was 0.88% in C. fernambucensis but ranged from 0.36 (Carnegiea gigantea) to 17.4% (Lophocereus schottii) in the other taxa. The genome lengths of the studied cacti are constituted by a high amount of transposable elements, ranging from ~ 57 to ~ 67%. Putative satellite DNAs are present in all species, excepting C. gigantea. The plastome of C. fernambucensis was ~ 104 kb, showing events of translocation, inversion, and gene loss. We observed a low number of shared unique orthologs, which may suggest gene duplication events and the simultaneous expression of paralogous genes. We recovered 37 genes that have undergone positive selection along the Cereus branch that are associated with different metabolic processes, such as improving photosynthesis during drought stress and nutrient absorption, which may be related to the adaptation to xeric areas of the Neotropics.

The HD-Zip I transcription factor MdHB7-like confers tolerance to salinity in transgenic apple (Malus domestica)

Salinity is a major environmental constraint that substantially limits global agricultural productivity. HD-Zip I transcription factors are involved in plant responses to salt stress, but little is known about the HD-Zip I genes in apple (Malus domestica). Here, we characterized the function of an apple HD-Zip I gene (MdHB7-like) and report that its expression is induced by salt stress. To further explore its role in salt stress, we created MdHB7-like overexpressing and RNAi transgenic apple plants. The overexpression of MdHB7-like improved the photosynthetic performance and reduced ROS and Na⁺ accumulation under salt stress. Plants that overexpressed MdHB7-like also showed increased accumulation of proline and soluble sugars, which may have played an important role in their salt stress tolerance. RNAi suppression of MdHB7-like had the opposite effects. Together, our results demonstrate that MdHB7-like is an important regulator of salt tolerance in apple. Our results provide new insights for future research on the mechanisms by which MdHB7-like promotes salt tolerance and provide a potential target for molecular breeding in apple.

Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus

Tomato chlorosis virus (ToCV), is one of the most devastating cultivated tomato viruses, seriously threatened the growth of crops worldwide. As the vector of ToCV, the whitefly Bemisia tabaci Mediterranean (MED) is mainly responsible for the rapid spread of ToCV. The current understanding of tomato plant responses to this virus and B. tabaci is very limited. To understand the molecular mechanism of the interaction between tomato, ToCV and B. tabaci, we adopted a next-generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed under the infection of B. tabaci and ToCV in tomato plants. Our data revealed that 6199 mRNAs were significantly regulated, and the differentially expressed genes were most significantly associated with the plant-pathogen interaction, the MAPK signaling pathway, the glyoxylate, and the carbon fixation in photosynthetic organisms and photosynthesis related proteins. Concomitantly, 242 differentially expressed miRNAs were detected, including novel putative miRNAs. Sly-miR159, sly-miR9471b-3p, and sly-miR162 were the most expressed miRNAs in each sample compare to control group. Moreover, we compared the similarities and differences of gene expression in tomato plant caused by infection or co-infection of B. tabaci and ToCV. Taken together, the analysis reported in this article lays a solid foundation for further research on the interaction between tomato, ToCV and B. tabaci, and provide evidence for the identification of potential key genes that influences virus transmission in tomato plants.

Transcriptomic profiling of atrazine phytotoxicity and comparative study of atrazine uptake, movement, and metabolism in Potamogeton crispus and Myriophyllum spicatum

The accumulation of atrazine in sediments raises wide concern due to its potential negative effects on aquatic environments. Here we collected sediments and different submerged macrophytes to simulate natural shallow lakes and to measure atrazine levels and submerged macrophyte biomass. We determined gene expressions in submerged macrophytes treated with or without atrazine. We also examined atrazine concentrations and its metabolite structures in submerged macrophytes. When the initial concentration of atrazine in sediments ranged from 0.1 to 2.0 mg kg^-1 dry weight (DW), atrazine levels in the pore water of the sediments ranged from 0.003 to 0.05 mg L^-1 in 90 days. Atrazine did not show obvious long-term effects on the biomass of Potamogeton crispus and Myriophyllum spicatum (P > 0.05). On day 90, gene expressions related to cell wall in P. crispus were changed by atrazine phytotoxicity. Moreover, the decrease in the number genes controlling light-harvesting chlorophyll a/b-binding proteins verified the toxic effects of atrazine on the photosynthesis of M. spicatum. Compared with unexposed plants on day 90, ribosome pathway was significantly enriched with differentially expressed genes after submerged macrophytes were exposed to 2.0 mg kg^-1 DW atrazine (P < 0.05). In addition, shoots and roots of P. crispus and M. spicatum could absorb the equal amount of atrazine (P > 0.05). Once absorbed by submerged macrophytes, atrazine was degraded into 1-hydroxyisopropylatrazine, hydroxyatrazine, deethylatrazine, didealkylatrazine, cyanuric acid, and biuret, and some of its metabolites could conjugate with organic acids, cysteinyl β-alanine, and glucose. This study establishes a foundation for aquatic ecological risk assessments and the phytoremediation of atrazine in sediments.

MdHB-7 Regulates Water Use Efficiency in Transgenic Apple (Malus domestica) Under Long-Term Moderate Water Deficit

Improved water use efficiency (WUE) promotes plant survival and crop yield under water deficit conditions. Although the plant-specific HD-Zip I transcription factors have important roles in plant adaptation to various abiotic stresses, including water deficit, their functions in regulating WUE of apple (Malus domestica) are poorly understood. We characterized the role of MdHB-7 in WUE regulation by subjecting MdHB-7 transgenic plants to long-term moderate soil water deficit. The long-term WUE (WUE_L) of transgenic apple plants with MdHB-7 overexpression or MdHB-7 RNA interference (RNAi) differed significantly from that of control plants. Upregulation of MdHB-7 caused reduced stomatal density, whereas the suppression of MdHB-7 increased stomatal density under both normal and long-term moderate soil water deficit conditions. Moderate reduction in stomatal density helped to improve the WUE of MdHB-7 overexpression transgenic plants, especially under water deficit conditions. MdHB-7 overexpression plants maintained high rates of photosynthesis that were conducive to the accumulation of biomass and the improvement of WUE_L. MdHB-7 overexpression also alleviated the inhibition of root growth caused by long-term moderate soil water deficit and improved root vitality and hydraulic conductivity, which were essential for improving plant WUE_L. By contrast, MdHB-7 RNA interference reduced the WUE_L of transgenic plants by inhibiting these factors under normal and long-term moderate soil water deficit conditions. Taken together, our results provide solid evidence for a crucial role of MdHB-7 in the regulation of apple WUE_L and provide new insights for improving the WUE of apple plants under moderate soil water deficit.