scholarly journals Identification and expression profile analysis of the sucrose phosphate synthase gene family in Litchi chinensis Sonn.

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4379 ◽  
Author(s):  
Dan Wang ◽  
Jietang Zhao ◽  
Bing Hu ◽  
Jiaqi Li ◽  
Yaqi Qin ◽  
...  
Keyword(s):  
Gene Family ◽  
Profile Analysis ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Sucrose Phosphate Synthase ◽  
Gene Families ◽  
Specific Expression ◽  
Litchi Chinensis ◽  
Sucrose Phosphate ◽  
Phosphate Synthase

Sucrose phosphate synthase (SPS, EC 2.4.1.14) is a key enzyme that regulates sucrose biosynthesis in plants. SPS is encoded by different gene families which display differential expression patterns and functional divergence. Genome-wide identification and expression analyses of SPS gene families have been performed in Arabidopsis, rice, and sugarcane, but a comprehensive analysis of the SPS gene family in Litchi chinensis Sonn. has not yet been reported. In the current study, four SPS gene (LcSPS1, LcSPS2, LcSPS3, and LcSPS4) were isolated from litchi. The genomic organization analysis indicated the four litchi SPS genes have very similar exon-intron structures. Phylogenetic tree showed LcSPS1-4 were grouped into different SPS families (LcSPS1 and LcSPS2 in A family, LcSPS3 in B family, and LcSPS4 in C family). LcSPS1 and LcSPS4 were strongly expressed in the flowers, while LcSPS3 most expressed in mature leaves. RT-qPCR results showed that LcSPS genes expressed differentially during aril development between cultivars with different hexose/sucrose ratios. A higher level of expression of LcSPS genes was detected in Wuheli, which accumulates higher sucrose in the aril at mature. The tissue- and developmental stage-specific expression of LcSPS1-4 genes uncovered in this study increase our understanding of the important roles played by these genes in litchi fruits.

scholarly journals Structure and Expression Analysis of Sucrose Phosphate Synthase, Sucrose Synthase and Invertase Gene Families in Solanum lycopersicum

2021 ◽  
Vol 22 (9) ◽  
pp. 4698
Author(s):  
Yaoke Duan ◽  
Lan Yang ◽  
Haijia Zhu ◽  
Jie Zhou ◽  
Hao Sun ◽  
...  
Keyword(s):  
Solanum Lycopersicum ◽  
Sucrose Synthase ◽  
Sucrose Phosphate Synthase ◽  
Gene Families ◽  
Tissue Expression ◽  
Tissue Expression Pattern ◽  
Structure Characteristics ◽  
Invertase Gene ◽  
Sucrose Phosphate ◽  
Phosphate Synthase

Sucrose phosphate synthase (SPS), sucrose synthase (SUS) and invertase (INV) are all encoded by multigene families. In tomato (Solanum lycopersicum), a comprehensive analysis of structure characteristics of these family genes is still lacking, and the functions of individual isoforms of these families are mostly unclear under stress. Here, the structure characteristics of the three families in tomato were analyzed; moreover, as a first step toward understanding the functions of isoforms of these proteins under stress, the tissue expression pattern and stress response of these genes were also investigated. The results showed that four SPS genes, six SUS genes and nineteen INV genes were identified in tomato. The subfamily differentiation of SlSPS and SlSUS might have completed before the split of monocotyledons and dicotyledons. The conserved motifs were mostly consistent within each protein family/subfamily. These genes demonstrated differential expressions among family members and tissues, and in response to polyethylene glycerol, NaCl, H2O2, abscisic acid or salicylic acid treatment. Our results suggest that each isoform of these families may have different functions in different tissues and under environmental stimuli. SlSPS1, SlSPS3, SlSUS1, SlSUS3, SlSUS4, SlINVAN5 and SlINVAN7 demonstrated consistent expression responses and may be the major genes responding to exogenous stimuli.

scholarly journals Evolution and Function of the Sucrose-Phosphate Synthase Gene Families in Wheat and Other Grasses

2004 ◽  
Vol 135 (3) ◽  
pp. 1753-1764 ◽  
Author(s):  
C. Kate Castleden ◽  
Naohiro Aoki ◽  
Vanessa J. Gillespie ◽  
Elspeth A. MacRae ◽  
W. Paul Quick ◽  
...  
Keyword(s):  
Sucrose Phosphate Synthase ◽  
Gene Families ◽  
And Function ◽  
Sucrose Phosphate ◽  
Phosphate Synthase

Tissue specificity and diurnal change in gene expression of the sucrose phosphate synthase gene family in rice

Plant Science ◽  
2011 ◽  
Vol 181 (2) ◽  
pp. 159-166 ◽  
Author(s):  
Masaki Okamura ◽  
Naohiro Aoki ◽  
Tatsuro Hirose ◽  
Madoka Yonekura ◽  
Chikara Ohto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Tissue Specificity ◽  
Sucrose Phosphate Synthase ◽  
Diurnal Change ◽  
Sucrose Phosphate ◽  
Phosphate Synthase

scholarly journals Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus

2022 ◽  
Vol 12 ◽  
Author(s):  
Rehman Sarwar ◽  
Rui Geng ◽  
Lei Li ◽  
Yue Shan ◽  
Ke-Ming Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Future Research ◽  
Plant Tolerance ◽  
Specific Expression ◽  
Biotic Stresses ◽  
Organ Specific ◽  
Duplication Events

BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.

scholarly journals Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Panpan Ma ◽  
Xingtan Zhang ◽  
Lanping Chen ◽  
Qian Zhao ◽  
Qing Zhang ◽  
...  
Keyword(s):  
Sugar Content ◽  
Expression Patterns ◽  
High Stress ◽  
Sucrose Phosphate Synthase ◽  
Saccharum Officinarum ◽  
Sugar Accumulation ◽  
Saccharum Spontaneum ◽  
Sugarcane Cultivar ◽  
Sucrose Phosphate ◽  
Phosphate Synthase

Abstract Background Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. Results In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. Conclusions SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.

scholarly journals Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Di Wu ◽  
Anqi Liu ◽  
Xiaoyu Qu ◽  
Jiayi Liang ◽  
Min Song
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Multigene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Specific Expression ◽  
Group I

Abstract Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

scholarly journals Structure and Evolution of the Actin Gene Family in Arabidopsis thaliana

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 587-602 ◽  
Author(s):  
John M McDowell ◽  
Shurong Huang ◽  
Elizabeth C McKinney ◽  
Yong-Qiang An ◽  
Richard B Meagher
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Higher Plants ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Gene Families ◽  
Plant Evolution ◽  
Actin Gene ◽  
Specific Expression ◽  
Phylogenetic Structure

Abstract Higher plants contain families of actin-encoding genes that are divergent and differentially expressed. Progress in understanding the functions and evolution of plant actins has been hindered by the large size of the actin gene families. In this study, we characterized the structure and evolution of the actin gene family in Arabidopsis thaliana. DNA blot analyses with gene-specific probes suggested that all 10 of the Arabidopsis actin gene family members have been isolated and established that Arabidopsis has a much simpler actin gene family than other plants that have been examined. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least two ancient classes of genes that diverged early in land plant evolution and may have separated vegetative from reproductive actins. Subsequent divergence produced a total of six distinct subclasses of actin, and five showed a distinct pattern of tissue specific expression. The concordance of expression patterns with the phylogenetic structure is discussed. These subclasses appear to be evolving independently, as no evidence of gene conversion was found. The Arabidopsis actin proteins have an unusually large number of nonconservative amino acid substitutions, which mapped to the surface of the actin molecule, and should effect protein-protein interactions.

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