Genome-wide analysis of the laccase (LAC) gene family in Aeluropus littoralis: A focus on identification, evolution and expression patterns in response to abiotic stresses and ABA treatment

Genome-wide identification of CA genes in cotton and the functional analysis of GhαCA4-D, GhβCA6-D and GhγCA2-D in response to drought and salt stresses

Carbonic anhydrases (CAs) are critical metalloenzymes, widely exist in organisms, which involve in many physiological processes, including response to adverse environmental conditions. Although CA genes have been comprehensive identified and analyzed in numerous plants, there are a few of reports in cotton. Therefore, we conducted an exhaustive research for CA genes from two tetraploid cotton species and their ancestral species. A total of 138 CA genes were found, and 45 of them belonged to Gossypium hirsutum. Phylogenetic relationships and sequences analysis showed that CA genes were categorized into three distinct subtypes: α-type, β-type and γ-type. The exon numbers of β-type members were highly variable. Various types of cis-elements, including drought inducibility, were identified in CA genes, suggesting that CA genes might be involved in the regulation of drought stress response. qRT-PCR was applied to assess the gene expression level in various tissues under drought stress. The results indicated that the expression levels of GhαCA4-D, GhβCA1-A, GhβCA1-D, GhβCA3-D and GhβCA6-D were significantly higher in leaves than that in stems and roots. The expression of GhαCA4-A, GhαCA8-A, GhαCA4-D, GhβCA3-D, GhβCA6-D and GhγCAL1-D was significantly upregulated in roots at severe drought treatment. The functions of GhαCA4-D, GhβCA6-D and GhγCA2-D were analyzed using virus-induced gene silencing (VIGS) technology. Compared to the controls, GhγCA2-D-silenced upland cotton seedlings were more sensitive to salt stress. However, the drought tolerance of GhαCA4-D and GhβCA6-D silenced plants was significantly decreased. Stomatal density, width and area were significantly higher in TRV:GhβCA6-D compared to TRV:00 inoculated plants. GhαCA4-D silenced plants were susceptible to oxidative stress, and silencing GhαCA4-D induced leave cell death. Our results will assist to make clear the regulatory mechanism of CA genes under abiotic stress.

Agro-physiological and transcriptome profiling reveal key genes associated with potato tuberization under different nitrogen regimes in aeroponics

Nitrogen (N) is a crucial nutrient for the growth and development of potatoes. However, excessive use of nitrogen fertilizers can have detrimental effects on human health, aquatic ecosystems, and the environment. Therefore, understanding the genes involved in nitrogen metabolism is essential for developing future strategies to improve nitrogen use efficiency (NUE) in plants. This study aimed to identify genes associated with high tuber yield in two contrasting potato varieties Kufri Jyoti (N inefficient) and Kufri Pukhraj (N efficient) grown under low and high nitrogen regimes using an aeroponics system. Both varieties were grown in aeroponics with two nitrogen doses (low N: 0.5 mM N; high N: 5 mM N) using a completely randomized design (CRD) with three replications over two years. The phenotypic results confirmed that Kufri Pukhraj was more nitrogen use efficient compared to Kufri Jyoti, particularly under low nitrogen conditions. Additionally, transcriptome analysis produced high-quality data ( ≥ Q20), ranging from 4.35 to 5.46 Gb per sample. Statistically significant genes (p ≤  0.05) were identified based on the reference potato genome. Differentially expressed genes (DEGs) were categorized as either up-regulated or down-regulated in leaf and tuber tissues. Transcriptome profiling of both tuber and leaf tissues revealed genes associated with traits contributing to high tuber yield under both high and low nitrogen conditions. The DEGs were further characterized through gene ontology (GO) annotation and KEGG pathway analysis. Selected genes were validated through real-time quantitative polymerase chain reaction (RT-qPCR) analysis. In summary, several genes were identified as being involved in high tuber yield component traits in potatoes under different nitrogen conditions. These included glutaredoxin, transcription factors (BTB/POZ, AP2/ERF, and MYB), nitrate transporter, aquaporin TIP1;3, glutamine synthetase, aminotransferase, GDSL esterase/lipase, sucrose synthase, UDP-glycosyltransferases, osmotin, xyloglucan endotransglucosylase/hydrolase, and laccases. Additionally, we identified overexpressed genes including cysteine protease inhibitor 1, miraculin, sterol desaturase, and pectinesterase in Kufri Pukhraj under low N stress. Our study highlights these genes' roles in enhancing tuber yield in potatoes cultivated under both high and low nitrogen in aeroponics.

The evolution and functional characterization of transcription factors E2Fs in lamprey, Lethenteron reissneri

The E2 promoter binding factors (E2Fs) are a group of transcriptional regulators that govern the cell cycle and play crucial roles in various cellular physiological processes, including proliferation and embryonic development. In this study, we identified four homologous genes-Lr-E2F3, Lr-E2F4, Lr-E2F5, and Lr-E2F8-from the lamprey (Lethenteron reissneri) genome database. Phylogenetic tree analysis was conducted to elucidate the evolutionary relationships within the E2F family across different species. Furthermore, analyses of motifs, domains, gene structures, and 3D structures reinforced the conservation of the E2F family. Notably, synteny analysis revealed that the neighboring genes of the Lr-E2Fs exhibited greater diversity compared to those in jawed vertebrates. Activity assays indicated that Lr-E2Fs may be involved in lamprey innate immunity mediated by NF-кB. Additionally, morphological observations of embryos microinjected with Cas9/sgRNA demonstrated that E2F-deficient lamprey embryos displayed embryonic lethality, suggesting that Lr-E2Fs play a significant role in lamprey embryonic development. In summary, our research not only provides new insights into the evolution of Lr-E2Fs but also offers valuable clues regarding their functional roles.

The function of HgLac in Heterodera glycines and its potential as a control target

The soybean cyst nematode (SCN; Heterodera glycines) is one of the most devastating pathogens for soybean production. The second stage juvenile (J2) invades the host root, develops and form white females which then become brown cysts enter the soil. The brown cyst wall plays a key role in protecting inside eggs from adverse environmental conditions. However, the function of cyst wall tanning (sclerotization and pigmentation) in nematodes is not clear. A browning-related gene discovered from the whole-genome sequencing was cloned and characterized in this study, the gene was confirmed to be the laccase gene and was named HgLac. HgLac mRNA and HgLac protein was detected in the epidermis of juveniles using in situ hybridization and immunolocalization techniques. The HgLac expression level was greater in fourth-stage juveniles (J4s) than in the other stages. Knockdown of HgLac by in vitro RNA interference (RNAi) significantly decreased the infectivity, development and reproduction of J2s but had no effect on cyst wall tanning. Further research revealed that HgLac expression in nematodes was significantly suppressed by 35.41-59.17 % through in planta RNAi, 52.96-58.19 % females could not tan successfully, and the female wall was very soft and fragile, with a low egg hatching rate (1.33 %), which was significantly lower than that of normal females (68.85 %). These results indicate that HgLac plays a key role in cyst wall tanning and suppressing the development and reproduction of the SCN, which provides new ideas for the use of this gene as a target to control SCN.

Genome-wide survey of chlorophyllase (CLH) gene family in seven Rosaceae and functional characterization of MdCLH1 in apple (Malus domestica) leaf photosynthesis

Chlorophyll, a crucial pigment in plant photosynthesis, undergoes dynamic synthesis and degradation processes throughout the growth cycle of plants. Chlorophyllase (CLH) plays a crucial role in the degradation of chlorophyll by removing the phytol group from chlorophyll A to produce chlorophyllide A. However, Rosaceae species remain underexplored in terms of understanding the functional divergences among CLH gene family members (CLHs) involved in chlorophyll catabolism and photosynthesis. The apple (Malus domestica) CLHs also requires further systematic characterization and identification. In this study, 20 CLHs (MdCLH1-4, FvCLH1-2, PpCLH1-2, PcCLH1-3, PaCLH1-2, RrCLH1-4, RcCLH1-3) were identified from seven species belonging to the Rosaceae family. The chromosomal distribution of these gene family members is mostly separate across all species, except in Rosa rugosa. The number of amino acids encoded by these genes ranges from 171 aa to 391 aa, possessing a theoretical isoelectric point (PI) of 5.46-9.59, and a relative molecular weight of 18313.07D to 42413.21D. Secondary structure predictions highlight α-helix and random coil conformations as the dominant structural elements of CLH proteins present in Rosaceae species. Subcellular localization predictions indicate that all CLH proteins are expressed in chloroplasts, while MdCLH4 is uniquely localized to the nucleus. Phylogenetic analysis reveals high homology and close evolutionary relationships among the genes in three subfamilies. All these 20 CLHs contain elements responsive to phytohormones, environmental stress, and light. Furthermore, transcriptomic profiling using geneChip expression array coupled with qRT-PCR analyses revealed a heightened transcriptional activity of MdCLHs in leaf tissues and protective tissue of annual shoots as compared to other plant components. Additional experimental evidence specifically indicates MdCLH1 is located in the chloroplasts of tobacco leaves. Notably, MdCLH1 transient expression in apple leaves decreased chlorophyll a, carotenoids, total chlorophyll content, non - photochemical quenching coefficient (NPQ), and intercellular CO₂ concentration (Ci), while increasing chlorophyll b content, effective PSII quantum yield [Y(II)], net photosynthetic rate (Pn), stomatal conductance (Gs), and electron transport rate (ETR). These suggest MdCLH1 enhances light energy conversion in PSII by modulating chlorophyll degradation, potentially improving photosynthetic efficiency and reducing the potential for photoinhibition. This study lays a solid foundation for further exploration into the functional roles of CLHs in the Rosaceae family.

Genome-wide analysis of the laccase gene family in Arachis hypogaea and functional characterization of AhLAC63 involved in lignin biosynthesis and abiotic stress

Plant laccases (LACs) play a vital role in lignification and participate in multiple biotic/abiotic stress responses. However, little is known about their role in lignin deposition and stress resistance in cultivated peanut (Arachis hypogaea L.). In this study, 80 putative peanut laccase genes (AhLACs) were identified and clustered into seven distinct phylogenetic groups. While the AhLAC members of group VI were lost, a novel specific group VIII was discovered in peanut. AhLACs within same group generally have similar gene structures and protein motif organizations. Expression pattern and subcellular cellular analysis revealed that AhLAC63 is a candidate gene involved in lignification and abiotic stress response. In addition, introducing AhLAC63 into the Arabidopsis laccase mutant (lac4 lac11) restored its lignin contents and abiotic stress tolerance. Moreover, the overexpression of AhLAC63 significantly altered phenylpropanoid metabolism flux and increased lignin content in peanut hairy roots. This study not only enables the further exploration of LAC biological functions in peanut, but also provides new gene resources for improving stress resistance in crops.

Insights into the Heat Shock Protein 70 (Hsp70) Family in Camelina sativa and Its Roles in Response to Salt Stress

Hsp70s, a group of heat shock proteins, are ancient proteins that play a crucial part in maintaining the stability of cells when faced with various internal and external stresses. In this research, there are 72 CsHSP70 genes present and verified in Camelina sativa, all of which exhibit a wide range of physicochemical characteristics. Through evolutionary analysis, the Hsp70 family was categorized into five primary groups, and numerous segmental duplications were anticipated among the CsHSP70 genes. The GO enrichment analysis of co-expression network elements revealed a significant association between key signaling terms, such as phosphorelay signal transduction, and MAPK cascade with the function of CsHsp70. An analysis of transcriptome data exposed to cold, drought, salinity, and cadmium stress demonstrated the varied expression profiles of CsHsp70 genes. The expression levels of CsHSP70 genes varied across various organs and stages of development in camelina, although some of them illustrated tissue-specific expression. qRT-PCR analysis further disclosed that CsHsp70-60, -52, and -13 were up-regulated and CsHsp70-03, -58, and -09 showed down-regulation in response to salinity. Furthermore, CsHsp70 genes are categorized as late-responsive elements to salinity stress. Through docking analysis, the current research revealed that CsHsp70 proteins interacted with ABA, BR, and MeJA.

Genome-wide identification of the Dof gene family: How it plays a part in mediating cold stress response in Prunus mume

DNA binding with a finger transcription factor (Dof) takes part in several plant physiological activities such as seed germination, flowering time, cold and drought resistance. Although the function, molecular phylogeny and expression pattern of Dof genes in Prunus mume was not clear yet. Here, the gene structure, motif, chromosome location and phylogenetic relationship of the Dof gene family in Prunus species was explored. We identified 24 members of the Dof gene family from P. mume, which were divided into 3 different subgroups. All these PmDof genes can be mapped to the pseudochromosome. Only one pair of tandem duplication genes are located in Chr3, whereas 8 pairs of segmentally duplicated PmDof genes located in Chr1, Chr2, Chr4, Chr5, and Chr7. Motif and gene structure analysis showed that each group had a similar conservative motif and similar exon/intron composition. Cis-acting elements analysis indicate that PmDofs may be involved in regulating abiotic stress response. Gene expression patterns showed that most PmDofs genes were specifically expressed in different tissues and at different stages. We next found that PmDofs genes display an obvious expression preference or specificity in cold stress response according to qRT-PCR analysis. We further observe a great cold resistance in PmDof10/11/20 OE lines, they showed lower electrolyte leakage rate, MDA content and higher soluble sugar/protein, POD/SOD/proline content than WT after -5 °C 6h freezing treatment. This research offers fresh perspectives on the development of PmDofs, enhancing our comprehension of the structure and role of plant Dof gene families.

Genome-wide identification of HIPP and mechanism of SlHIPP4/7/9/21/26/32 mediated phytohormones response to Cd, osmotic, and salt stresses in tomato

Heavy-metal-associated isoprenylated plant proteins (HIPPs) contributed to abiotic tolerance in vascular plants. Up to now, the HIPP gene family of tomato (Solanum lycopersicum L.) had not been thoroughly understood. In the present study, 34 SlHIPP genes were identified from the tomato genome using the Hidden Markov Model (HMM). The phylogenetic analysis revealed that the evolution of SlHIPPs was highly conserved. The cis-acting element analysis indicated that SlHIPP genes might be involved in phytohormones and abiotic stresses. We constructed venn diagram with 17 genes containing stress-related motifs as well as 15 genes and 19 genes expressing in leaves and roots in RNA-seq data, suggesting that SlHIPP4/7/9/21/26/32 were selected as candidate genes for study. The quantitative real-time PCR (qRT-PCR) analysis showed that 6 candidate genes were indicated to be involved in osmotic and salt stress tolerance and SlHIPP7/21/26/32 responded to cadmium (Cd) tolerance. The virus-induced silencing of 6 candidate genes caused growth inhibition in stress conditions, further illustrating that 6 candidate genes played a positive role in abiotic conditions. Importantly, the phytohormone analysis implied that 6 candidate genes mediated abscisic acid (ABA), salicylic acid (SA), gibberellin (GA3), auxin (IAA), or methyl jasmonate (MeJA) response to Cd, osmotic, or salt stress tolerance. These findings indicated that SlHIPP4/7/9/21/26/32 were key regulators of abiotic stress responses in tomato seedlings, functioning through multiple phytohormone pathways.

Heterologous expression of AaLac1 gene in hairy roots and its role in secondary metabolism under PEG-induced osmotic stress condition in Artemisia annua L

This study explores the Laccase gene (AaLac) family along with AaLac1 expression in hairy roots of A. annua. 42 AaLacs were identified by detecting three conserved domains: Cu-oxidase, Cu oxidase-2, and Cu oxidase-3. The physicochemical properties show that AaLacs are proteins with 541-1075 amino acids. These proteins are stable, with an instability index less than 40. Phylogenetic and motif studies have shown structural variants in AaLacs, suggesting functional divergence. 22 AaLac cis-regulatory elements were selected for their roles in drought stress, metabolic modulations, defense, and stress responses. A comparison of AtLac and AaLac proteins showed that 11 AtLacs mitigates stress reactions. In silico expression, analysis of 11 AtLacs showed that AtLac84 may function under osmotic stress. Thus, the Homolog AaLac1 was selected by expression profiling. The real-time PCR results showed that AaLac1 enhances osmotic stress tolerance in shoot and root samples. It was also used to analyze AaLac1, ADS, and CYP71AV1 gene expression in hairy roots via induction. The transformed hairy roots exhibited a greater capacity for PEG-induced osmotic stress tolerance in contrast to the untransformed roots. The gene expression analysis also depicted a significant increment in expression of AaLac1, ADS, and CYP71AV1 genes to 3.8, 6.9, and 3.1 folds respectively. The transformed hairy roots exhibited a significant increase of 2.2 and 1.4 fold in flavonoid and phenolic content respectively. Also, lignin content and artemisinin content increased by 7.05 folds and 95.6% with respect to the control. Thus, transformed hairy roots of A. annua under PEG-induced osmotic stress demonstrate the involvement of the AaLac1 gene in stress responses, lignin biosynthesis, and secondary metabolism production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01516-8.

How lignin biosynthesis responds to nitrogen in plants: a scoping review

Nitrogen (N) plays a critical role in the functioning of key amino acids and synthetic enzymes responsible for the various stages of lignin biosynthesis. However, the precise mechanisms through which N influences lignin biosynthesis have not been fully elucidated. This scoping review explores how lignin biosynthesis responds to N in plants. A systematic search of the literature in several databases was conducted using relevant keywords. Only 44 of the 1842 selected studies contained a range of plant species, experimental conditions, and research approaches. Lignin content, structure, and biosynthetic pathways in response to N are discussed, and possible response mechanisms of lignin under low N are proposed. Among the selected studies, 64.52% of the studies reter to lignin content found a negative correlation between N availability and lignin content. Usually, high N decreases the lignin content, delays cell lignification, increases p-hydroxyphenyl propane (H) monomer content, and regulates lignin synthesis through the expression of key genes (PAL, 4CL, CCR, CAD, COMT, LAC, and POD) encoding miRNAs and transcription factors (e.g., MYB, bHLH). N deficiency enhances lignin synthesis through the accumulation of phenylpropanoids, phenolics, and soluble carbohydrates, and indirect changes in phytohormones, secondary metabolites, etc. This review provides new insights and important references for future studies on the regulation of lignin biosynthesis.

Genome-wide survey of KT/HAK/KUP genes in the genus Citrullus and analysis of their involvement in K+-deficiency and drought stress responses in between C. lanatus and C. amarus

BACKGROUND

The KT/HAK/KUP is the largest K+ transporter family in plants, playing crucial roles in K+ absorption, transport, and defense against environmental stress. Sweet watermelon is an economically significant horticultural crop belonging to the genus Citrullus, with a high demand for K+ during its growth process. However, a comprehensive analysis of the KT/HAK/KUP gene family in watermelon has not been reported.

RESULTS

14 KT/HAK/KUP genes were identified in the genomes of each of seven Citrullus species. These KT/HAK/KUPs in watermelon were unevenly distributed across seven chromosomes. Segmental duplication is the primary driving force behind the expansion of the KT/HAK/KUP family, subjected to purifying selection during domestication (Ka/Ks < 1), and all KT/HAK/KUPs exhibit conserved motifs and could be phylogenetically classified into four groups. The promoters of KT/HAK/KUPs contain numerous cis-regulatory elements related to plant growth and development, phytohormone response, and stress response. Under K+ deficiency, the growth of watermelon seedlings was significantly inhibited, with cultivated watermelon experiencing greater impacts (canopy width, redox enzyme activity) compared to the wild type. All KT/HAK/KUPs in C. lanatus and C. amarus exhibit specific expression responses to K+-deficiency and drought stress by qRT-PCR. Notably, ClG42_07g0120700/CaPI482276_07g014010 were predominantly expressed in roots and were further induced by K+-deficiency and drought stress. Additionally, the K+ transport capacity of ClG42_07g0120700 under low K+ stress was confirmed by yeast functional complementation assay.

CONCLUSIONS

KT/HAK/KUP genes in watermelon were systematically identified and analyzed at the pangenome level and provide a foundation for understanding the classification and functions of the KT/HAK/KUPs in watermelon plants.

Phenotypic and transcriptomics characterization uncovers genes underlying tuber yield traits and gene expression marker development in potato under aeroponics

MAIN CONCLUSION

Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log2 fold change) and down-regulated (< -2 Log2 fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time-quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics.

Transcriptomic Analyses Reveal That Coffea arabica and Coffea canephora Have More Complex Responses under Combined Heat and Drought than under Individual Stressors

Increasing exposure to unfavorable temperatures and water deficit imposes major constraints on most crops worldwide. Despite several studies regarding coffee responses to abiotic stresses, transcriptome modulation due to simultaneous stresses remains poorly understood. This study unravels transcriptomic responses under the combined action of drought and temperature in leaves from the two most traded species: Coffea canephora cv. Conilon Clone 153 (CL153) and C. arabica cv. Icatu. Substantial transcriptomic changes were found, especially in response to the combination of stresses that cannot be explained by an additive effect. A large number of genes were involved in stress responses, with photosynthesis and other physiologically related genes usually being negatively affected. In both genotypes, genes encoding for protective proteins, such as dehydrins and heat shock proteins, were positively regulated. Transcription factors (TFs), including MADS-box genes, were down-regulated, although responses were genotype-dependent. In contrast to Icatu, only a few drought- and heat-responsive DEGs were recorded in CL153, which also reacted more significantly in terms of the number of DEGs and enriched GO terms, suggesting a high ability to cope with stresses. This research provides novel insights into the molecular mechanisms underlying leaf Coffea responses to drought and heat, revealing their influence on gene expression.

The Analysis, Description, and Examination of the Maize LAC Gene Family's Reaction to Abiotic and Biotic Stress

Laccase (LAC) is a diverse group of genes found throughout the plant genome essential for plant growth and the response to stress by converting monolignin into intricate lignin formations. However, a comprehensive investigation of maize laccase has not yet been documented. A bioinformatics approach was utilized in this research to conduct a thorough examination of maize (Zea mays L.), resulting in the identification and categorization of 22 laccase genes (ZmLAC) into six subfamilies. The gene structure and motifs of each subgroup were largely consistent. The distribution of the 22 LAC genes was uneven among the maize chromosomes, with the exception of chromosome 9. The differentiation of the genes was based on fragment replication, and the differentiation time was about 33.37 million years ago. ZmLAC proteins are primarily acidic proteins. There are 18 cis-acting elements in the promoter sequences of the maize LAC gene family associated with growth and development, stress, hormones, light response, and stress response. The analysis of tissue-specific expression revealed a high expression of the maize LAC gene family prior to the V9 stage, with minimal expression at post-V9. Upon reviewing the RNA-seq information from the publicly available transcriptome, it was discovered that ZmLAC5, ZmLAC10, and ZmLAC17 exhibited significant expression levels when exposed to various biotic and abiotic stress factors, suggesting their crucial involvement in stress responses and potential value for further research. This study offers an understanding of the functions of the LAC genes in maize's response to biotic and abiotic stress, along with a theoretical basis for comprehending the molecular processes at play.

Genome-wide identification and expression analysis of the HAK/KUP/KT gene family in Moso bamboo

The K+ uptake permease/high-affinity K+/K+ transporter (KUP/HAK/KT) family is the most prominent group of potassium (K+) transporters, playing a key role in K+ uptake, transport, plant growth and development, and stress tolerance. However, the presence and functions of the KUP/HAK/KT family in Moso bamboo (Phyllostachys edulis (Carriere) J. Houzeau), the fastest-growing plant, have not been studied. In this study, we identified 41 KUP/HAK/KT genes (PeHAKs) distributed across 18 chromosomal scaffolds of the Moso bamboo genome. PeHAK is a typical membrane protein with a conserved structural domain and motifs. Phylogenetic tree analysis classified PeHAKs into four distinct clusters, while collinearity analysis revealed gene duplications resulting from purifying selection, including both tandem and segmental duplications. Enrichment analysis of promoter cis-acting elements suggested their plausible role in abiotic stress response and hormone induction. Transcriptomic data and STEM analyses indicated that PeHAKs were involved in tissue and organ development, rapid growth, and responded to different abiotic stress conditions. Subcellular localization analysis demonstrated that PeHAKs are predominantly expressed at the cell membrane. In-situ PCR experiments confirmed that PeHAK was mainly expressed in the lateral root primordia. Furthermore, the involvement of PeHAKs in potassium ion transport was confirmed by studying the potassium ion transport properties of a yeast mutant. Additionally, through homology modeling, we revealed the structural properties of HAK as a transmembrane protein associated with potassium ion transport. This research provides a solid basis for understanding the classification, characterization, and functional analysis of the PeHAK family in Moso bamboo.

Identification of the lateral organ boundary domain gene family and its preservation by exogenous salicylic acid in Cerasus humilis

The gene family known as the Lateral Organ Boundary Domain (LBD) is responsible for producing transcription factors unique to plants, which play a crucial role in controlling diverse biological activities, including their growth and development. This research focused on examining Cerasus humilis'ChLBD gene, owing to its significant ecological, economic, and nutritional benefits. Examining the ChLBD gene family's member count, physicochemical characteristics, phylogenetic evolution, gene configuration, and motif revealed 41 ChLBD gene family members spread across 8 chromosomes, with ChLBD gene's full-length coding sequences (CDSs) ranging from 327 to 1737 base pairs, and the protein sequence's length spanning 109 (ChLBD30)-579 (ChLBD35) amino acids. The molecular weights vary from 12.068 (ChLBD30) to 62.748 (ChLBD35) kDa, and the isoelectric points span from 4.74 (ChLBD20) to 9.19 (ChLBD3). Categorizing them into two evolutionary subfamilies: class I with 5 branches, class II with 2, the majority of genes with a single intron, and most members of the same subclade sharing comparable motif structures. The results of collinearity analysis showed that there were 3 pairs of tandem repeat genes and 12 pairs of fragment repeat genes in the Cerasus humilis genome, and in the interspecific collinearity analysis, the number of collinear gene pairs with apples belonging to the same family of Rosaceae was the highest. Examination of cis-acting elements revealed that methyl jasmonate response elements stood out as the most abundant, extensively dispersed in the promoter areas of class 1 and class 2 ChLBD. Genetic transcript analysis revealed that during Cerasus humilis' growth and maturation, ChLBD developed varied control mechanisms, with ChLBD27 and ChLBD40 potentially playing a role in managing color alterations in fruit ripening. In addition, the quality of calcium fruit will be affected by the environment during transportation and storage, and it is particularly important to use appropriate means to preserve the fruit. The research used salicylic acid-treated Cerasus humilis as the research object and employed qRT-PCR to examine the expression of six ChLBD genes throughout storage. Variations in the expression of the ChLBD gene were observed when exposed to salicylic acid, indicating that salicylic acid could influence ChLBD gene expression during the storage of fruits. This study's findings lay the groundwork for additional research into the biological role of the LBD gene in Cerasus humilis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01438-5.

Comparative Analysis of the Effect of Gamma-, Electron, and Proton Irradiation on Transcriptomic Profile of Hordeum vulgare L. Seedlings: In Search for Molecular Contributors to Abiotic Stress Resilience

The development of adaptation strategies for crops under ever-changing climate conditions is a critically important food security issue. Studies of barley responses to ionising radiation showed that this evolutionarily ancient stress factor can be successfully used to identify molecular pathways involved in adaptation to a range of abiotic stressors. In order to identify potential molecular contributors to abiotic stress resilience, we examined the transcriptomic profiles of barley seedlings after exposure to γ-rays, electrons, and protons. A total of 553 unique differentially expressed genes with increased expression and 124 with decreased expression were detected. Among all types of radiation, the highest number of differentially expressed genes was observed in electron-irradiated samples (428 upregulated and 56 downregulated genes). Significant upregulation after exposure to the three types of radiation was shown by a set of ROS-responsive genes, genes involved in DNA repair, cell wall metabolism, auxin biosynthesis and signalling, as well as photosynthesis-related genes. Most of these genes are known to be involved in plant ROS-mediated responses to other abiotic stressors, especially with genotoxic components, such as heavy metals and drought. Ultimately, the modulation of molecular pathways of plant responses to ionising radiation may be a prospective tool for stress tolerance programmes.

NRAMP gene family in Kandelia obovata: genome-wide identification, expression analysis, and response to five different copper stress conditions

Natural resistance-associated macrophage proteins (NRAMPs) are a class of metal transporters found in plants that exhibit diverse functions across different species. Transporter proteins facilitate the absorption, distribution, and sequestration of metallic elements within various plant tissues. Despite the extensive identification of NRAMP family genes in various species, a full analysis of these genes in tree species is still necessary. Genome-wide identification and bioinformatics analysis were performed to understand the roles of NRAMP genes in copper (CuCl2) stress in Kandelia obovata (Ko). In Arachis hypogaea L., Populus trichocarpa, Vitis vinifera, Phaseolus vulgaris L., Camellia sinensis, Spirodela polyrhiza, Glycine max L. and Solanum lycopersicum, a genome-wide study of the NRAMP gene family was performed earlier. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and CuCl2 were all investigated in this research. In order to comprehend the notable functions of the NRAMP gene family in Kandelia obovata, a comprehensive investigation was conducted at the genomic level. This study successfully found five NRAMP genes, encompassing one gene pair resulting from whole-genome duplication and a gene that had undergone segmental duplication. The examination of chromosomal position revealed an unequal distribution of the KoNRAMP genes across chromosomes 1, 2, 5, 7, and 18. The KoNRAMPs can be classified into three subgroups (I, II, and SLC) based on phylogeny and synteny analyses, similar to Solanum lycopersicum. Examining cis-regulatory elements in the promoters revealed five hormone-correlated responsive elements and four stress-related responsive elements. The genomic architecture and properties of 10 highly conserved motifs are similar among members of the NRAMP gene family. The conducted investigations demonstrated that the expression levels of all five genes exhibited alterations in response to different levels of CuCl2 stress. The results of this study offer crucial insights into the roles of KoNRAMPs in the response of Kandelia obovata to CuCl2 stress.

Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata

Akebia trifoliata is an economically important, self-incompatible fruit tree in the Lardizabalaceae family. Asexual propagation is the main strategy used to maintain excellent agronomic traits. However, the generation of adventitious roots during asexual propagation is very difficult. To study the important role of the WUSCHEL-related homeobox (WOX) transcription factor in adventitious root growth and development, we characterized this transcription factor family in the whole genome of A. trifoliata. A total of 10 AktWOXs were identified, with the following characteristics: length (657~11,328 bp), exon number (2~5), isoelectric point (5.65~9.03), amino acid number (176~361 AA) and molecular weight (20.500~40.173 kDa), and their corresponding expression sequence could also be detectable in the public transcriptomic data for A. trifoliata fruit. A total of 10 AktWOXs were classified into modern (6), intermediate (2) and ancient clades (2) and all AktWOXs had undergone strong purifying selection during evolution. The expression profile of AktWOXs during A. trifoliata adventitious root formation indicated that AktWOXs play an important role in the regulation of adventitious root development. Overall, this is the first study to identify and characterize the WOX family in A. trifoliata and will be helpful for further research on A. trifoliata adventitious root formation.

Genome-Wide Identification, Characterization, and Expression Analysis of the Copper-Containing Amine Oxidase Gene Family in Mangrove Kandelia obovata

Copper-containing amine oxidases (CuAOs) are known to have significant involvement in the process of polyamine catabolism, as well as serving crucial functions in plant development and response to abiotic stress. A genome-wide investigation of the CuAO protein family was previously carried out in sweet orange (Citrus sinensis) and sweet cherry (Prunus avium L.). Six CuAO (KoCuAO1-KoCuAO6) genes were discovered for the first time in the Kandelia obovata (Ko) genome through a genome-wide analysis conducted to better understand the key roles of the CuAO gene family in Kandelia obovata. This study encompassed an investigation into various aspects of gene analysis, including gene characterization and identification, subcellular localization, chromosomal distributions, phylogenetic tree analysis, gene structure analysis, motif analysis, duplication analysis, cis-regulatory element identification, domain and 3D structural variation analysis, as well as expression profiling in leaves under five different treatments of copper (CuCl2). Phylogenetic analysis suggests that these KoCuAOs, like sweet cherry, may be subdivided into three subgroups. Examining the chromosomal location revealed an unequal distribution of the KoCuAO genes across four out of the 18 chromosomes in Kandelia obovata. Six KoCuAO genes have coding regions with 106 and 159 amino acids and exons with 4 and 12 amino acids. Additionally, we discovered that the 2.5 kb upstream promoter region of the KoCuAOs predicted many cis elements linked to phytohormones and stress responses. According to the expression investigations, CuCl2 treatments caused up- and downregulation of all six genes. In conclusion, our work provides a comprehensive overview of the expression pattern and functional variety of the Kandelia obovata CuAO gene family, which will facilitate future functional characterization of each KoCuAO gene.

Genome-wide identification of RNA recognition motif (RRM1) in Brassica rapa and functional analysis of RNA-binding protein (BrRBP) under low-temperature stress

BACKGROUND

The RNA recognition motif (RRM) is primarily engaged in the processing of mRNA and rRNA following gene transcription as well as the regulation of RNA transport; it is critical in preserving RNA stability.

RESULTS

In this study, we identified 102 members of the RRM1 gene family in Brassica rapa, which were dispersed across 10 chromosomes with the ninth chromosome being the most extensively distributed. The RRM1 gene family members of Brassica rapa and Arabidopsis thaliana were grouped into 14 subclades (I-XIV) using phylogenetic analysis. Moreover, the results of transcriptome analysis and RT-qPCR indicated that the expression of Brapa05T000840 was upregulated in the cultivars 'Longyou 7' and 'Longyou 99' following exposure to cold stress at a temperature of 4 °C for 24 h. The levels of expression in the leaves and growth cones of the 'Longyou 7' variety were found to be significantly higher than those observed in the 'Longyou 99' variety under conditions of low temperature and NaCl stress. It illustrates the involvement of the RRM1 gene in the physiological response to both low temperature and salt stress. In addition, it was observed that the survival rate of transgenic BrRBP (Brapa05T000840) Arabidopsis thaliana plants was notably higher compared to that of wild-type plants when subjected to varying durations of low temperature treatment. Furthermore, the expression of the BrRBP gene in transgenic plants exhibited an upward trend as the duration of low temperature treatment increased, reaching its peak at 24 h. The in-vivo enzymatic activity of reactive oxygen species-scavenging enzymes were found to be significantly elevated in comparison to wild-type plants, suggesting that the BrRBP gene may enhance the cold tolerance of Arabidopsis thaliana.

CONCLUSIONS

This study offers a significant foundation for comprehending the regulation mechanism of the RRM1 gene family in winter Brassica rapa subjected to cold stress, as well as for finding key genes associated with cold resistance.

Genome-Wide Analysis of Flax (Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors

Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17 LuGRF genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17 LuGRFs (88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades; LuGRF genes were found in four clades. Most LuGRF gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of LuGRF genes were also analyzed. The three-dimensional structure of LuGRF proteins was predicted using homology modeling. The transcript expression data indicated that most LuGRF family members were highly expressed in flax fruit and embryos, whereas LuGRF3, LuGRF12 and LuGRF16 were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both LuGRF1 and LuGRF11 were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense. LuGRF1 was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of LuGRF gene function and obtaining improved flax breeding lines.

Analysis of Auxin-Encoding Gene Family in Vigna radiata and It's Cross-Species Expression Modulating Waterlogging Tolerance in Wild Vigna umbellata

Mungbean is known to be susceptible to waterlogging (WL) stress. Some of the wild species have the potential to tolerate this through various physiological and molecular mechanisms. Auxin Response Factor (ARF) and Auxin/Indole Acetic Acid (AUX/IAA), an early responsive gene family, has multiple functions in growth, development, and stress tolerance. Here, we report the first comprehensive analysis of the ARF and AUX/IAA gene family in mungbean. A total of 26 ARF and 19 AUX/IAA genes were identified from the mungbean genome. The ARF and AUX/IAA candidates were clearly grouped into two major clades. Further, the subgrouping within the major clades indicated the presence of significant diversity. The gene structure, motif analysis, and protein characterization provided the clue for further fundamental research. Out of the10 selected candidate genes, VrARF-5, VrARF-11, VrARF-25, and VrAUX/IAA-9 were found to significantly multiple-fold gene expression in the hypocotyl region of WL-tolerant wild relatives (PRR 2008-2) provides new insight into a role in the induction of lateral root formation under WL stress. The analysis provides an insight into the structural diversity of ARF and AUX/IAA genes in mungbean. These results increase our understanding of ARF and AUX/IAA genes and therefore offer robust information for functional investigations, which can be taken up in the future and will form a foundation for improving tolerance against waterlogging stress.

Genome-Wide Identification and Expression Analysis of the Copper Transporter (COPT/Ctr) Gene Family in Kandelia obovata, a Typical Mangrove Plant

The copper transporter (COPT/Ctr) gene family plays a critical part in maintaining the balance of the metal, and many diverse species depend on COPT to move copper (Cu) across the cell membrane. In Arabidopsis thaliana, Oryza sativa, Medicago sativa, Zea mays, Populus trichocarpa, Vitis vinifera, and Solanum lycopersicum, a genome-wide study of the COPT protein family was performed. To understand the major roles of the COPT gene family in Kandelia obovata (Ko), a genome-wide study identified four COPT genes in the Kandelia obovata genome for the first time. The domain and 3D structural variation, phylogenetic tree, chromosomal distributions, gene structure, motif analysis, subcellular localization, cis-regulatory elements, synteny and duplication analysis, and expression profiles in leaves and Cu were all investigated in this research. Structural and sequence investigations show that most KoCOPTs have three transmembrane domains (TMDs). According to phylogenetic research, these KoCOPTs might be divided into two subgroups, just like Populus trichocarpa. KoCOPT gene segmental duplications and positive selection pressure were discovered by universal analysis. According to gene structure and motif analysis, most KoCOPT genes showed consistent exon-intron and motif organization within the same group. In addition, we found five hormones and four stress- and seven light-responsive cis-elements in the KoCOPTs promoters. The expression studies revealed that all four genes changed their expression levels in response to copper (CuCl2) treatments. In summary, our study offers a thorough overview of the Kandelia obovata COPT gene family's expression pattern and functional diversity, making it easier to characterize each KoCOPT gene's function in the future.

FlbZIP12 gene enhances drought tolerance via modulating flavonoid biosynthesis in Fagopyrum leptopodum

Karst lands provide a poor substrate to support plant growth, as they are low in nutrients and water content. Common buckwheat (Fagopyrum esculentum) is becoming a popular crop for its gluten-free grains and their high levels of phenolic compounds, but buckwheat yields are affected by high water requirements during grain filling. Here, we describe a wild population of drought-tolerant Fagopyrum leptopodum and its potential for enhancing drought tolerance in cultivated buckwheat. We determined that the expression of a gene encoding a Basic leucine zipper (bZIP) transcription factor, FlbZIP12, from F. leptopodum is induced by abiotic stresses, including treatment with the phytohormone abscisic acid, salt, and polyethylene glycol. In addition, we show that overexpressing FlbZIP12 in Tartary buckwheat (Fagopyrum tataricum) root hairs promoted drought tolerance by increasing the activities of the enzymes superoxide dismutase and catalase, decreasing malondialdehyde content, and upregulating the expression of stress-related genes. Notably, FlbZIP12 overexpression induced the expression of key genes involved in flavonoid biosynthesis. We also determined that FlbZIP12 interacts with protein kinases from the FlSnRK2 family in vitro and in vivo. Taken together, our results provide a theoretical basis for improving drought tolerance in buckwheat via modulating the expression of FlbZIP12 and flavonoid contents.

New insights into comprehensive analysis of magnesium transporter (MGT) gene family in rice (Oryza sativa L.)

Magnesium transporters (MGTs) regulate magnesium absorption, transport, and redistribution in higher plants. To investigate the role of the Oryza sativa MGTs gene family members under salt stress, this study analyzed the protein properties, gene structure, phylogenetic relationship, synteny patterns, expression, and co-expression networks of 23 non-redundant OsMGT. The evolutionary relationship of the OsMGT gene family was fully consistent with their functional domain, and were divided into three main classes based on the conserved domain: MMgT, CorA-like, and NIPA. The α/β patterns in the protein structures were highly similar in the CorA-like and NIPA members, with the conserved structures in the Mg2+-binding and catalytic regions. The CorA-like clade-related proteins demonstrated the highest numbers of protein channels with Pro, Ser, Lys, Gly, and Tyr, as the critical binding residues. The expression analysis of OsMGT genes in various tissues showed that MGTs' gene family may possess critical functions during rice development. Gene expression analysis of candidate OsMGT using reverse-transcription quantitative real-time PCR (RT-qPCR) found that four OsMGT genes exhibited different expression patterns in salt-sensitive and salt-tolerant rice genotypes. We hypothesize that the OsMGT gene family members may be involved in responses to salt stress. These findings could be useful for further functional investigation of MGTs as well as defining their involvement in abiotic stress studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03735-4.

Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp. revealed their role in multiple stresses

Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.

Genome-wide characterization, evolutionary analysis, and expression pattern analysis of the trihelix transcription factor family and gene expression analysis under MeJA treatment in Panax ginseng

Panax ginseng is a well-known medicinal plant with several pharmacological uses in China. The trihelix family transcription factors, also known as GT factors, can be involved in the regulation of growth and developmental processes in plants. There have been no in-depth reports or systematic studies about the trihelix transcription factor in ginseng. In this study, the structure, chromosomal localization, gene duplication, phylogeny, functional differentiation, expression patterns and coexpression interactions of trihelix transcripts were analysed using bioinformatics methods based on the ginseng transcriptome database. Thirty-two trihelix transcription factor genes were identified in ginseng, and these genes were alternatively spliced to obtain 218 transcripts. These transcripts were unevenly distributed on different chromosomes of ginseng, and phylogenetic analysis classified the PgGT transcripts into five subgroups. Gene Ontology (GO) analysis classified PgGT transcripts into eight functional subclasses, indicating that they are functionally diverse. The expression pattern analysis of 218 PgGT transcripts revealed that their expression was tissue-specific and spatiotemporally-specific in 14 different tissues of 4-year-old ginseng, 4 different ages of ginseng roots, and 42 farmers' cultivars of 4-year-old ginseng roots. Despite the differences in the expression patterns of these transcripts, coexpression network analysis revealed that these transcripts could be expressed synergistically in ginseng. In addition, two randomly selected PgGT transcripts in each of the five different subfamilies were subjected to methyl jasmonate treatment at different times, and PgGT was able to respond to the regulation of methy1 jasmonate. These results provide a theoretical basis and gene resources for an in-depth study of the function of trihelix genes in other plants.

Genome-Wide Detection of SPX Family and Profiling of CoSPX-MFS3 in Regulating Low-Phosphate Stress in Tea-Oil Camellia

Camellia oleifera a member of the family Theaceae, is a phosphorus (P) tolerator native to southern China. The SPX gene family critically regulates plant growth and development and maintains phosphate (Pi) homeostasis. However, the involvement of SPX genes in Pi signaling in Tea-Oil Camellia remains unknown. In this work, 20 SPX genes were identified and categorized into four subgroups. Conserved domains, motifs, gene structure, chromosomal location and gene duplication events were also investigated in the SPX gene family. Defense and stress responsiveness cis-elements were identified in the SPX gene promoters, which participated in low-Pi stress responses. Based on transcriptome data and qRT-PCR results, nine CoSPX genes had similar expression patterns and eight genes (except CoPHO1H3) were up-regulated at 30 days after exposure to low-Pi stress. CoSPX-MFS3 was selected as a key candidate gene by WGCNA analysis. CoSPX-MFS3 was a tonoplast protein. Overexpression of CoSPX-MFS3 in Arabidopsis promoted the accumulation of total P content and decreased the anthocyanin content. Overexpression of CoSPX-MFS3 could enhance low-Pi tolerance by increased biomass and organic acid contents in transgenic Arabidopsis lines. Furthermore, the expression patterns of seven phosphate starvation genes were higher in transgenic Arabidopsis than those in the wild type. These results highlight novel physiological roles of the SPX family genes in C. oleifera under low-Pi stress, and lays the foundation for a deeper knowledge of the response mechanism of C. oleifera to low-Pi stress.

Characterization of HSP70 family in watermelon (Citrullus lanatus): identification, structure, evolution, and potential function in response to ABA, cold and drought stress

Watermelon (Citrullus lanatus) as a crop with important economic value, is widely cultivated around the world. The heat shock protein 70 (HSP70) family in plant is indispensable under stress conditions. However, no comprehensive analysis of watermelon HSP70 family is reported to date. In this study, 12 ClHSP70 genes were identified from watermelon, which were unevenly located in 7 out of 11 chromosomes and divided into three subfamilies. ClHSP70 proteins were predicted to be localized primarily in cytoplasm, chloroplast, and endoplasmic reticulum. Two pairs of segmental repeats and 1 pair of tandem repeats existed in ClHSP70 genes, and ClHSP70s underwent strong purification selection. There were many abscisic acid (ABA) and abiotic stress response elements in ClHSP70 promoters. Additionally, the transcriptional levels of ClHSP70s in roots, stems, true leaves, and cotyledons were also analyzed. Some of ClHSP70 genes were also strongly induced by ABA. Furthermore, ClHSP70s also had different degrees of response to drought and cold stress. The above data indicate that ClHSP70s may be participated in growth and development, signal transduction and abiotic stress response, laying a foundation for further analysis of the function of ClHSP70s in biological processes.

Genome-Wide Characteristics of GH9B Family Members in Melon and Their Expression Profiles under Exogenous Hormone and Far-Red Light Treatment during the Grafting Healing Process

β-1,4-glucanase can not only promote the wound healing of grafted seedlings but can also have a positive effect on a plant's cell wall construction. As a critical gene of β-1,4-glucanase, GH9B is involved in cell wall remodeling and intercellular adhesion and plays a vital role in grafting healing. However, the GH9B family members have not yet been characterized for melons. In this study, 18 CmGH9Bs were identified from the melon genome, and these CmGH9Bs were located on 15 chromosomes. Our phylogenetic analysis of these CmGH9B genes and GH9B genes from other species divided them into three clusters. The gene structure and conserved functional domains of CmGH9Bs in different populations differed significantly. However, CmGH9Bs responded to cis elements such as low temperature, exogenous hormones, drought, and injury induction. The expression profiles of CmGH9Bs were different. During the graft healing process of the melon scion grafted onto the squash rootstock, both exogenous naphthyl acetic acid (NAA) and far-red light treatment significantly induced the upregulated expression of CmGH9B14 related to the graft healing process. The results provided a technical possibility for managing the graft healing of melon grafted onto squash by regulating CmGH9B14 expression.