- Genome-wide characterization of the SPL gene family involved in the age. - Results: In Jatropha, 15 JcSPL genes were identified. - Phylogenetic analysis revealed that most of the JcSPLs were closely related to SPLs from woody plant rather than herbaceous plant and distantly related to monocotyledon SPLs. - By combination of target prediction and degradome sequencing analysis, 10 of the 15 JcSPLs were shown to be targets of JcmiR156. - It is interesting that the expression levels of JcSPL3 were the highest in all tissues examined in 7- or 10-year-old plants and exhibited increasing trend with plant age, suggesting its important role in the regulation of age development in Jatropha. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - The other group AtSPL10, AtSPL11 and AtSPL2 control morphological change in association with shoot maturation in the re- productive phase and the lateral root development [17, 18]. - Given that overexpres- sion of specific SPL gene could accelerate leaf initiation rate, increase biomass yield, enhanced salt tolerance and essential oil content, we ask if SPL is involved in the production of oil in J. - Some of the 15 identified SPL genes were highly conserved based on gene structure, conserved motifs, as well as clustering level. - To gain an understanding of the evolutionary status of SPLs from J. - Furthermore, most of the JcSPL genes showed a closer relationship with woody plant Glycine and Populus SPL genes rather than herbaceous. - plant Arabidopsis SPL genes, and JcSPL genes were ra- ther distantly related to the rice SPL genes. - Overall structure analysis of all plant SPL proteins re- vealed that clade 1 were the smallest of the SPL proteins, while clade 6 and clade 7 were the largest (Fig. - Identification of SPL genes in Jatropha. - To identify the SPL genes in the Jatropha genome, the SBP domain was used as a query to search against the Jatropha genome. - Gene structure, motif and sequence analysis of JcSPL genes. - The pos- ition of intron in the SBP domain were highly conserved and located in the 47th amino acid, which were also found in Arabidopsis [6] and Populus [10]. - The in- tron number existing in the 15 JcSPLs ranged from 1 to 10. - 2 Sequence alignment and logo of the JcSPLs. - a Multiple alignment of the JcSPLs. - b Sequence logo of the SBP domain from the JcSPLs. - It was found that all JcSPLs showed repetitive sequence features including either simple se- quence repeat (SSR) or tandem repeat (TR) in the pro- moter and gene regions (Fig. - The cis-acting elements in the promoter regions of all JcSPLs were investigated (Fig. - The cis-act- ing elements involved in the light response were the. - 3 Gene structure and motif analysis of the JcSPLs. - b Distribution of the conserved motifs in the JcSPLs. - 4 Distribution of repetitive sequences and motifs in the JcSPLs. - a The number of repetitive sequences in the promoter and genomic DNA sequences of JcSPLs. - b The number of cis-acting elements found in the promoter regions of JcSPLs. - The putative elements involved in growth and develop- ment and stress response were absent in the promoter regions of JcSPL4 and JcSPL6. - There were seven and four JcSPL genes containing the CAT-box and GCN4 motif, which were functional in the meristem and endosperm expression, respectively. - In order to get deep understanding of the functional roles of JcSPL genes in Jatropha, we evalu- ated the potential regulation of JcSPLs by miRNA through both psRNATarget prediction and degradome sequencing. - The MFold-predicted sec- ondary structure of the miR156 precussor sequence. - Most miR156- targeted JcSPL genes were clustered into Group 1–4 (Fig. - The JcmiR156 target sites for three JcSPLs in Group 1 were located in the 3′ UTRs, while the target sites for all the other JcSPLs were in their last exons.. - The cleavage sites in the JcSPL gene sequences were clearly shown in T-plots and were confirmed to be exactly the same as predicted sites (Additional file 12). - Expression patterns of JcSPL genes. - In Jatropha, there were dramatic variability in the leaf morphology from different ages of plants (Add- itional file 13). - 6 Expression patterns of the JcSPLs in different tissues. - There were eight JcSPL genes (JcSPL that showed higher expression in 7-year-old root tissue com- pared to root from other stages, while four JcSPL genes (JcSPL1/7/12/14) showed higher expression in 1-year-old. - However, other JcSPL genes even in the same subgroup exhibited diversified expression patterns, indicating that they could play specific roles in various tissues under different de- velopmental stages.. - Confocal microscopy observation of the JcSPL3-GFP florescence signals showed that JcSPL3 were mainly distributed in the nucleus (Add- itional file 14), indicating its potential binding ability in vivo.. - 7 Expression patterns of the JcSPLs in different developmental stages. - The expression level of JcSPL3 in the overexpressed lines was about 50 times more than the wild-type (Fig. - The average number of rosette leaves at flowering ranged from 4 to 6 in the transgenic plants, and was 12.5 in the wild-type plants (Fig. - In addition, the siliques of transgenic plants were approximately 50% as long as those of the control plants (Fig. - These data indicated that JcSPL3 may act as a floral activator and might be involved in the Jatropha flowering process.. - After filtering the short and partial sequences in the Pfam database, a total of 833 full-length SPL genes were found from 60 species which represent plant line- ages of green algae, moss, lycopodiophyta and angio- sperm. - However, no SPL genes were discovered in the Pfam database from gymnosperms. - To verify the sequences of JcSPL genes retrieved from the J. - The cDNA amp- lification results showed that there was a point mutation in the gene XM Additional file 3). - This relatively small number of gene family was also reported for other transcription fac- tor families in the Jatropha genome, such as the WRKY gene family, which have not undergone any recent gene duplication [36]. - According to the phylogen- etic tree, three pairs of JcSPL genes were presumed to be segment duplicated genes. - Moreover, JcSPL3/4/5 were relatively small and had a miR156 tar- get site in the 3′ UTR, which were also similar to AtSPL3/4/5, suggesting that JcSPL3/4/5 may have similar function in regulating flowering time and phase transi- tion in Jatropha.. - Gene structure and conserved motifs analysis revealed that members in the same group always showed similar structure and motifs (Fig. - Moreover, there were about two-thirds of the JcSPLs contained the miR156 target sites and nine JcSPLs were confirmed by degradome sequencing to be cleaved by miR156 (Add- itional file 12). - The complementary site to miR156 in the three small JcSPLs in Group 1 located in the 3′-UTR region, whereas in other seven JcSPLs it located in the last exon. - Previous reports have shown that most of paralogous SPL genes in the same group exhibited similar expres- sion patterns [10, 38]. - In Jatropha, three genes JcSPL1, JcSPL12 and JcSPL14 belonging to Group 7 showed simi- lar expression patterns, whereas other genes even in the same group showed distinct expression, suggesting spe- cific functions of these genes. - Interestingly, the expres- sion levels of JcSPL3 increased significantly with the age of the plant in both leaf and root tissues (Fig. - In Jatropha, there was a significant variability in the morph- ology of the leaves from 1-month- and 1-year-old shoots of plants. - These suggest that JcSPL3 could also play a role in the root development (Fig. - Interestingly, the expression patterns of JcSPL3 indicate its important role in the regulation of age development in Jatropha. - Analysis of JcSPL genes. - All putative proteins were fur- ther confirmed to contain SBP domain in the PFAM database. - Originally 21 JcSPL genes were retrieved. - The repetitive sequence analysis in the promoter (2.0 kb upstream of the coding sequence) and coding se- quence of JcSPLs were determined by SSRIT database (http://archive.gramene.org/db/markers/ssrtool) and Tandem Repeat Finder database (https://tandem.bu.edu/. - The cis-acting elements analysis in the pro- moter region of all JcSPLs genes were performed by using the PlantCARE database (http://www.dna.affrc.go.. - The sequence of JcmiR156a-f was obtained from the data in the paper by Galli et al. - Fully expanded leaves, stem and root were harvested from 1-month-old plants grown in the greenhouse. - T-plots were generated according to the abun- dance of the resulting mRNA tags relative to the overall profile of degradome reads that matched the target. - In category 4, only one raw read was matched at the cleavage position of the transcript.. - The RNA Ligase-Mediated (RLM) 5′-RACE experiment was performed following the instructions of the RACE kit FirstChoice™ RLM-RACE Kit (Invitrogen). - The coding sequence of JcSPL3 was cloned from the leaf cDNA library and fused to C-terminal Green florescence protein (GFP) tag (JcSPL3-GFP) in the ex- pression vector pCambia1301-GFP. - Detailed information of the plant SPL proteins used for phylogenetic analysis.. - Sequence information of identified JcSPL genes.. - a Schematic representation of the alternative processing of predicted JcSPL3 genes. - Chromosomal localization of the JcSPLs. - Chromosomal localization of the JcSPLs based on the linkage map. - The Ka/Ks ratios of the JcSPLs family.. - E-value and consensus sequence of twenty motifs identified in the JcSPLs.. - Detailed information of the cis-acting elements in the promoters of JcSPLs.. - Secondary structure of the JcMIR156 family.. - Target plots of the targets cleaved by the miR156 family through degradome sequencing. - The T-plots show the distribution of the degradome tags along the full-length of the target mRNA se- quence (bottom). - JCY and GTY participated in the sequence analysis and data interpretation. - played no role in the design of the study or collection, analysis and interpretation of data.. - The datasets used and analyzed during the current study are available in the manuscript and its additional files.. - Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. - A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. - Comparative analysis of the SBP-box gene families in P. - Molecular characterisation of the Arabidopsis SBP-box genes. - Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh. - Molecular characterization of the SPL gene family in Populus trichocarpa. - Functional evolution in the plant SQUAMOSA- PROMOTER BINDING PROTEIN-LIKE (SPL) gene family. - with shoot maturation in the reproductive phase. - Novel positive regulatory role for the SPL6 transcription factor in the N TIR-NB-LRR receptor-mediated plant innate immunity. - Genome-wide identification and characterization of SQUAMOSA-promoter-binding protein (SBP) genes involved in the flowering development of Citrus Clementina.. - Genome-wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza
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