scholarly journals GhGPAT12/25 Are Essential for the Formation of Anther Cuticle and Pollen Exine in Cotton (Gossypium hirsutum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Meng Zhang ◽  
Hengling Wei ◽  
Pengbo Hao ◽  
Aimin Wu ◽  
Qiang Ma ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Regulatory Mechanism ◽  
Anther Development ◽  
Biological Processes ◽  
Rna Seq ◽  
Loss Of Function ◽  
Virus Induced Gene Silencing ◽  
Cuticular Waxes ◽  
Pollen Exine ◽  
Anther Cuticle

Glycerol-3-phosphate acyltransferases (GPATs), critical for multiple biological processes like male fertility, have been extensively characterized. However, their precise functions and underlying regulatory mechanism in cotton anther development are unclear. This research demonstrated the importance of GhGPAT12/25 (a paralogs pair on A12/D12 sub-chromosome of cotton) to regulate the degradation of tapetum, anther cuticle formation, and pollen exine development. GhGPAT12 and GhGPAT25 exhibited specifically detected transcripts in tapetum and pollen exine during the early anther developmental stages. GhGPAT12/25 are sn-2 glycerol-3-phosphate acyltransferases and can transfer the acyl group of palmitoyl-CoA to glycerol-3-phosphate (G3P). CRISPR/Cas9-mediated knockout identified the functional redundancy of GhGPAT12 and GhGPAT25. Knockout of both genes caused completely male sterility associated with abnormal anther cuticle, swollen tapetum, and inviable microspores with defective exine and irregular unrestricted shape. RNA-seq analysis showed that the loss of function of GhGPAT12/25 affects the processes of wax metabolic, glycerol monomer biosynthesis, and transport. Consistently, cuticular waxes were dramatically reduced in mutant anthers. Yeast one-hybrid system (Y1H), virus-induced gene silencing (VIGS), and dual-luciferase (LUC) assays illustrated that GhMYB80s are likely to directly activate the expression of GhGPAT12/25. This study provides important insights for revealing the regulatory mechanism underlying anther development in cotton.

scholarly journals Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation

2022 ◽  
Vol 23 (2) ◽  
pp. 746
Author(s):  
Bo Li ◽  
Xiangzhan Zhang ◽  
Ruiwei Duan ◽  
Chunhong Han ◽  
Jian Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Developmental Stages ◽  
Genomic Analysis ◽  
Pyrus Communis ◽  
Anthocyanin Content ◽  
Anthocyanin Accumulation ◽  
Rna Seq ◽  
Virus Induced Gene Silencing ◽  
Functional Identification ◽  
Glutathione S Transferase

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding.

scholarly journals Comparison of transcriptomic and proteomic analyses to construct a model for the promotion of starch synthesis by ABA in Euryale ferox Salisb. seeds

2020 ◽  
Author(s):  
Peng Wu ◽  
Xiang Li ◽  
Xian Liu ◽  
Xu Xu ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Seed Quality ◽  
Developmental Stages ◽  
Regulatory Mechanism ◽  
Starch Content ◽  
Starch Synthesis ◽  
Rna Seq ◽  
Hub Genes ◽  
Network Analyses ◽  
Euryale Ferox ◽  
Main Factor

Abstract Background: Euryale ferox Salisb. is an annual aquatic herb and the only species belonging to the genus Euryale in the Nymphaeaceae family. E. ferox seeds are used in medicine and diets. Starch is the main factor affecting E. ferox seed quality, but its regulatory mechanism has not been elucidated. Results: Herein, four time points of seed development, including after flowering T1 (10 days), T2 (20 days), T3 (30 days) and T4 (40 days), were investigated by using RNA-Seq and iTRAQ technology. Using weighted gene co-expression network analyses (WGCNAs), co-expressed genes and hub genes were identified for each module. Of particular importance are the discoveries of specific modules for seed starch during the seed developmental stages. The candidate regulators of seed starch are involved in the hormonal signaling pathways. Three ABA signaling receptor kinases, EfPYR1, EfSnRK2.1 and EfSnRK2.2, were identified as hub genes functioning in starch synthesis during the seed maturation process. The changes in expression pattern, ABA and starch content also indicated that ABA is positively correlated with starch. Conclusions: Together, these results indicate that E. ferox seed accumulation of starch is promoted by ABA, providing new insights into the regulatory mechanism of starch synthesis in E. ferox seeds.

scholarly journals RiceLncPedia: a comprehensive database of rice long non-coding RNAs

2020 ◽  
Author(s):  
Zhengfeng Zhang ◽  
Yao Xu ◽  
Fei Yang ◽  
Benze Xiao ◽  
Guoliang Li
Keyword(s):  
Experimental Validation ◽  
Developmental Stages ◽  
Data Sets ◽  
Omics Data ◽  
Biological Processes ◽  
Rna Seq ◽  
Current Version ◽  
Non Coding Rnas ◽  
Systematic Identification ◽  
Different Tissues

ABSTRACTLong non-coding RNAs (lncRNAs) play significant functions in various biological processes including differentiation, development and adaptation to different environments. Although multi research focused on lncRNAs in rice, the systematic identification and annotation of lncRNAs expressed in different tissues, developmental stages under diverse conditions are still scarce. This impacts the elucidation of their functional significance and the further research on them. Here, RiceLncPedia (http://218.199.68.191:10092/) is constructed including rice lncRNAs explored from 2313 publically available rice RNA-seq libraries and characterize them with multi-omics data sets. In the current version, RiceLncPedia shows 6978 lncRNAs with abundant features: (i) expression profile across 2313 rice RNA-seq libraries; (ii) an online genome browser for rice lncRNAs; (iii) genome SNPs in lncRNA transcripts; (iv) lncRNA associations with phenotype; (v) overlap of lncRNAs with transposons; and (vi) LncRNA-miRNA interactions and lncRNAs as the precursors of miRNAs. In total, RiceLncPedia imported numerous of rice lncRNAs during development under various environments as well as their features extracted from multi-omics data and thus serve as a fruitful resource for rice-related research communities. RiceLncPedia will be further updated with experimental validation, functions association and epigenetic characteristics to greatly facilitate future investigation on rice lncRNAs.

scholarly journals Comparison of transcriptomic and proteomic analyses to construct a new model for the promotion of starch synthesis by ABA in Euryale ferox Salisb. seeds

2019 ◽  
Author(s):  
Peng Wu ◽  
Xiang Li ◽  
Xian Liu ◽  
Xu Xu ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Seed Quality ◽  
Developmental Stages ◽  
Regulatory Mechanism ◽  
Starch Content ◽  
Starch Synthesis ◽  
Rna Seq ◽  
Hub Genes ◽  
Network Analyses ◽  
Euryale Ferox ◽  
Main Factor

Abstract Background: Euryale ferox Salisb. is an annual aquatic herb and the only species belonging to the genus Euryale in the Nymphaeaceae family. E. ferox seeds are used in medicine and diet s. Starch is the main factor affecting E. ferox seed quality, but its regulatory mechanism has not been elucidated. Results: Herein, four time points of seed development, including after flowering T1 (10 days), T2 (20 days), T3 (30 days) and T4 (40 days), were investigated by using RNA-Seq and iTRAQ technology. Using weighted gene co-expression network analyses (WGCNAs), co-expressed genes and hub genes were identified for each module. Of particular importance are the discoveries of specific modules for seed starch during the seed developmental stages. The candidate regulators of seed starch are involved in the hormonal signaling pathways. Three ABA signaling receptor kinases, EfPYR1, EfSnRK2.1 and EfSnRK2.2 , were identified as hub genes functioning in starch synthesis during the seed maturation process. The changes in expression pattern, ABA and starch content also indicated that ABA is positively correlated with starch. Conclusions: Together, these results indicate that E. ferox seed accumulation of starch is promoted by ABA, providing new insights into the regulatory mechanism of starch synthesis in E. ferox seeds.

scholarly journals Systematic analysis of RNA-seq-based gene co-expression across multiple plants

2017 ◽  
Author(s):  
Hua Yu ◽  
Bingke Jiao ◽  
Chengzhi Liang
Keyword(s):  
Plant Species ◽  
Regulatory Mechanism ◽  
Gene Expression Regulation ◽  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Rna Seq ◽  
Systematic Analysis ◽  
Gene Modules ◽  
Species Specific

AbstractThe complex cellular network was formed by the interacting gene modules. Building the high-quality RNA-seq-based Gene Co-expression Network (GCN) is critical for uncovering these modules and understanding the phenotypes of an organism. Here, we established and analyzed the RNA-seq-based GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed modules. Taking rice as an example, we associated these modules with biological functions and agronomic traits by enrichment analysis, and discovered a large number of conditin-specific or tissue-specific modules. In addition, we also explored the regulatory mechanism of the modules by enrichment of the known cis-elements, transcription factors and miRNA targets. Their coherent enrichment with the inferred functions of the modules revealed their synergistic effect on the gene expression regulation. Moreover, the comparative analysis of gene co-expression was performed to identify conserved and species-specific functional modules across 4 plant species. We discovered that the modules shared across 4 plants participate in the basic biological processes, whereas the species-specific modules were involved in the spatiotemporal-specific processes linking the genotypes to phenotypes. Our research provides the massive modules relating to the cellular activities and agronomic traits in several model and crop plant species.

scholarly journals Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1932 ◽  
Author(s):  
Efejiro Ashano ◽  
Itunuoluwa Isewon ◽  
Jelili Oyelade ◽  
Ezekiel Adebiyi
Keyword(s):  
Time Course ◽  
Developmental Stages ◽  
Regulatory Elements ◽  
Development Stage ◽  
Functional Enrichment ◽  
Developmental Cycle ◽  
Significant Activity ◽  
Biological Processes ◽  
Rna Seq ◽  
Time Course Data

In this study, we interpreted RNA-seq time-course data of three developmental stages of Plasmodium species by clustering genes based on similarities in their expression profile without prior knowledge of the gene function. Functional enrichment of clusters of upregulated genes at specific time-points reveals potential targetable biological processes with information on their timings. We identified common consensus sequences that these clusters shared as potential points of coordinated transcriptional control. Five cluster groups showed upregulated profile patterns of biological interest. This included two clusters from the Intraerythrocytic Developmental Cycle (cluster 4 = 16 genes, and cluster 9 = 32 genes), one from the sexual development stage (cluster 2 = 851 genes), and two from the gamete-fertilization stage in the mosquito host (cluster 4 = 153 genes, and cluster 9 = 258 genes). The IDC expressed the least numbers of genes with only 1448 genes showing any significant activity of the 5020 genes (~29%) in the experiment. Gene ontology (GO) enrichment analysis of these clusters revealed a total of 671 uncharacterized genes implicated in 14 biological processes and components associated with these stages, some of which are currently being investigated as drug targets in on-going research. Five putative transcription regulatory binding motifs shared by members of each cluster were also identified, one of which was also identified in a previous study by separate researchers. Our study shows stage-specific genes and biological processes that may be important in antimalarial drug research efforts. In addition, timed-coordinated control of separate processes may explain the paucity of factors in parasites.

Transcriptome Analysis Reveals Candidate Genes During the Prepupal-pupal Transition in the Oriental Armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2020 ◽  
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Pupal Stage ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Rna Seq ◽  
Mythimna Separata ◽  
Expression Levels ◽  
Lepidoptera Noctuidae

Abstract Background Metamorphosis ensures the transformation of a larva of the holometabolous insects into a reproductive adult through a transitory pupal stage. Understanding how changes in expression levels of genes during the prepupal-pupal transition will inform us of how the metamorphosis arises. Results In this study, mature larvae (ML), wandering (W), 1 day (P1), 5 days (P5), and 10 days (P10) after pupation of the Mythimna separata (Walker), a notorious migratory pest of agricultural crops, were selected, forming five groups. RNA-Seq revealed that the draft transcriptome assembly contained 140562 contigs, and more than half (74,059) were similar to sequence at NCBI (e value < e− 3), including 22884, 23534, 26643, and 33238 differentially expressed genes (DEGs) in ML vs W, W vs P1, P1 vs P5, and P5-vs-P10, respectively. Comparative transcriptomics revealed the enrichment of biological processes related to the membrane and integral component of membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, enabled us to delineate and partially validate the metabolic pathway in M. separata. Of these DEGs, 33 CP, 18 20E, and 7 JH genes were differentially expressed across the developmental stages. Correlation analysis uncovered that the relative expression levels of 10 selected CP, 20E, and JH-related genes obtained by real-time PCR quantitative (RT-qPCR) matched well with their FPKM values derived from RNA-seq. Conclusions The data gave here represent an important first step to uncover the molecular mechanism of metamorphosis in M. separata, which also provide valuable information for manipulation of insect development and metamorphosis using the obtained DEGs as targets and broaden the applications of available tools for insect pest control.

scholarly journals Latent periodic process inference from single-cell RNA-seq data

2019 ◽  
Author(s):  
Shaoheng Liang ◽  
Fang Wang ◽  
Jincheng Han ◽  
Ken Chen
Keyword(s):  
Cell Cycle ◽  
Developmental Stages ◽  
High Dimensional ◽  
Biological Processes ◽  
Periodic Process ◽  
Rna Seq ◽  
Cell Cycles ◽  
Periodic Processes ◽  
Cell Subpopulations ◽  
Multicellular Organisms

AbstractConvoluted biological processes underlie the development of multicellular organisms and diseases. Advances in scRNA-seq make it possible to study these processes from cells at various developmental stages. Achieving accurate characterization is challenging, however, particularly for periodic processes, such as cell cycles. To address this, we developed Cyclum, a novel AutoEncoder approach that characterizes circular trajectories in the high-dimensional gene expression space. Cyclum substantially improves the accuracy and robustness of cell-cycle characterization beyond existing approaches. Applying Cyclum to removing cell-cycle effects leads to substantially improved delineations of cell subpopulations, which is useful for establishing various cell atlases and studying tumor heterogeneity. Cyclum is available at https://github.com/KChen-lab/cyclum.

scholarly journals Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 315
Author(s):  
Hailin Liu ◽  
Xin Han ◽  
Jue Ruan ◽  
Lian Xu ◽  
Bing He
Keyword(s):  
Ginkgo Biloba ◽  
Leaf Development ◽  
Developmental Stages ◽  
Leaf Growth ◽  
Rna Seq ◽  
Final Size ◽  
Dioecious Species ◽  
Related Factors ◽  
New Genes ◽  
Gene Modules

The final size of plant leaves is strictly controlled by environmental and genetic factors, which coordinate cell expansion and cell cycle activity in space and time; however, the regulatory mechanisms of leaf growth are still poorly understood. Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics, and its fan-shaped leaves are unique in gymnosperms, while the mechanism of G. biloba leaf development remains unclear. In this study we studied the transcriptome of G. biloba leaves at three developmental stages using high-throughput RNA-seq technology. Approximately 4167 differentially expressed genes (DEGs) were obtained, and a total of 12,137 genes were structure optimized together with 732 new genes identified. More than 50 growth-related factors and gene modules were identified based on DEG and Weighted Gene Co-expression Network Analysis. These results could remarkably expand the existing transcriptome resources of G. biloba, and provide references for subsequent analysis of ginkgo leaf development.

scholarly journals Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1268
Author(s):  
Shengchao Zhang ◽  
Sibtain Ahmad ◽  
Yuxia Zhang ◽  
Guohua Hua ◽  
Jianming Yi
Keyword(s):  
Mammary Gland ◽  
Crude Protein ◽  
Regulatory Mechanism ◽  
Differentially Expressed ◽  
Milk Replacer ◽  
Rna Seq ◽  
Fat Pad ◽  
Mammary Fat Pad ◽  
Non Coding Rnas ◽  
Gland Development

Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs’ quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.

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