Identification, Analysis and Gene Cloning of the SWEET Gene Family Provide Insights into Sugar Transport in Pomegranate (Punica granatum)

Genome-wide identification and characterization of the sucrose invertase gene family in Hemerocallis citrina

Background

Sucrose invertase is an important catalytic enzyme that is widely distributed in plants and can irreversibly hydrolyze sucrose into fructose and glucose. Daylily is an important perennial flower worldwide and a traditional vegetable in East Asia. Previous studies have suggested that sucrose invertase is involved in the aging of daylily flowers. However, knowledge about the number, physicochemical properties, and expression patterns of daylily sucrose invertases is still lacking. Identifying the daylily sucrose invertase family genes in the genome is highly important for understanding phylogenetic evolution and determining the genetic function of sucrose invertase.

Methods

To obtain basic knowledge about the number, classification, sequence composition, and physicochemical properties of sucrose invertases in daylily, bioinformatics software was used to analyze the genome of Hemerocallis citrina (H. citrina), and the basic properties of sucrose invertase genes and proteins were obtained. Then, combined with transcriptome data from flower organs at different developmental stages, the expression patterns of each gene were clarified. Finally, the reliability of the transcriptome data was verified by quantitative real-time polymerase chain reaction (PCR).

Results

Through software analysis, 35 sucrose invertases were identified from the H. citrina genome and named HcINV1-HcINV35; these enzymes belong to three subfamilies: cell wall invertases, vacuolar invertases, and chloroplast invertases. The amino acid composition, motif types, promoter composition, gene structure, protein physicochemical properties, gene chromosomal localization, and evolutionary adaptability of daylily invertases were determined; these results provided a comprehensive understanding of daylily invertases. The transcriptome expression profile combined with fluorescence quantitative reverse transcription-polymerase chain reaction (RT‒PCR) analysis suggested that almost all daylily invertase genes were expressed in flower organs, but even genes belonging to the same subfamily did not exhibit the same expression pattern at different developmental stages, suggesting that there may be redundancy or dissimilation in the function of daylily sucrose invertases.

Genome-wide analysis of the SWEET gene family in Hemerocallis citrina and functional characterization of HcSWEET4a in response to salt stress

Sugars will be eventually effluxed transporters (SWEETs) have been confirmed to play diverse physiological roles in plant growth, development and stress response. However, the characteristics and functions of the SWEET genes in Hemerocallis citrina remain unclear and poorly elucidated. In this study, the whole genome of Hemerocallis citrina was utilized to conduct bioinformatics analysis and a total of 19 HcSWEET genes were successfully identified. Analysis of the physicochemical properties indicated dominant differences among these HcSWEETs. A phylogenetic analysis revealed that HcSWEET proteins can be divided into 4 clades ranging from Clade I to IV, where proteins within the same clade exhibited shared conserved motifs and gene structures. Five to six exons were contained in the majority of HcSWEET genes, which were unevenly distributed across 11 chromosomes. The gene duplication analysis showed the presence of 4 gene pairs. Comparative syntenic maps revealed that the HcSWEET gene family might present more closed homology in monocotyledons than dicotyledons. Cis-acting element analysis of HcSWEET genes indicated key responsiveness to various hormones, light, and stresses. Additionally, transcriptome sequencing analysis suggested that most HcSWEET genes had a relatively higher expression in roots, and HcSWEET4a was significantly up-regulated under salt stress. Overexpression further verified the possibility that HcSWEET4a was involved in response to salt stress, which provides novel insights and facilitates in-depth studies of the functional analysis of HcSWEETs in resistance to abiotic stress.

Genome-wide identification of SWEET genes reveals their roles during seed development in peanuts

Sugar Will Eventually be Exported Transporter (SWEET) proteins are highly conserved in various organisms and play crucial roles in sugar transport processes. However, SWEET proteins in peanuts, an essential leguminous crop worldwide, remain lacking in systematic characterization. Here, we identified 94 SWEET genes encoding the conservative MtN3/saliva domains in three peanut species, including 47 in Arachis hypogea, 23 in Arachis duranensis, and 24 in Arachis ipaensis. We observed significant variations in the exon-intron structure of these genes, while the motifs and domain structures remained highly conserved. Phylogenetic analysis enabled us to categorize the predicted 286 SWEET proteins from eleven species into seven distinct groups. Whole genome duplication/segment duplication and tandem duplication were the primary mechanisms contributing to the expansion of the total number of SWEET genes. In addition, an investigation of cis-elements in the potential promoter regions and expression profiles across 22 samples uncovered the diverse expression patterns of AhSWEET genes in peanuts. AhSWEET24, with the highest expression level in seeds from A. hypogaea Tifrunner, was observed to be localized on both the plasma membrane and endoplasmic reticulum membrane. Moreover, qRT-PCR results suggested that twelve seed-expressed AhSWEET genes were important in the regulation of seed development across four different peanut varieties. Together, our results provide a foundational basis for future investigations into the functions of SWEET genes in peanuts, especially in the process of seed development.

Hormonal Regulation and Transcriptomic Insights into Flower Development in Hydrangea paniculata 'Vanilla Strawberry'

Understanding the molecular mechanisms that regulate flower growth, development, and opening is of paramount importance, yet these processes remain less explored at the genetic level. Flower development in Hydrangea paniculata 'Vanilla Strawberry' is finely tuned through hormonal signals, yet the genetic underpinnings are not well defined. This study addresses the gap by examining the influence of gibberellic acid (GA3), salicylic acid (SA), and ethylene (ETH) on the flowering traits and underlying molecular responses. Treatment with 100 mg/L SA significantly improved chlorophyll content and bolstered the accumulation of soluble sugars and proteins, advancing the flowering onset by 6 days and lengthening the flowering period by 11 days. Concurrently, this treatment enhanced inflorescence dimensions, increasing length, width, and petal area by 22.76%, 26.74%, and 27.45%, respectively. Contrastingly, 100 mg/L GA3 expanded inflorescence size but postponed flowering initiation and decreased inflorescence count. Higher concentrations of SA and GA3, as well as any concentration of ETH, resulted in delayed flowering and inferior inflorescence attributes. A physiological analysis over 50 days revealed that these regulators variably affected sugar and protein levels and modified antioxidant enzyme activities. An RNA-seq analysis during floral development highlighted significant transcriptomic reprogramming, with SA treatment downregulating Myb transcription factors, implicating them in the modulation of flowering timing and stress adaptation. These findings illuminate the complex interplay between hormonal treatments, gene expression, and flowering phenotypes in Hydrangea paniculata, offering valuable perspectives for ornamental horticulture optimization.

Identification of Candidate Expansin Genes Associated with Seed Weight in Pomegranate (Punica granatum L.)

Seed weight is an important target trait in pomegranate breeding and culture. Expansins act by loosening plant cell walls and cellulosic materials, permitting turgor-driven cell enlargement. However, the role of expansin genes (EXPs) in pomegranate seed weight remains elusive. A total of 29 PgrEXPs were identified in the 'Dabenzi' genome. These genes were classified into four subfamilies and 14 subgroups, including 22 PgrEXPAs, 5 PgrEXPBs, 1 PgrEXPLA, and 1 PgrEXPLB. Transcriptome analysis of PgrEXPs in different tissues (root, leaf, flower, peel, and seed testa) in 'Dabenzi', and the seed testa of the hard-seeded pomegranate cultivar 'Dabenzi' and soft-seeded cultivar 'Tunisia' at three development stages showed that three PgrEXPs (PgrEXPA11, PgrEXPA22, PgrEXPA6) were highly expressed throughout seed development, especially in the sarcotesta. SNP/Indel markers of these PgrEXPs were developed and used to genotype 101 pomegranate accessions. The association of polymorphic PgrEXPs with seed weight-related traits (100-seed weight, 100-kernel weight, 100-sarcotesta weight, and the percentage of 100-sarcotesta to 100-seed weight) were analyzed. PgrEXP22 was significantly associated with 100-seed weight and 100-sarcotesta weight and is a likely candidate for regulating seed weight and sarcotesta development in particular. This study provides an effective tool for the genetic improvement of seed weight in pomegranate breeding programs.

Genome-Wide Investigation and Characterization of SWEET Gene Family with Focus on Their Evolution and Expression during Hormone and Abiotic Stress Response in Maize

The sugar will eventually be exported transporters (SWEET) family is an important group of transport carriers for carbon partitioning in plants and has important functions in growth, development, and abiotic stress tolerance. Although the SWEET family is an important sugar transporter, little is known of the functions of the SWEET family in maize (Zea mays), especially in response to abiotic stresses. To further explore the response pattern of maize SWEET to abiotic stress, a bioinformatics-based approach was used to predict and identify the maize SWEET gene (ZmSWEET) family. Twenty-four ZmSWEET genes were identified using the MaizeGDB database. Phylogenetic analysis resolved these twenty-four genes into four clades. One tandem and five segmental duplication events were identified, which played a major role in ZmSWEET family expansion. Synteny analysis provided insight into the evolutionary characteristics of the ZmSWEET genes with those of three graminaceous crop species. A heatmap showed that most ZmSWEET genes responded to at least one type of abiotic stress. By an abscisic acid signaling pathway, among which five genes were significantly induced under NaCl treatment, eight were obviously up-regulated under PEG treatment and five were up-regulated under Cd stress, revealing their potential functions in response to abiotic stress. These findings will help to explain the evolutionary links of the ZmSWEET family and contribute to future studies on the functional characteristics of ZmSWEET genes, and then improve abiotic stress tolerance in maize through molecular breeding.

Identification of sugar transporter (SWEET) genes involved in pomegranate seed coat sugar accumulation

Sugar content of the outer seed coat and hardness of the inner seed coat are important traits of the pomegranate fruit. The translocation of sugars across biological membranes, mediated by SWEET transporters, is critical to seed development. In this study, we identified 16 PgrSWEET genes distributed on six chromosomes in the pomegranate genome. According to the phylogenetic analysis, PgrSWEET proteins were divided into four groups. Tandem and segmental duplications contributed to the expansion of the PgrSWEET family, while functional redundancy and diversification may have occurred among SWEET members according to analyses of evolution and gene expression. RNA-seq and qRT-PCR analyses revealed that PgrSWEET1a and PgrSWEET9 were highly expressed in the inner seed coat, and the expression levels gradually increased during seed development. Moreover, the relative expression levels of PgrSWEET1a and PgrSWEET9 in a hard-seeded cultivar were higher than those in a soft-seeded cultivar, indicating that PgrSWEET1a and PgrSWEET9 might function in the inner seed coat development by accumulating sugar metabolites. We also found that PgrSWEET2 was highly expressed in the outer seed coat during seed development, and the protein was localized to the tonoplast, indicating that PgrSWEET2 is likely a candidate regulating sugar accumulation or reutilization in the vacuoles of the outer seed coat. Genes encoding transcription factors probably regulating the candidate PgrSWEET genes were chosen by co-expression analysis. These results not only helped to characterize PgrSWEET genes but also provided an insight into their functions in relation to seed coat development.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03248-6.

Characterization of the SWEET Gene Family in Longan (Dimocarpus longan) and the Role of DlSWEET1 in Cold Tolerance

Sugars will eventually be exported transporters (SWEET), a group of relatively novel sugar transporters, that play important roles in phloem loading, seed and fruit development, pollen development, and stress response in plants. Longan (Dimocarpus longan), a subtropic fruit tree with high economic value, is sensitive to cold. However, whether the SWEET gene family plays a role in conferring cold tolerance upon longan remains unknown. Here, a total of 20 longan SWEET (DlSWEET) genes were identified, and their phylogenetic relationships, gene structures, cis-acting elements, and tissue-specific expression patterns were systematically analyzed. This family is divided into four clades. Gene structures and motifs analyses indicated that the majority of DlSWEETs in each clade shared similar exon–intron organization and conserved motifs. Tissue-specific gene expression suggested diverse possible functions for DlSWEET genes. Cis-elements analysis and quantitative real-time PCR (qRT-PCR) analysis revealed that DlSWEET1 responded to cold stress. Notably, the overexpression of DlSWEET1 improved cold tolerance in transgenic Arabidopsis, suggesting that DlSWEET1 might play a positive role in D. longan’s responses to cold stress. Together, these results contribute to a better understanding of SWEET genes, which could serve as a foundation for the further functional identification of these genes.