New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics

Identification of the SWEET gene family and functional characterization of PsSWEET1a and PsSWEET17b in the regulation of sugar accumulation in 'Fengtang' plum (Prunus salicina Lindl.)

BACKGROUND

'Fengtang' plum is a cultivar known for its significant sugar accumulation. Although various studies have been conducted on sugar metabolism, the specific molecular mechanisms underlying the high sugar accumulation in 'Fengtang' plum remain largely unexplored. Here, we present the role of the Sugars Will Eventually be Exported Transporters (SWEETs) family in regulating sugar accumulation in 'Fengtang' plum fruits.

RESULTS

In this study, 18 PsSWEET genes were identified based on homology with Arabidopsis genes and the Pfam database (ID: PF03083). Alignment of multiple sequences revealed that the seven alpha-helical transmembrane regions (7-TMs) are largely conserved in the PsSWEET family. Phylogenetic analysis demonstrated that the 18 SWEET family members could be categorized into four clades. Nine predicted motifs were identified within the PsSWEET genes of plum. The PsSWEET genes were unevenly distributed across five chromosomes, and synteny analysis revealed three pairs of fragmented duplication events. PsSWEET1a and PsSWEET17b are pivotal in 'Fengtang' plum fruit development. Subcellular localization analyses indicated that PsSWEET1a is localized to the nucleus and cytoplasm, while PsSWEET17b is associated with the vacuolar membrane. Gene function was further validated through transient silencing and overexpression of the PsSWEET1a and PsSWEET17b genes in plum fruits, which significantly impacted their soluble sugar content. Heterologous expression of PsSWEET1a and PsSWEET17b in tomato resulted in an increase in soluble sugar content due to the modulation of sugar accumulation-related genes and enzyme activities.

CONCLUSION

The genes PsSWEET1a and PsSWEET17b, which regulate the content of soluble sugar in plum fruit, were successfully identified. This study provides a comprehensive insight into the SWEET gene family of plum, offering novel perspectives on the regulation of sugar accumulation in fruit and laying a critical foundation for further enhancement of plum fruit quality.

Genome-Wide Identification of the SWEET Gene Family and Functional Analysis of BraSWEET10 in Winter B. rapa (Brassica rapa L.) Under Low-Temperature Stress

Sugars will eventually be exported transporter (SWEET), a class of glucose transport proteins, is crucial in plants for glucose transport by redistribution of sugars and regulates growth, development, and stress tolerance. Although the SWEET family has been studied in many plants, little is known about its function in winter B. rapa (Brassica rapa L.). Bioinformatics approaches were adopted to identify the SWEET gene (BraSWEETs) family in B. rapa to investigate its role during overwintering. From the whole-genome data, 31 BraSWEET genes were identified. Gene expansion was realized by tandem and fragment duplication, and the 31 genes were classified into four branches by phylogenetic analysis. As indicated by exon-intron structure, cis-acting elements, MEME (Multiple EM for Motif Elicitation) motifs, and protein structure, BraSWEETs were evolutionarily conserved. According to the heat map, 23 BraSWEET genes were differentially expressed during overwintering, revealing their potential functions in response to low-temperature stress and involvement in the overwintering memory-formation mechanism. BraSWEET10 is mainly associated with plant reproductive growth and may be crucial in the formation of overwintering memory in B. rapa. The BraSWEET10 gene was cloned into B. rapa (Longyou-7, L7). The BraSWEET10 protein contained seven transmembrane structural domains. Real-time fluorescence quantitative PCR (qRT-PCR) showed that the BraSWEET10 gene responded to low-temperature stress. BraSWEET10 was localized to the cell membrane. The root length of overexpressing transgenic A. thaliana was significantly higher than that of wild-type (WT) A. thaliana under low temperatures. Our findings suggest that this gene may be important for the adaptation of winter B. rapa to low-temperature stress. Overall, the findings are expected to contribute to understanding the evolutionary links of the BraSWEET family and lay the foundation for future studies on the functional characteristics of BraSWEET genes.

Characterization of the SWEET Gene Family in Blueberry (Vaccinium corymbosum L.) and the Role of VcSWEET6 Related to Sugar Accumulation in Fruit Development

Sugars will eventually be exported transporters (SWEETs) are essential transmembrane proteins involved in plant growth, stress responses, and plant-pathogen interactions. Despite their importance, systematic studies on SWEETs in blueberries (Vaccinium corymbosum L.) are limited. Blueberries are recognized for their rapid growth and the significant impact of sugar content on fruit flavor, yet the role of the SWEET gene family in sugar accumulation during fruit development remains unclear. In this study, 23 SWEET genes were identified in blueberry, and their phylogenetic relationships, duplication events, gene structures, cis-regulatory elements, and expression profiles were systematically analyzed. The VcSWEET gene family was classified into four clades. Structural and motif analysis revealed conserved exon-intron organization within each clade. RT-qPCR analysis showed widespread expression of VcSWEETs across various tissues and developmental stages, correlating with promoter cis-elements. VcSWEET6a, in particular, was specifically expressed in fruit and showed reduced expression during fruit maturation. Subcellular localization indicated that VcSWEET6a is located in the endoplasmic reticulum. Functional assays in yeast confirmed its role in glucose and fructose uptake, with transport activity inhibited at higher sugar concentrations. Overexpression of VcSWEET6a in blueberries resulted in reduced sugar accumulation. These findings offer valuable insights into the role of VcSWEETs in blueberry sugar metabolism.

The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum

Modern sugarcane, a highly allo-autopolyploid organism, has a very complex genome. In the present study, the karyotype and genome architecture of modern sugarcane were investigated, resulting in a genome assembly of 97 chromosomes (8.84 Gb). The allopolyploid genome was divided into subgenomes from Saccharum officinarum (Soh) and S. spontaneum (Ssh), with Soh dominance in the Saccharum hybrid (S. hybrid). Genome shock affected transcriptome dynamics during allopolyploidization. Analysis of an inbreeding population with 192 individuals revealed the underlying genetic basis of transgressive segregation. Population genomics of 310 Saccharum accessions clarified the breeding history of modern sugarcane. Using the haplotype-resolved S. hybrid genome as a reference, genome-wide association studies identified a potential candidate gene for sugar content from S. spontaneum. These findings illuminate the complex genome evolution of allopolyploids, offering opportunities for genomic enhancements and innovative breeding strategies for sugarcane.

Regulatory network of the late-recruited primary decarboxylase C4NADP-ME in sugarcane

In agronomically important C4 grasses, efficient CO2 delivery to Rubisco is facilitated by NADP-malic enzyme (C4NADP-ME), which decarboxylates malate in bundle sheath cells. However, understanding the molecular regulation of the C4NADP-ME gene in sugarcane (Saccharum spp.) is hindered by its complex genetic background. Enzymatic activity assays demonstrated that decarboxylation in sugarcane Saccharum spontaneum predominantly relies on the NADP-ME pathway, similar to sorghum (Sorghum bicolor) and maize (Zea mays). Comparative genomics analysis revealed the recruitment of 8 core C4 shuttle genes, including C4NADP-ME (SsC4NADP-ME2), in the C4 pathway of sugarcane. Contrasting to sorghum and maize, the expression of SsC4NADP-ME2 in sugarcane is regulated by different transcription factors (TFs). We propose a gene regulatory network for SsC4NADP-ME2, involving candidate TFs identified through gene coexpression analysis and yeast 1-hybrid experiment. Among these, ABA INSENSITIVE5 (ABI5) was validated as the predominant regulator of SsC4NADP-ME2 expression, binding to a G-box within its promoter region. Interestingly, the core element ACGT within the regulatory G-box was conserved in sugarcane, sorghum, maize, and rice (Oryza sativa), suggesting an ancient regulatory code utilized in C4 photosynthesis. This study offers insights into SsC4NADP-ME2 regulation, crucial for optimizing sugarcane as a bioenergy crop.

Genome wide identification of BjSWEET gene family and drought response analysis of BjSWEET12 and BjSWEET17 genes in Brassica juncea

BACKGROUND

Sugars Will Eventually be Exported Transporter (SWEET) gene family is a unique type of sugar transporter that plays a vital role in metabolic regulation, growth, development, and stress response in multiple species. This study aimed to systematically identify the SWEET gene family members and detect the regulation of gene expression and their potential roles of the SWEET gene family in Brassica juncea.

RESULTS

A total of 66 BjSWEET (Brassica juncea Sugar Will Eventually be Exported Transporter) genes distributed across 17 chromosomes were identified. The gene structure and motifs were relatively conserved, with all members containing the MtN3/saliva domain. Phylogenetic analysis revealed that the SWEET gene family can be classified into four subfamilies (Clades I, II, III, and IV). Collinearity analysis revealed that there were 118 pairs of segment duplicates, indicating that some BjSWEET genes were obtained via segmental duplication. The promoter regions of the BjSWEET genes contained many plant hormone-related response elements, stress-related response elements, growth and development elements, and light-responsive regulatory elements. Furthermore, analysis of the expression profiles revealed that the expression levels of the BjSWEET genes differed among the eight different tissues. qRT‒PCR analysis of six selected BjSWEET genes revealed that the expression levels of BjSWEET17.2, BjSWEET17.4, BjSWEET12.2, and BjSWEET12.3 were significantly upregulated under drought treatment, suggesting that these genes may respond to drought stress in B. juncea.

CONCLUSION

This study systematically identified and analyzed the SWEET gene family members in B. juncea for the first time, laying the foundation for further research on the molecular mechanisms of drought resistance in B. juncea and providing theoretical guidance for the application of these genes in other species.

Genome-wide identification and expression analyses of SWEET gene family reveal potential roles in plant development, fruit ripening and abiotic stress responses in cranberry (Vaccinium macrocarpon Ait)

The sugars will eventually be exported transporter (SWEET) family is a novel class of sugar transporters that play a crucial role in plant growth, development, and responses to stress. Cranberry (Vaccinium macrocarpon Ait.) is a nutritious berry with economic importance, but little is known about SWEET gene family functions in this small fruit. In this research, 13 VmSWEET genes belonging to four clades were identified in the cranberry genome for the first time. In the conserved domains, we observed seven phosphorylation sites and four amino acid residues that might be crucial for the binding function. The majority of VmSWEET genes in each clade shared similar gene structures and conserved motifs, showing that the VmSWEET genes were highly conserved during evolution. Chromosomal localization and duplication analyses showed that VmSWEET genes were unevenly distributed in eight chromosomes and two pairs of them displayed synteny. A total of 79 cis-acting elements were predicted in the promoter regions of VmSWEETs including elements responsive to plant hormones, light, growth and development and stress responses. qRT-PCR analysis showed that VmSWEET10.1 was highly expressed in flowers, VmSWEET16 was highly expressed in upright and runner stems, and VmSWEET3 was highly expressed in the leaves of both types of stems. In fruit, the expression of VmSWEET14 and VmSWEET16 was highest of all members during the young fruit stage and were downregulated as fruit matured. The expression of VmSWEET4 was higher during later developmental stages than earlier developmental stages. Furthermore, qRT-PCR results revealed a significant up-regulation of VmSWEET10.2, under osmotic, saline, salt-alkali, and aluminum stress conditions, suggesting it has a crucial role in mediating plant responses to various environmental stresses. Overall, these results provide new insights into the characteristics and evolution of VmSWEET genes. Moreover, the candidate VmSWEET genes involved in the growth, development and abiotic stress responses can be used for molecular breeding to improve cranberry fruit quality and abiotic stress resistance.

Genome-wide identification of Gα family in grass carp (Ctenopharyngodon idella) and reproductive regulation functional characteristics of Cignaq

BACKGROUND

The Gα family plays a crucial role in the complex reproductive regulatory network of teleosts. However, the characterization and function of Gα family members, especially Gαq, remain poorly understood in teleosts. To analyze the characterization, expression, and function of grass carp (Ctenopharyngodon idella) Gαq, we identified the Gα family members in grass carp genome, and analyzed the expression, distribution, and signal transduction of Gαq/gnaq. We also explored the role of Gαq in the reproductive regulation of grass carp.

RESULTS

Our results showed that the grass carp genome contains 27 Gα genes with 46 isoforms, which are divided into four subfamilies: Gαs, Gαi/o, Gαq/11, and Gα12/13. The expression level of Cignaq in the testis was the highest and significantly higher than in other tissues, followed by the hypothalamus and brain. The luteinizing hormone receptor (LHR) was mainly localized to the nucleus in grass carp oocytes, with signals also present in follicular cells. In contrast, Gαq signal was mainly found in the cytoplasm of oocytes, with no signal in follicular cells. In the testis, Gαq and LHR were co-localized in the cytoplasm. Furthermore, the grass carp Gαq recombinant protein significantly promoted Cipgr expression.

CONCLUSIONS

These results provided preliminary evidence for understanding the role of Gαq in the reproductive regulation of teleosts.

Sugar sensing in C4 source leaves: a gap that needs to be filled

Plant growth depends on sugar production and export by photosynthesizing source leaves and sugar allocation and import by sink tissues (grains, roots, stems, and young leaves). Photosynthesis and sink demand are tightly coordinated through metabolic (substrate, allosteric) feedback and signalling (sugar, hormones) mechanisms. Sugar signalling integrates sugar production with plant development and environmental cues. In C3 plants (e.g. wheat and rice), it is well documented that sugar accumulation in source leaves, due to source-sink imbalance, negatively feeds back on photosynthesis and plant productivity. However, we have a limited understanding about the molecular mechanisms underlying those feedback regulations, especially in C4 plants (e.g. maize, sorghum, and sugarcane). Recent work with the C4 model plant Setaria viridis suggested that C4 leaves have different sugar sensing thresholds and behaviours relative to C3 counterparts. Addressing this research priority is critical because improving crop yield requires a better understanding of how plants coordinate source activity with sink demand. Here we review the literature, present a model of action for sugar sensing in C4 source leaves, and suggest ways forward.

Genome-Wide Analysis of the Auxin/Indoleacetic Acid (Aux/IAA) Gene Family in Autopolyploid Sugarcane (Saccharum spontaneum)

The auxin/indoleacetic acid (Aux/IAA) family plays a central role in regulating gene expression during auxin signal transduction. Nonetheless, there is limited knowledge regarding this gene family in sugarcane. In this study, 92 members of the IAA family were identified in Saccharum spontaneum, distributed on 32 chromosomes, and classified into three clusters based on phylogeny and motif compositions. Segmental duplication and recombination events contributed largely to the expansion of this superfamily. Additionally, cis-acting elements in the promoters of SsIAAs involved in plant hormone regulation and stress responsiveness were predicted. Transcriptomics data revealed that most SsIAA expressions were significantly higher in stems and basal parts of leaves, and at nighttime, suggesting that these genes might be involved in sugar transport. QRT-PCR assays confirmed that cold and salt stress significantly induced four and five SsIAAs, respectively. GFP-subcellular localization showed that SsIAA23 and SsIAA12a were localized in the nucleus, consistent with the results of bioinformatics analysis. In conclusion, to a certain extent, the functional redundancy of family members caused by the expansion of the sugarcane IAA gene family is related to stress resistance and regeneration of sugarcane as a perennial crop. This study reveals the gene evolution and function of the SsIAA gene family in sugarcane, laying the foundation for further research on its mode of action.

Genome-wide identification of JAZ gene family in sugarcane and function analysis of ScJAZ1/2 in drought stress response and flowering regulation

The JASMONATE ZIM DOMAIN (JAZ) proteins are a key inhibitors of the jasmonic acid (JA) signaling pathway that play an important role in the regulation of plant growth and development and environmental stress responses. However, there is no systematic identification and functional analysis of JAZ gene family members in sugarcane. In this study, a total of 49 SsJAZ genes were identified from the wild sugarcane species Saccharum spontaneum genome that were unevenly distributed on 13 chromosomes. Phylogenetic analysis showed that all SsJAZ members can be divided into six groups, and most of the SsJAZ genes contained photoreactive and ABA-responsive elements. RNA-seq analysis revealed that SsJAZ1-1/2/3/4 and SsJAZ7-1 were significantly upregulated under drought stress. The transcript level of ScJAZ1 which is the homologous gene of SsJAZ1 in modern sugarcane cultivars was upregulated by JA, PEG, and abscisic acid (ABA). Moreover, ScJAZ1 can interact with three other JAZ proteins to form heterodimers. The spatial and temporal expression analysis showed that SsJAZ2-1/2/3/4 were highly expressed in different tissues and growth stages and during the day-night rhythm between 10:00 and 18:00. Overexpression of ScJAZ2 in Arabidopsis accelerated flowering through activating the expression of AtSOC1, AtFT, and AtLFY. Moreover, the transcription level of ScJAZ2 was about 30-fold in the early-flowering sugarcane variety than that of the non-flowering variety, indicating ScJAZ2 positively regulated flowering. This first systematic analysis of the JAZ gene family and function analysis of ScJAZ1/2 in sugarcane provide key candidate genes and lay the foundation for sugarcane breeding.

Transcriptome and small RNA analysis unveils novel insights into the C4 gene regulation in sugarcane

MAIN CONCLUSION

This study reveals miRNA indirect regulation of C4 genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a. C4 photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C4 genes in sugarcane remains elusive. We have identified 384 miRNAs along the leaf gradients, including 293 known miRNAs and 91 novel miRNAs. Among these, 86 unique miRNAs exhibited differential expression patterns, and we identified 3511 potential expressed targets of these differentially expressed miRNAs (DEmiRNAs). Analyses using Pearson correlation coefficient (PCC) and Gene Ontology (GO) enrichment revealed that targets of miRNAs with positive correlations are integral to chlorophyll-related photosynthetic processes. In contrast, negatively correlated pairs are primarily associated with metabolic functions. It is worth noting that no C4 genes were predicted as targets of DEmiRNAs. Our application of weighted gene co-expression network analysis (WGCNA) led to a gene regulatory network (GRN) suggesting miRNAs might indirectly regulate C4 genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C4 genes, targeted by miR171y and miR171am, and exhibiting a negative correlation with miRNA expression along the leaf gradient. This study sheds light on the complex involvement of miRNAs in regulating C4 genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.

Current perspectives on the regulatory mechanisms of sucrose accumulation in sugarcane

Sugars transported from leaves (source) to stems (sink) energize cell growth, elongation, and maintenance. which are regulated by a variety of genes. This review reflects progress and prospects in the regulatory mechanism for maximum sucrose accumulation, including the role of sucrose metabolizing enzymes, sugar transporters and the elucidation of post-transcriptional control of sucrose-induced regulation of translation (SIRT) in the accumulation of sucrose. The current review suggests that SIRT is emerging as a significant mechanism controlling Scbzip44 activities in response to endogenous sugar signals (via the negative feedback mechanism). Sucrose-controlled upstream open reading frame (SC-uORF) exists at the 5' leader region of Scbzip44's main ORF, which inhibits sucrose accumulation through post-transcriptional regulatory mechanisms. Sucrose transporters (SWEET1a/4a/4b/13c, TST, SUT1, SUT4 and SUT5) are crucial for sucrose translocation from source to sink. Particularly, SWEET13c was found to be a major contributor to the efflux in the transportation of stems. Tonoplast sugar transporters (TSTs), which import sucrose into the vacuole, suggest their tissue-specific role from source to sink. Sucrose cleavage has generally been linked with invertase isozymes, whereas sucrose synthase (SuSy)-catalyzed metabolism has been associated with biosynthetic processes such as UDP-Glc, cellulose, hemicellulose and other polymers. However, other two key sucrose-metabolizing enzymes, such as sucrose-6-phosphate phosphohydrolase (S6PP) and sucrose phosphate synthase (SPS) isoforms, have been linked with sucrose biosynthesis. These findings suggest that manipulation of genes, such as overexpression of SPS genes and sucrose transporter genes, silencing of the SC-uORF of Scbzip44 (removing the 5' leader region of the main ORF that is called SIRT-Insensitive) and downregulation of the invertase genes, may lead to maximum sucrose accumulation. This review provides an overview of sugarcane sucrose-regulating systems and baseline information for the development of cultivars with higher sucrose accumulation.

Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum

BACKGROUND

Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes.

RESULTS

Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases.

CONCLUSIONS

This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.

Molecular Cloning, Expression Analysis, and Functional Analysis of Nine IbSWEETs in Ipomoea batatas (L.) Lam

Sugar Will Eventually be Exported Transporter (SWEET) genes play an important regulatory role in plants' growth and development, stress response, and sugar metabolism, but there are few reports on the role of SWEET proteins in sweet potato. In this study, nine IbSWEET genes were obtained via PCR amplification from the cDNA of sweet potato. Phylogenetic analysis showed that nine IbSWEETs separately belong to four clades (Clade I~IV) and contain two MtN3/saliva domains or PQ-loop superfamily and six~seven transmembrane domains. Protein interaction prediction showed that seven SWEETs interact with other proteins, and SWEETs interact with each other (SWEET1 and SWEET12; SWEET2 and SWEET17) to form heterodimers. qRT-PCR analysis showed that IbSWEETs were tissue-specific, and IbSWEET1b was highly expressed during root growth and development. In addition to high expression in leaves, IbSWEET15 was also highly expressed during root expansion, and IbSWEET7, 10a, 10b, and 12 showed higher expression in the leaves. The expression of SWEETs showed a significant positive/negative correlation with the content of soluble sugar and starch in storage roots. Under abiotic stress treatment, IbSWEET7 showed a strong response to PEG treatment, while IbSWEET10a, 10b, and 12 responded significantly to 4 °C treatment and, also, at 1 h after ABA, to NaCl treatment. A yeast mutant complementation assay showed that IbSWEET7 had fructose, mannose, and glucose transport activity; IbSWEET15 had glucose transport activity and weaker sucrose transport activity; and all nine IbSWEETs could transport 2-deoxyglucose. These results provide a basis for further elucidating the functions of SWEET genes and promoting molecular breeding in sweet potato.

Spatial expression patterns of genes encoding sugar sensors in leaves of C4 and C3 grasses

BACKGROUND AND AIMS

The mechanisms of sugar sensing in grasses remain elusive, especially those using C4 photosynthesis even though a large proportion of the world's agricultural crops utilize this pathway. We addressed this gap by comparing the expression of genes encoding components of sugar sensors in C3 and C4 grasses, with a focus on source tissues of C4 grasses. Given C4 plants evolved into a two-cell carbon fixation system, it was hypothesized this may have also changed how sugars were sensed.

METHODS

For six C3 and eight C4 grasses, putative sugar sensor genes were identified for target of rapamycin (TOR), SNF1-related kinase 1 (SnRK1), hexokinase (HXK) and those involved in the metabolism of the sugar sensing metabolite trehalose-6-phosphate (T6P) using publicly available RNA deep sequencing data. For several of these grasses, expression was compared in three ways: source (leaf) versus sink (seed), along the gradient of the leaf, and bundle sheath versus mesophyll cells.

KEY RESULTS

No positive selection of codons associated with the evolution of C4 photosynthesis was identified in sugar sensor proteins here. Expressions of genes encoding sugar sensors were relatively ubiquitous between source and sink tissues as well as along the leaf gradient of both C4 and C3 grasses. Across C4 grasses, SnRK1β1 and TPS1 were preferentially expressed in the mesophyll and bundle sheath cells, respectively. Species-specific differences of gene expression between the two cell types were also apparent.

CONCLUSIONS

This comprehensive transcriptomic study provides an initial foundation for elucidating sugar-sensing genes within major C4 and C3 crops. This study provides some evidence that C4 and C3 grasses do not differ in how sugars are sensed. While sugar sensor gene expression has a degree of stability along the leaf, there are some contrasts between the mesophyll and bundle sheath cells.

Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

BACKGROUND

Dendrobium officinale Kimura et Migo (D. officinale) is a well-known traditional Chinese medicine with high content polysaccharides in stems. The SWEET (Sugars Will Eventually be Exported Transporters) family is a novel class of sugar transporters mediating sugar translocation among adjacent cells of plants. The expression patterns of SWEETs and whether they are associated with stress response in D. officinale remains uncovered.

RESULTS

Here, 25 SWEET genes were screened out from D. officinale genome, most of which typically contained seven transmembrane domains (TMs) and harbored two conserved MtN3/saliva domains. Using multi-omics data and bioinformatic approaches, the evolutionary relationship, conserved motifs, chromosomal location, expression patterns, correlationship and interaction network were further analyzed. DoSWEETs were intensively located in nine chromosomes. Phylogenetic analysis revealed that DoSWEETs were divided into four clades, and conserved motif 3 specifically existed in DoSWEETs from clade II. Different tissue-specific expression patterns of DoSWEETs suggested the division of their roles in sugar transport. In particular, DoSWEET5b, 5c, and 7d displayed relatively high expression levels in stems. DoSWEET2b and 16 were significantly regulated under cold, drought, and MeJA treatment, which were further verified using RT-qPCR. Correlation analysis and interaction network prediction discovered the internal relationship of DoSWEET family.

CONCLUSIONS

Taken together, the identification and analysis of the 25 DoSWEETs in this study provide basic information for further functional verification in D. officinale.

The role of SWEET4 proteins in the post-phloem sugar transport pathway of Setaria viridis sink tissues

In the developing seeds of all higher plants, filial cells are symplastically isolated from the maternal tissue supplying photosynthate to the reproductive structure. Photoassimilates must be transported apoplastically, crossing several membrane barriers, a process facilitated by sugar transporters. Sugars Will Eventually be Exported Transporters (SWEETs) have been proposed to play a crucial role in apoplastic sugar transport during phloem unloading and the post-phloem pathway in sink tissues. Evidence for this is presented here for developing seeds of the C4 model grass Setaria viridis. Using immunolocalization, SvSWEET4 was detected in various maternal and filial tissues within the seed along the sugar transport pathway, in the vascular parenchyma of the pedicel, and in the xylem parenchyma of the stem. Expression of SvSWEET4a in Xenopus laevis oocytes indicated that it functions as a high-capacity glucose and sucrose transporter. Carbohydrate and transcriptional profiling of Setaria seed heads showed that there were some developmental shifts in hexose and sucrose content and consistent expression of SvSWEET4 homologues. Collectively, these results provide evidence for the involvement of SWEETs in the apoplastic transport pathway of sink tissues and allow a pathway for post-phloem sugar transport into the seed to be proposed.

Transcriptome dynamics provides insights into divergences of the photosynthesis pathway between Saccharum officinarum and Saccharum spontaneum

Saccharum spontaneum and Saccharum officinarum contributed to the genetic background of modern sugarcane cultivars. Saccharum spontaneum has shown a higher net photosynthetic rate and lower soluble sugar than S. officinarum. Here, we analyzed 198 RNA-sequencing samples to investigate the molecular mechanisms for the divergences of photosynthesis and sugar accumulation between the two Saccharum species. We constructed gene co-expression networks based on differentially expressed genes (DEGs) both for leaf developmental gradients and diurnal rhythm. Our results suggested that the divergence of sugar accumulation may be attributed to the enrichment of major carbohydrate metabolism and the oxidative pentose phosphate pathway. Compared with S. officinarum, S. spontaneum DEGs showed a high enrichment of photosynthesis and contained more complex regulation of photosynthesis-related genes. Noticeably, S. spontaneum lacked gene interactions with sulfur assimilation stimulated by photorespiration. In S. spontaneum, core genes related to clock and photorespiration displayed a sensitive regulation by the diurnal rhythm and phase-shift. Small subunit of Rubisco (RBCS) displayed higher expression in the source tissues of S. spontaneum. Additionally, it was more sensitive under a diurnal rhythm, and had more complex gene networks than that in S. officinarum. This indicates that the differential regulation of RBCS Rubisco contributed to photosynthesis capacity divergence in both Saccharum species.

Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum

BACKGROUND

B-box (BBX) zinc-finger transcription factors play crucial roles in plant growth, development, and abiotic stress responses. Nevertheless, little information is available on sugarcane (Saccharum spp.) BBX genes and their expression profiles.

RESULTS

In the present study, we characterized 25 SsBBX genes in the Saccharum spontaneum genome database. The phylogenetic relationships, gene structures, and expression patterns of these genes during plant growth and under low-nitrogen conditions were systematically analyzed. The SsBBXs were divided into five groups based on phylogenetic analysis. The evolutionary analysis further revealed that whole-genome duplications or segmental duplications were the main driving force for the expansion of the SsBBX gene family. The expression data suggested that many BBX genes (e.g., SsBBX1 and SsBBX13) may be helpful in both plant growth and low-nitrogen stress tolerance.

CONCLUSIONS

The results of this study offer new evolutionary insight into the BBX family members in how sugarcane grows and responds to stress, which will facilitate their utilization in cultivated sugarcane breeding.

Genome-wide characterization and expression analysis of the growth-regulating factor family in Saccharum

BACKGROUND

Growth regulating factors (GRFs) are transcription factors that regulate diverse biological and physiological processes in plants, including growth, development, and abiotic stress. Although GRF family genes have been studied in a variety of plant species, knowledge about the identification and expression patterns of GRFs in sugarcane (Saccharum spp.) is still lacking.

RESULTS

In the present study, a comprehensive analysis was conducted in the genome of wild sugarcane (Saccharum spontaneum) and 10 SsGRF genes were identified and characterized. The phylogenetic relationship, gene structure, and expression profiling of these genes were analyzed entirely under both regular growth and low-nitrogen stress conditions. Phylogenetic analysis suggested that the 10 SsGRF members were categorized into six clusters. Gene structure analysis indicated that the SsGRF members in the same group were greatly conserved. Expression profiling demonstrated that most SsGRF genes were extremely expressed in immature tissues, implying their critical roles in sugarcane growth and development. Expression analysis based on transcriptome data and real-time quantitative PCR verification revealed that GRF1 and GRF3 were distinctly differentially expressed in response to low-nitrogen stress, which meant that they were additional participated in sugarcane stress tolerance.

CONCLUSION

Our study provides a scientific basis for the potential functional prediction of SsGRF and will be further scrutinized by examining their regulatory network in sugarcane development and abiotic stress response, and ultimately facilitating their application in cultivated sugarcane breeding.

Phylogenetic analysis and structural prediction reveal the potential functional diversity between green algae SWEET transporters

Sugar-Will-Eventually-be-Exported-Transporters (SWEETs) are an important family of sugar transporters that appear to be ubiquitous in all organisms. Recent research has determined the structure of SWEETs in higher plants, identified specific residues required for monosaccharide or disaccharide transport, and begun to understand the specific functions of individual plant SWEET proteins. However, in green algae (Chlorophyta) these transporters are poorly characterised. This study identified SWEET proteins from across representative Chlorophyta with the aim to characterise their phylogenetic relationships and perform protein structure modelling in order to inform functional prediction. The algal genomes analysed encoded between one and six SWEET proteins, which is much less than a typical higher plant. Phylogenetic analysis identified distinct clusters of over 70 SWEET protein sequences, taken from almost 30 algal genomes. These clusters remain separate from representative higher or non-vascular plant SWEETs, but are close to fungi SWEETs. Subcellular localisation predictions and analysis of conserved amino acid residues revealed variation between SWEET proteins of different clusters, suggesting different functionality. These findings also showed conservation of key residues at the substrate-binding site, indicating a similar mechanism of substrate selectivity and transport to previously characterised higher plant monosaccharide-transporting SWEET proteins. Future work is now required to confirm the predicted sugar transport specificity and determine the functional role of these algal SWEET proteins.

Functional characterization and analysis of transcriptional regulation of sugar transporter SWEET13c in sugarcane Saccharum spontaneum

BACKGROUND

Sugarcane is an important crop for sugar production worldwide. The Sugars Will Eventually be Exported Transporters (SWEETs) are a group of sugar transporters recently identified in sugarcane. In Saccharum spontaneum, SsSWEET13c played a role in the sucrose transportation from the source to the sink tissues, which was found to be mainly active in the mature leaf. However, the function and regulation of SWEETs in sugarcane remain elusive despite extensive studies performed on sugar metabolism.

RESULTS

In this study, we showed that SsSWEET13c is a member of SWEET gene family in S. spontaneum, constituting highest circadian rhythm-dependent expression. It is a functional gene that facilitates plant root elongation and increase fresh weight of Arabidopsis thaliana, when overexpressed. Furthermore, yeast one-hybrid assays indicate that 20 potential transcription factors (TFs) could bind to the SsSWEET13c promoter in S. spontaneum. We combined transcriptome data from developmental gradient leaf with distinct times during circadian cycles and stems/leaves at different growth stages. We have uncovered that 14 out of 20 TFs exhibited positive/negative gene expression patterns relative to SsSWEET13c. In the source tissues, SsSWEET13c was mainly positively regulated by SsbHLH34, SsTFIIIA-a, SsMYR2, SsRAP2.4 and SsbHLH035, while negatively regulated by SsABS5, SsTFIIIA-b and SsERF4. During the circadian rhythm, it was noticed that SsSWEET13c was more active in the morning than in the afternoon. It was likely due to the high level of sugar accumulation at night, which was negatively regulated by SsbZIP44, and positively regulated by SsbHLH34. Furthermore, in the sink tissues, SsSWEET13c was also active for sugar accumulation, which was positively regulated by SsbZIP44, SsTFIIIA-b, SsbHLH34 and SsTFIIIA-a, and negatively regulated by SsERF4, SsHB36, SsDEL1 and SsABS5. Our results were further supported by one-to-one yeast hybridization assay which verified that 12 potential TFs could bind to the promoter of SsSWEET13c.

CONCLUSIONS

A module of the regulatory network was proposed for the SsSWEET13c in the developmental gradient of leaf and circadian rhythm in S. spontaneum. These results provide a novel understanding of the function and regulation of SWEET13c during the sugar transport and biomass production in S. spontaneum.

Evolutionary and Gene Expression Analyses Reveal New Insights into the Role of LSU Gene-Family in Plant Responses to Sulfate-Deficiency

LSU proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. In the last few years, LSUs have arisen as relevant hubs in protein–protein interaction networks, in which they play relevant roles in the response to abiotic and biotic stresses. Most of our knowledge on LSU genomic organization, expression and function comes from studies in Arabidopsis and tobacco, while little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole-genome sequences available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta-specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Protein sequence analyses showed four new motifs that further support the subgroup classification by phylogenetic analyses. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S deficiency, suggesting that these genes might play a key role in S stress responses. In summary, our results indicate that LSU genes belong to the Spermatophyta-specific gene family and their response to S deficiency is conserved in angiosperms.

Contributions of sugar transporters to crop yield and fruit quality

The flux, distribution, and storage of soluble sugars regulate crop yield in terms of starch, oil, protein, and total carbohydrates, and affect the quality of many horticultural products. Sugar transporters contribute to phloem loading and unloading. The mechanisms of phloem loading have been studied in detail, but the complex and diverse mechanisms of phloem unloading and sugar storage in sink organs are less explored. Unloading and subsequent transport mechanisms for carbohydrates vary in different sink organs. Analyzing the transport and storage mechanisms of carbohydrates in important storage organs, such as cereal seeds, fruits, or stems of sugarcane, will provide information for genetic improvements to increase crop yield and fruit quality. This review discusses current research progress on sugar transporters involved in carbohydrate unloading and storage in sink organs. The roles of sugar transporters in crop yield and the accumulation of sugars are also discussed to highlight their contribution to efficient breeding.

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

Members of the sugars will eventually be exported transporter (SWEET) family regulate the transport of different sugars through the cell membrane and control the distribution of sugars inside and outside the cell. The SWEET gene family also plays important roles in plant growth and development and physiological processes. So far, there are no reports on the SWEET family in pomegranate. Meanwhile, pomegranate is rich in sugar, and three published pomegranate genome sequences provide resources for the study of the SWEET gene family. 20 PgSWEETs from pomegranate and the known Arabidopsis and grape SWEETs were divided into four clades (Ⅰ, Ⅱ, Ⅲ and Ⅳ) according to the phylogenetic relationships. PgSWEETs of the same clade share similar gene structures, predicting their similar biological functions. RNA-Seq data suggested that PgSWEET genes have a tissue-specific expression pattern. Foliar application of tripotassium phosphate significantly increased the total soluble sugar content of pomegranate fruits and leaves and significantly affected the expression levels of PgSWEETs. The plant growth hormone regulator assay also significantly affected the PgSWEETs expression both in buds of bisexual and functional male flowers. Among them, we selected PgSWEET17a as a candidate gene that plays a role in fructose transport in leaves. The 798 bp CDS sequence of PgSWEET17a was cloned, which encodes 265 amino acids. The subcellular localization of PgSWEET17a showed that it was localized to the cell membrane, indicating its involvement in sugar transport. Transient expression results showed that tobacco fructose content was significantly increased with the up-regulation of PgSWEET17a, while both sucrose and glucose contents were significantly down-regulated. The integration of the PgSWEET phylogenetic tree, gene structure and RNA-Seq data provide a genome-wide trait and expression pattern. Our findings suggest that tripotassium phosphate and plant exogenous hormone treatments could alter PgSWEET expression patterns. These provide a reference for further functional verification and sugar metabolism pathway regulation of PgSWEETs.

Elucidating the role of SWEET13 in phloem loading of the C4 grass Setaria viridis

Photosynthetic efficiency and sink demand are tightly correlated with rates of phloem loading, where maintaining low cytosolic sugar concentrations is paramount to prevent the downregulation of photosynthesis. Sugars Will Eventually be Exported Transporters (SWEETs) are thought to have a pivotal role in the apoplastic phloem loading of C₄ grasses. SWEETs have not been well studied in C₄ species, and their investigation is complicated by photosynthesis taking place across two cell types and, therefore, photoassimilate export can occur from either one. SWEET13 homologues in C₄ grasses have been proposed to facilitate apoplastic phloem loading. Here, we provide evidence for this hypothesis using the C₄ grass Setaria viridis. Expression analyses on the leaf gradient of C₄ species Setaria and Sorghum bicolor show abundant transcript levels for SWEET13 homologues. Carbohydrate profiling along the Setaria leaf shows total sugar content to be significantly higher in the mature leaf tip compared with the younger tissue at the base. We present the first known immunolocalization results for SvSWEET13a and SvSWEET13b using novel isoform-specific antisera. These results show localization to the bundle sheath and phloem parenchyma cells of both minor and major veins. We further present the first transport kinetics study of C₄ monocot SWEETs by using a Xenopus laevis oocyte heterologous expression system. We demonstrate that SvSWEET13a and SvSWEET13b are high-capacity transporters of glucose and sucrose, with a higher apparent V_max for sucrose, compared with glucose, typical of clade III SWEETs. Collectively, these results provide evidence for an apoplastic phloem loading pathway in Setaria and possibly other C₄ species.

Sugar transporters of the SWEET family and their role in arbuscular mycorrhiza

Plant sugar transporters play an essential role in the organism’s productivity by carrying out carbohydrate transportation from source cells in the leaves to sink cells in the cortex. In addition, they aid in the regulation of a substantial part of the exchange of nutrients with microorganisms in the rhizosphere (bacteria and fungi), an ty essential to the formation of symbiotic relationships. This review pays special attention to carbohydrate nutrition during the development of arbuscular mycorrhiza (AM), a symbiosis of plants with fungi from the Glomeromycotina subdivision. This relationship results in the host plant receiving micronutrients from the mycosymbiont, mainly phosphorus, and the fungus receiving carbon assimilation products in return. While the eff icient nutrient transport pathways in AM symbiosis are yet to be discovered, SWEET sugar transporters are one of the three key families of plant carbohydrate transporters. Specif ic AM symbiosis transporters can be identif ied among the SWEET proteins. The survey provides data on the study history, structure and localization, phylogeny and functions of the SWEET proteins. A high variability of both the SWEET proteins themselves and their functions is noted along with the fact that the same proteins may perform different functions in different plants. A special role is given to the SWEET transporters in AM development. SWEET transporters can also play a key role in abiotic stress tolerance, thus allowing plants to adapt to adverse environmental conditions. The development of knowledge about symbiotic systems will contribute to the creation of microbial preparations for use in agriculture in the Russian Federation.

Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane

Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.

Improving C4 photosynthesis to increase productivity under optimal and suboptimal conditions

Although improving photosynthetic efficiency is widely recognized as an underutilized strategy to increase crop yields, research in this area is strongly biased towards species with C3 photosynthesis relative to C4 species. Here, we outline potential strategies for improving C4 photosynthesis to increase yields in crops by reviewing the major bottlenecks limiting the C4 NADP-malic enzyme pathway under optimal and suboptimal conditions. Recent experimental results demonstrate that steady-state C4 photosynthesis under non-stressed conditions can be enhanced by increasing Rubisco content or electron transport capacity, both of which may also stimulate CO2 assimilation at supraoptimal temperatures. Several additional putative bottlenecks for photosynthetic performance under drought, heat, or chilling stress or during photosynthetic induction await further experimental verification. Based on source-sink interactions in maize, sugarcane, and sorghum, alleviating these photosynthetic bottlenecks during establishment and growth of the harvestable parts are likely to improve yield. The expected benefits are also shown to be augmented by the increasing trend in planting density, which increases the impact of photosynthetic source limitation on crop yields.

Genome-wide identification of candidate aquaporins involved in water accumulation of pomegranate outer seed coat

Aquaporins (AQPs) are a class of highly conserved integral membrane proteins that facilitate the uptake and transport of water and other small molecules across cell membranes. However, little is known about AQP genes in pomegranate (Punica granatum L.) and their potential role in water accumulation of the outer seed coat. We identified 38 PgrAQP genes in the pomegranate genome and divided them into five subfamilies based on a comparative analysis. Purifying selection played a role in the evolution of PgrAQP genes and a whole-genome duplication event in Myrtales may have contributed to the expansion of PgrTIP, PgrSIP, and PgrXIP genes. Transcriptome data analysis revealed that the PgrAQP genes exhibited different tissue-specific expression patterns. Among them, the transcript abundance of PgrPIPs were significantly higher than that of other subfamilies. The mRNA transcription levels of PgrPIP1.3, PgrPIP2.8, and PgrSIP1.2 showed a significant linear relationship with water accumulation in seed coats, indicating that PgrPIP1.3/PgrPIP2.8 located in the plasma membrane and PgrSIP1.2 proteins located on the tonoplast may be involved in water accumulation and contribute to the cell expansion of the outer seed coat, which then develops into juicy edible flesh. Overall, our results provided not only information on the characteristics and evolution of PgrAQPs, but also insights on the genetic improvement of outer seed coats.

Genome-wide identification and expression profiling of DREB genes in Saccharum spontaneum

Background

The dehydration-responsive element-binding proteins (DREBs) are important transcription factors that interact with a DRE/CRT (C-repeat) sequence and involve in response to multiple abiotic stresses in plants. Modern sugarcane are hybrids from the cross between Saccharum spontaneum and Saccharum officinarum, and the high sugar content is considered to the attribution of S. officinaurm, while the stress tolerance is attributed to S. spontaneum. To understand the molecular and evolutionary characterization and gene functions of the DREBs in sugarcane, based on the recent availability of the whole genome information, the present study performed a genome-wide in silico analysis of DREB genes and transcriptome analysis in the polyploidy S. spontaneum.

Results

Twelve DREB1 genes and six DREB2 genes were identified in S. spontaneum genome and all proteins contained a conserved AP2/ERF domain. Eleven SsDREB1 allele genes were assumed to be originated from tandem duplications, and two of them may be derived after the split of S. spontaneum and the proximal diploid species sorghum, suggesting tandem duplication contributed to the expansion of DREB1-type genes in sugarcane. Phylogenetic analysis revealed that one DREB2 gene was lost during the evolution of sugarcane. Expression profiling showed different SsDREB genes with variable expression levels in the different tissues, indicating seven SsDREB genes were likely involved in the development and photosynthesis of S. spontaneum. Furthermore, SsDREB1F, SsDREB1L, SsDREB2D, and SsDREB2F were up-regulated under drought and cold condition, suggesting that these four genes may be involved in both dehydration and cold response in sugarcane.

Conclusions

These findings demonstrated the important role of DREBs not only in the stress response, but also in the development and photosynthesis of S. spontaneum.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07799-5.

Plant SWEETs: from sugar transport to plant-pathogen interaction and more unexpected physiological roles

Sugars Will Eventually be Exported Transporters (SWEETs) have important roles in numerous physiological mechanisms where sugar efflux is critical, including phloem loading, nectar secretion, seed nutrient filling, among other less expected functions. They mediate low affinity and high capacity transport, and in angiosperms this family is composed by 20 paralogs on average. As SWEETs facilitate the efflux of sugars, they are highly susceptible to hijacking by pathogens, making them central players in plant-pathogen interaction. For instance, several species from the Xanthomonas genus are able to upregulate the transcription of SWEET transporters in rice (Oryza sativa), upon the secretion of transcription-activator-like effectors. Other pathogens, such as Botrytis cinerea or Erysiphe necator, are also capable of increasing SWEET expression. However, the opposite behavior has been observed in some cases, as overexpression of the tonoplast AtSWEET2 during Pythium irregulare infection restricted sugar availability to the pathogen, rendering plants more resistant. Therefore, a clear-cut role for SWEET transporters during plant-pathogen interactions has so far been difficult to define, as the metabolic signatures and their regulatory nodes, which decide the susceptibility or resistance responses, remain poorly understood. This fuels the still ongoing scientific question: what roles can SWEETs play during plant-pathogen interaction? Likewise, the roles of SWEET transporters in response to abiotic stresses are little understood. Here, in addition to their relevance in biotic stress, we also provide a small glimpse of SWEETs importance during plant abiotic stress, and briefly debate their importance in the particular case of grapevine (Vitis vinifera) due to its socioeconomic impact.

Genome-wide identification and transcriptional analysis of ammonium transporters in Saccharum

Ammonium transporters (AMTs) are plasma membrane proteins that exclusively transport ammonium/ammonia. It is essential for the nitrogen demand of plantsby AMT-mediated acquisition of ammonium from soils. The molecular characteristics and evolutionary history of AMTs in Saccharum spp. remain unclear. We comprehensively evaluated the AMT gene family in the latest release of the S. spontaneum genome and identified 6 novel AMT genes. These genes belong to 3 clusters: AMT2 (2 genes), AMT3 (3 genes), and AMT4 (one gene). Evolutionary analyses suggested that the S. spontaneum AMT gene family may have expanded via whole-genome duplication events. All of the 6 AMT genes are located on 5 chromosomes of S. spontaneum. Expression analyses revealed that AMT3;2 was highly expressed in leaves and in the daytime, and AMT2;1/3;2/4 were dynamic expressed in different leaf segments, as well as AMT2;1/3;2 demonstrated a high transcript accumulation level in leaves and roots and were significantly dynamic expressed under low-nitrogen conditions. The results suggest the functional roles of AMT genes on tissue expression and ammonium absorption in Saccharum. This study will provide some reference information for further elucidation of the functional mechanism and regulation of expression of the AMT gene family in Saccharum.

SWEET Transporters and the Potential Functions of These Sequences in Tea (Camellia sinensis)

Tea (Camellia sinensis) is an important economic beverage crop. Its flowers and leaves could be used as healthcare tea for its medicinal value. SWEET proteins were recently identified in plants as sugar transporters, which participate in diverse physiological processes, including pathogen nutrition, seed filling, nectar secretion, and phloem loading. Although SWEET genes have been characterized and identified in model plants, such as Arabidopsis thaliana and Oryza sativa, there is very little knowledge of these genes in C. sinensis. In this study, 28 CsSWEETs were identified in C. sinensis and further phylogenetically divided into four subfamilies with A. thaliana. These identified CsSWEETs contained seven transmembrane helixes (TMHs) which were generated by an ancestral three-TMH unit with an internal duplication experience. Microsynteny analysis revealed that the large-scale duplication events were the main driving forces for members from CsSWEET family expansion in C. sinensis. The expression profiles of the 28 CsSWEETs revealed that some genes were highly expressed in reproductive tissues. Among them, CsSWEET1a might play crucial roles in the efflux of sucrose, and CsSWEET17b could control fructose content as a hexose transporter in C. sinensis. Remarkably, CsSWEET12 and CsSWEET17c were specifically expressed in flowers, indicating that these two genes might be involved in sugar transport during flower development. The expression patterns of all CsSWEETs were differentially regulated under cold and drought treatments. This work provided a systematic understanding of the members from the CsSWEET gene family, which would be helpful for further functional studies of CsSWEETs in C. sinensis.

Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential

Sugarcane (Saccharum spp.), a C₄ grass, has a peculiar feature: it accumulates, gradient-wise, large amounts of carbon (C) as sucrose in its culms through a complex pathway. Apart from being a sustainable crop concerning C efficiency and bioenergetic yield per hectare, sugarcane is used as feedstock for producing ethanol, sugar, high-value compounds, and products (e.g., polymers and succinate), and bioelectricity, earning the title of the world's leading biomass crop. Commercial cultivars, hybrids bearing high levels of polyploidy, and aneuploidy, are selected from a large number of crosses among suitable parental genotypes followed by the cloning of superior individuals among the progeny. Traditionally, these classical breeding strategies have been favoring the selection of cultivars with high sucrose content and resistance to environmental stresses. A current paradigm change in sugarcane breeding programs aims to alter the balance of C partitioning as a means to provide more plasticity in the sustainable use of this biomass for metabolic engineering and green chemistry. The recently available sugarcane genetic assemblies powered by data science provide exciting perspectives to increase biomass, as the current sugarcane yield is roughly 20% of its predicted potential. Nowadays, several molecular phenotyping tools can be applied to meet the predicted sugarcane C potential, mainly targeting two competing pathways: sucrose production/storage and biomass accumulation. Here we discuss how molecular phenotyping can be a powerful tool to assist breeding programs and which strategies could be adopted depending on the desired final products. We also tackle the advances in genetic markers and mapping as well as how functional genomics and genetic transformation might be able to improve yield and saccharification rates. Finally, we review how "omics" advances are promising to speed up plant breeding and reach the unexplored potential of sugarcane in terms of sucrose and biomass production.

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

New insights into the evolution and functional divergence of the CIPK gene family in Saccharum

Background

Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses.

Results

In this study, 48 CIPK genes (SsCIPKs) were identified from the genome of Saccharum spontaneum. Phylogenetic reconstruction suggested that the SsCIPK gene family may have undergone six gene duplication events from the last common ancestor (LCA) of SsCIPKs. Whole-genome duplications (WGDs) served as the driving force for the amplification of SsCIPKs. The Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that the duplicated genes were possibly under strong purifying selection pressure. The divergence time of these duplicated genes had an average duplication time of approximately 35.66 Mya, suggesting that these duplication events occurred after the divergence of the monocots and eudicots (165 Mya). The evolution of gene structure analysis showed that the SsCIPK family genes may involve intron losses. Ten ScCIPK genes were amplified from sugarcane (Saccharum spp. hybrids). The results of real-time quantitative polymerase chain reaction (qRT-PCR) demonstrated that these ten ScCIPK genes had different expression patterns under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) stresses. Prokaryotic expression implied that the recombinant proteins of ScCIPK3, − 15 and − 17 could only slightly enhance growth under salinity stress conditions, but the ScCIPK21 did not. Transient N. benthamiana plants overexpressing ScCIPKs demonstrated that the ScCIPK genes were involved in responding to external stressors through the ethylene synthesis pathway as well as to bacterial infections.

Conclusions

In generally, a comprehensive genome-wide analysis of evolutionary relationship, gene structure, motif composition, and gene duplications of SsCIPK family genes were performed in S. spontaneum. The functional study of expression patterns in sugarcane and allogenic expressions in E. coli and N. benthamiana showed that ScCIPKs played various roles in response to different stresses. Thus, these results improve our understanding of the evolution of the CIPK gene family in sugarcane as well as provide a basis for in-depth functional studies of CIPK genes in sugarcane.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07264-9.

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

Dof transcription factors plant-specific and associates with growth and development in plants. We conducted comprehensive and systematic analyses of Dof transcription factors in sugarcane, and identified 29 SsDof transcription factors in sugarcane genome. Those SsDof genes were divided into five groups, with similar gene structures and conserved motifs within the same groups. Segmental duplications are predominant in the evolution of Dof in sugarcane. Cis-element analysis suggested that the functions of SsDofs were involved in growth and development, hormones and abiotic stresses responses in sugarcane. Expression patterns indicated that SsDof7, SsDof23 and SsDof24 had a comparatively high expression in all detected tissues, indicating these genes are crucial in sugarcane growth and development. Moreover, we examined the transcription levels of SsDofs under four plant hormone treatments, SsDof7-3 and SsDof7-4 were down-regulated after ABA treatment, while SsDof7-1 and SsDof7-2 were induced after the same treatment, indicating different alleles may play different roles in response to plant hormones. We also analyzed SsDofs' expression profiling under four abiotic stresses, SsDof5 and SsDof28 significantly responded to these four stresses, indicating they are associate with abiotic stresses responses. Collectively, our results yielded allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane, and their cis-elements could be crucial for sugarcane improvement.

Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum

BACKGROUND

Plant genomes contain a large number of HAK/KUP/KT transporters, which play important roles in potassium uptake and translocation, osmotic potential regulation, salt tolerance, root morphogenesis and plant development. Potassium deficiency in the soil of a sugarcane planting area is serious. However, the HAK/KUP/KT gene family remains to be characterized in sugarcane (Saccharum).

RESULTS

In this study, 30 HAK/KUP/KT genes were identified in Saccharum spontaneum. Phylogenetics, duplication events, gene structures and expression patterns were analyzed. Phylogenetic analysis of the HAK/KUP/KT genes from 15 representative plants showed that this gene family is divided into four groups (clades I-IV). Both ancient whole-genome duplication (WGD) and recent gene duplication contributed to the expansion of the HAK/KUP/KT gene family. Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that purifying selection was the main force driving the evolution of HAK/KUP/KT genes. The divergence time of the HAK/KUP/KT gene family was estimated to range from 134.8 to 233.7 Mya based on Ks analysis, suggesting that it is an ancient gene family in plants. Gene structure analysis showed that the HAK/KUP/KT genes were accompanied by intron gain/loss in the process of evolution. RNA-seq data analysis demonstrated that the HAK/KUP/KT genes from clades II and III were mainly constitutively expressed in various tissues, while most genes from clades I and IV had no or very low expression in the tested tissues at different developmental stages. The expression of SsHAK1 and SsHAK21 was upregulated in response to low-K⁺ stress. Yeast functional complementation analysis revealed that SsHAK1 and SsHAK21 could rescue K⁺ uptake in a yeast mutant.

CONCLUSIONS

This study provided insights into the evolutionary history of HAK/KUP/KT genes. HAK7/9/18 were mainly expressed in the upper photosynthetic zone and mature zone of the stem. HAK7/9/18/25 were regulated by sunlight. SsHAK1 and SsHAK21 played important roles in mediating potassium acquisition under limited K⁺ supply. Our results provide valuable information and key candidate genes for further studies on the function of HAK/KUP/KT genes in Saccharum.

Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement

BACKGROUND

Sorghum bicolor (L.) is an important bioenergy source. The stems of sweet sorghum function as carbon sinks and accumulate large amounts of sugars and lignocellulosic biomass and considerable amounts of starch, therefore providing a model of carbon allocation and accumulation for other bioenergy crops. While omics data sets for sugar accumulation have been reported in different genotypes, the common features of primary metabolism in sweet genotypes remain unclear. To obtain a cohesive and comparative picture of carbohydrate metabolism between sorghum genotypes, we compared the phenotypes and transcriptome dynamics of sugar-accumulating internodes among three different sweet genotypes (Della, Rio, and SIL-05) and two non-sweet genotypes (BTx406 and R9188).

RESULTS

Field experiments showed that Della and Rio had similar dynamics and internode patterns of sugar concentration, albeit distinct other phenotypes. Interestingly, cellulose synthases for primary cell wall and key genes in starch synthesis and degradation were coordinately upregulated in sweet genotypes. Sweet sorghums maintained active monolignol biosynthesis compared to the non-sweet genotypes. Comparative RNA-seq results support the role of candidate Tonoplast Sugar Transporter gene (TST), but not the Sugars Will Eventually be Exported Transporter genes (SWEETs) in the different sugar accumulations between sweet and non-sweet genotypes.

CONCLUSIONS

Comparisons of the expression dynamics of carbon metabolic genes across the RNA-seq data sets identify several candidate genes with contrasting expression patterns between sweet and non-sweet sorghum lines, including genes required for cellulose and monolignol synthesis (CesA, PTAL, and CCR), starch metabolism (AGPase, SS, SBE, and G6P-translocator SbGPT2), and sucrose metabolism and transport (TPP and TST2). The common transcriptome features of primary metabolism identified here suggest the metabolic networks contributing to carbon sink strength in sorghum internodes, prioritize the candidate genes for manipulating carbon allocation with bioenergy purposes, and provide a comparative and cohesive picture of the complexity of carbon sink strength in sorghum stem.

Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

Background

Sugarcane served as the model plant for discovery of the C₄ photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynthesis. In plants, the magnesium transporter (MGT) family is composed of a number of membrane proteins, which play crucial roles in maintaining Mg homeostasis. However, to date there is no information available on the genomics of MGTs in sugarcane due to the complexity of the Saccharum genome.

Results

Here, we identified 10 MGTs from the Saccharum spontaneum genome. Phylogenetic analysis of MGTs suggested that the MGTs contained at least 5 last common ancestors before the origin of angiosperms. Gene structure analysis suggested that MGTs family of dicotyledon may be accompanied by intron loss and pseudoexon phenomena during evolution. The pairwise synonymous substitution rates corresponding to a divergence time ranged from 142.3 to 236.6 Mya, demonstrating that the MGTs are an ancient gene family in plants. Both the phylogeny and Ks analyses indicated that SsMGT1/SsMGT2 originated from the recent ρWGD, and SsMGT7/SsMGT8 originated from the recent σ WGD. These 4 recently duplicated genes were shown low expression levels and assumed to be functionally redundant. MGT6, MGT9 and MGT10 weredominant genes in the MGT family and werepredicted to be located inthe chloroplast. Of the 3 dominant MGTs, SsMGT6 expression levels were found to be induced in the light period, while SsMGT9 and SsMTG10 displayed high expression levels in the dark period. These results suggested that SsMGT6 may have a function complementary to SsMGT9 and SsMTG10 that follows thecircadian clock for MGT in the leaf tissues of S. spontaneum. MGT3, MGT7 and MGT10 had higher expression levels Insaccharum officinarum than in S. spontaneum, suggesting their functional divergence after the split of S. spontaneum and S. officinarum.

Conclusions

This study of gene evolution and expression of MGTs in S. spontaneum provided basis for the comprehensive genomic study of the entire MGT genes family in Saccharum. The results are valuable for further functional analyses of MGT genes and utilization of the MGTs for Saccharum genetic improvement.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5437-3) contains supplementary material, which is available to authorized users.