- Eleven BnLPPs genes were identified in the rapeseed genome. - Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. - By evaluating cis -elements in the promoters, we recognized six hormone- and seven stress-responsive elements.. - Further, six putative miRNAs were identified targeting three BnLPP genes. - Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. - The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/. - Conclusions: This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. - The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.. - Phospholipids exist in the cellular membranes of an or- ganism. - 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. - In short, LPPs are members of the PAP superfamily and catalyze the dephosphorylation of phosphorous lipids, which play a vital role in numerous physiological functions, including cell migration, proliferation, and differentiation [3, 4].. - Recently, significant progress has been made in the PAP superfamily. - The complete rapeseed genome sequence allows the identification and analysis of LPP genes in the rapeseed genome. - In the current study, 11 BnLPPs genes were obtained containing the complete PAP2 functional domain (Table 1). - Six genes were positioned in the A subge- nome, and five genes were positioned in the C subge- nome (Table 1). - Detailed characteristics of 11 BnLPP genes are presented in Table 1. - The subcellular location prediction revealed that 10 BnLPP proteins were positioned in the plasma membrane, while BnLPP1C was located in the endoplasmic reticulum.. - To understand the sequence characteristics, we per- formed a multiple sequence alignment analysis of the 11 BnLPP proteins using DNAMAN software with the de- fault parameters. - Notably, the conserved amino acids in the PAP2 domain were found to be essential for enzymatic activity. - To determine the BnLPP genes family’s evolutionary relationships with (A) thaliana and the (B) napus ances- tor species, based on the neighbor-joining (NJ) method, an unrooted phylogenetic tree was constructed between 25 LPP genes (11 from B. - In the aligned amino acids, invariant ones were marked with black, and the conserved ones were marked with blue and 5/5), purple and 4/5), and cyan (2/4 and 3/5). - Black bars represented the six transmembrane regions, and red bars represented the three domains of the phosphatase motif. - We also found that similar struc- tures usually exist in the same group, e.g., the group I members have one intron and two exons. - In the genomic position, the positive. - Interestingly, BnLPPs in the same group tends to have similar motif composition (Fig. - Chromosomal distribution and synteny analysis of BnLPP genes. - The chromosomal location of 11 BnLPPs was evaluated, and the result shows that 8 out of the 19 chromosomes had BnLPP genes (Table 1).. - Additionally, we also identified 6 and 4 LPPs genes in the B. - Our find- ings show that these genes were similar to those in the A and C sub-genomes of B. - olera- cea and two-four homologous genes in the B. - These results indicate that allotetraploidy was the main force for the rapid expansion of the LPP gene family in B. - Overall, our results indicate that the LPP gene family’s expansion in the B. - Cis -Elements in the promoters of BnLPPs. - In order to explore gene function and regulation pat- terns, we studied the cis-elements in the region of 2000 bp upstream of the initiation codon of each BnLPPs. - Overall, 13 putative cis-elements were predicted in the BnLPPs promoter (Fig. - Relatively more light-responsive cis-elements were observed in the BnLPPs promoters (Additional file 6). - 5, most of the hormone- and stress-responsive elements were specific to some genes highlighting their crucial role in hormone and stress response mechanisms.. - Functional annotation analysis of BnLPP genes. - To further discriminate the BnLPP genes’ functions, we implemented gene ontology (GO) annotation and en- richment analysis based on three classes, i.e., biological process (BP), molecular function (MF), and cellular com- ponent (CC). - These GO terms boost our understanding of the precise gene functions. - Nearly all GO-CC terms are consistent with the subcellular localization of the BnLPP proteins. - In short, GO enrichment outcomes validate the functional role of BnLPP genes in numerous biological, cellular, and molecular processes that were associated with phosphatase activity, hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation.. - Genome-wide analysis of miRNA targeting BnLPP genes In recent years, numerous researchers have discovered that microRNA (miRNA)-mediated regulation is accom- panying plants’ stress responses. - 5 Cis -elements that are related to different stress and hormone responses in the putative promoters of BnLPPs . - Cis -elements with similar functions were displayed in the same color. - knowledge of miRNAs connected with BnLPP gene regulation, we identified six putative miRNAs targeting three BnLPP genes (Fig. - Our results showed that four members of the bna- miR156 family targeted one gene (BnLPP3D), and two members of the bna-miR396 family targeted two genes (BnLPP4A and BnLPP4B) (Fig. - To demonstrate the expression patterns of the BnLPP genes, we examined eight tissues/organs (roots, stem, leaves, flower, petal, stamen, stigma, and silique) of rape- seed at various growth phases by qRT-PCR (Fig. - expression profiles of BnLPP genes varied in the various tissues/organs. - Expression patterns of BnLPP genes under different stress and phytohormone treatments. - 6 a A network diagram of the regulatory relationships between the presumed miRNAs and particular BnLPP genes. - was used to examine 11 BnLPP genes’ expression pat- terns at different time points after PEG, NaCl, and cold (Fig. - 8 Expression profiles of 11 BnLPPs under abiotic stress.The datawerenormalized to β-actin . - The heatmap showed the change ratio of the BnLPPs expression levels under NaCl, cold,and PEG stress. - A genome-wide analysis is a crucial method for clarifying the biological functions of the LPP family associates in a particular plant species. - So far, there is no comprehensive study of the LPP gene family in rape- seed. - The accessibility of the whole rapeseed genome permits the genome-wide characterization of the LPP family genes, which may further be used for rapeseed improvement.. - In the present study, a total of 11 BnLPP genes (six on A- and five on C-subgenome) were identified in the rapeseed genome (Table 1), which surpasses the number of genes identified from closely related species (4 BoLPPs, 6 BraLPPs, and 4 AtLPPs genes) (Additional file. - This evidence supports the role of asymmetrical evolution in the evolutionary success of polyploidy as well as their phenotypic novelty and adaptation [24, 25]. - Further, the results indicated that most duplicated LPP genes were lost after Brassica genome triplication, which was more than 35 % of lost genes in the Brassica lineage via a deletion mechanism [24]. - These arrange- ments in the phylogenetic tree were further established. - 9 Expression profiles of 11 BnLPP genes in response to different hormones. - The heatmap showed the change ratio of the BnLPPs expression levels under ABA, GA, IAA, and KT. - Almost all BnLPPs were predicted to be localized in the plasma membrane except BnLPP1C, specifically lo- calized in the endoplasmic reticulum. - However, the ex- pression profiles of BnLPP genes varied in the various tissues. - Notably, some genes showed higher expression levels in leaves, stigma, stem, roots, and stamens, suggesting that BnLPPs might play tissue-specific roles in the rapeseed development.. - Analysis of the cis-acting elements indicated that BnLPPs might respond to different stress and hormone signaling (Fig. - Likewise, the cis-elements analysis showed that BnLPP genes are involved in responding to various. - In the current study, the expression of both BnLPP2A and BnLPP2B was in- creased by ABA, suggesting that AtLPP2 and BnLPP2A/. - Hence, we identified six putative miRNAs (be- longing to two families, i.e., bna-miR156 and bna- miR396) targeting three BnLPP genes (Fig. - In the present study, we identified 11 BnLPPs, four BoLPPs, six BraLPPs, and four AtLPPs genes via genome-wide analysis. - stress and hormone-related cis-elements were also iden- tified in BnLPPs, appropriately explaining the induction of the BnLPPs by stress and hormone. - For the first time, we have predicted that two miRNAs families were tar- geting the three BnLPP genes. - In conclusion, the exten- sive data collected in the present study can be used for upcoming functional analysis of BnLPP genes in rape- seed growth, development, response to hormone and abiotic stresses.. - Eleven BnLPP genes were finally identified in the rapeseed genome. - The genome sequences of the B. - Prediction of putative miRNA targeting BnLPP genes and functional annotation analysis. - In the current study, the BnLPPs CDS sequences were used to predict targeted miRNAs using the psRNATar- get server (http://plantgrn.noble.org/psRNATarget/. - download.html) software was used to create the inter- action network between the prophesied miRNAs and the equivalent target BnLPP genes.. - In the present study, Westar, a rapeseed variety, was provided by the Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), China, and was used for stress treatments. - The samples were harvested after 0 (CK and 12 h of the treatments and were stored at − 80 ℃ for subsequent analysis.. - β -actin was used as an internal control, and all the primers used in the present study are listed in Additional file 1. - Sequences of the primers used in this study.. - The protein sequences of the LPP gene family in (A) thaliana, (B) oleracea, B. - Cis -elements in the promoters of putative BnLPP genes.. - The GO enrichment analysis of BnLPP genes.. - All authors have read and approved the final version of the manuscript.. - However, most of the data is available in additional files. - The sequences of Brassica napus , Brassica oleracea , and Brassica rapa are available in the GENOSCOPE database (https://wwwdev.genoscope.cns.fr/brassicanapus/data/) and Phytozome v12.1 (https://phytozome.jgi.doe.gov/pz/portal.html#).. - Further, we also have appropriate permissions from the Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China, to use the Westar (a rapeseed cultivar) seed specimens in the present study.. - Discoveries of the phosphatidate phosphatase genes in yeast published in the Journal of Biological Chemistry. - Isolation and Characterization of the Saccharomyces cerevisiae LPP1 Gene Encoding a Mg2+-independent Phosphatidate Phosphatase. - Regulation of the Saccharomyces cerevisiae DPP1-encoded Diacylglycerol Pyrophosphate Phosphatase by Zinc. - Regulation of Cellular Diacylglycerol through Lipid Phosphate Phosphatases Is Required for Pathogenesis of the Rice Blast Fungus, Magnaporthe oryzae. - regulation of the atlpp1 gene in response to stress. - Anatomical and Transcriptomic Studies of the Coleorhiza Reveal the Importance of This Tissue in Regulating Dormancy in Barley. - Mutagenesis of the phosphatase sequence motif in diacylglycerol pyrophosphate phosphatase from Saccharomyces cerevisiae. - The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. - Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
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