scholarly journals Gene regulation network analyses of pistil development in papaya

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Zhenyang Liao ◽  
Fei Dong ◽  
Juan Liu ◽  
Lele Xu ◽  
Amy Marshall-Colon ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Developmental Stages ◽  
Differentially Expressed ◽  
Algorithm Analysis ◽  
Male And Female ◽  
Pistil Abortion ◽  
Pistil Development ◽  
Female Flowers

Abstract Background The pistil is an essential part of flowers that functions in the differentiation of the sexes and reproduction in plants. The stigma on the pistil can accept pollen to allow fertilization and seed development. Papaya (Carica papaya L.) is a dioecious plant, where female flowers exhibit normal pistil, while the male flowers exhibit aborted pistil at a late stage of pistil development. Results The developmental stages of papaya pistil were analyzed after first dividing it into slices representing the primordium stage 1 (S1), the pre-meiotic stages S2, post-meiotic stage S3, and the mitotic stage S4. The SS scoring algorithm analysis of genes preferentially expressed at different stages revealed differentially expressed genes between male and female flowers. A transcription factor regulatory network for each stage based on the genes that are differentially expressed between male and female flowers was constructed. Some transcription factors related to pistil development were revealed based on the analysis of regulatory networks such as CpAGL11, CpHEC2, and CpSUPL. Based on the specific expression of genes, constructed a gene regulatory subnetwork with CpAGL11-CpSUPL-CpHEC2 functioning as the core. Analysis of the functionally enriched terms in this network reveals several differentially expressed genes related to auxin/ brassinosteroid signal transduction in the plant hormone signal transduction pathway. At the same time, significant differences in the expression of auxin and brassinosteroid synthesis-related genes between male and female flowers at different developmental stages were detected. Conclusions The pistil abortion of papaya might be caused by the lack of expression or decreased expression of some transcription factors and hormone-related genes, affecting hormone signal transduction or hormone biosynthesis. Analysis of aborted and normally developing pistil in papaya provided new insights into the molecular mechanism of pistil development and sex differentiation in dioecious papaya.

scholarly journals A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

2020 ◽  
Author(s):  
Shunkai Hu ◽  
Mi Zhang ◽  
Yiqing Yang ◽  
Wei Xuan ◽  
Zhongwei Zou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Lateral Roots ◽  
Nitrogen Concentration ◽  
Tea Plant ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Tea Plants ◽  
Low Nitrogen

Abstract Abstract Background Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. Lateral roots (LRs) of tea plant are the main organ used for tea plant to absorb soil moisture and nutrients. Lateral roots formation and development are tightly regulated by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. Results A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion This study provides new insights into the mechanisms associated with nitrogen and auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level.

scholarly journals Transgene-associated human growth hormone expression in pancreatic β-cells impairs identification of sex-based gene expression differences

2019 ◽  
Vol 316 (2) ◽  
pp. E196-E209 ◽  
Author(s):  
Jennifer S. Stancill ◽  
Anna B. Osipovich ◽  
Jean-Philippe Cartailler ◽  
Mark A. Magnuson
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Growth Hormone ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Human Growth ◽  
Differentially Expressed ◽  
Β Cells ◽  
Pancreatic Β Cells ◽  
Male And Female

Fluorescent protein reporter genes are widely used to identify and sort murine pancreatic β-cells. In this study, we compared use of the MIP-GFP transgene, which exhibits aberrant expression of human growth hormone (hGH), with a newly derived Ins2Apple allele that lacks hGH expression on the expression of sex-specific genes. β-Cells from MIP-GFP transgenic mice exhibit changes in the expression of 7,733 genes, or greater than half of their transcriptome, compared with β-cells from Ins2Apple/+ mice. To determine how these differences might affect a typical differential gene expression study, we analyzed the effect of sex on gene expression using both reporter lines. Six hundred fifty-seven differentially expressed genes were identified between male and female β-cells containing the Ins2Apple allele. Female β-cells exhibit higher expression of Xist, Tmed9, Arpc3, Eml2, and several islet-enriched transcription factors, including Nkx2-2 and Hnf4a, whereas male β-cells exhibited a generally higher expression of genes involved in cell cycle regulation. In marked contrast, the same male vs. female comparison of β-cells containing the MIP-GFP transgene revealed only 115 differentially expressed genes, and comparison of the 2 lists of differentially expressed genes revealed only 17 that were common to both analyses. These results indicate that 1) male and female β-cells differ in their expression of key transcription factors and cell cycle regulators and 2) the MIP-GFP transgene may attenuate sex-specific differences that distinguish male and female β-cells, thereby impairing the identification of sex-specific variations.

scholarly journals A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

2020 ◽  
Author(s):  
Shunkai Hu(Former Corresponding Author) ◽  
Mi Zhang ◽  
Yiqing Yang ◽  
Wei Xuan ◽  
Zhongwei Zou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Lateral Roots ◽  
Nitrogen Concentration ◽  
Tea Plant ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Tea Plants ◽  
Low Nitrogen

Abstract Background: Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. Lateral roots (LRs) of tea plant are the main organ used for tea plant to absorb soil moisture and nutrients. Lateral roots formation and development are tightly regulated by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. Results: A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion: This study provides new insights into the mechanisms associated with nitrogen and auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level.

scholarly journals A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

2020 ◽  
Author(s):  
Shunkai Hu ◽  
Mi Zhang ◽  
Yiqing Yang ◽  
Wei Xuan ◽  
Zhongwei Zou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Lateral Roots ◽  
Nitrogen Concentration ◽  
Tea Plant ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Tea Plants ◽  
Low Nitrogen

Abstract Background Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. Lateral roots (LRs) of tea plant are the main organ used for tea plant to absorb soil moisture and nutrients. Lateral roots formation and development are tightly regulated by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. Results A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion This study provides new insights into the mechanisms associated with nitrogen and auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level.

scholarly journals A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

2019 ◽  
Author(s):  
Shunkai Hu ◽  
Yiqing Yang ◽  
Mi Zhang ◽  
Wei Xuan ◽  
Zhongwei Zou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Nitrogen Metabolism ◽  
Differentially Expressed Genes ◽  
Lateral Roots ◽  
Nitrogen Concentration ◽  
Tea Plant ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Low Nitrogen

Abstract Lateral roots (LRs) are the main organ for tea plant to absorb soil moisture and nutrients. Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. LRs formation and development are limited by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in LRs of tea plant treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of genes expression; thus, regulated lateral roots formation. Furthermore, metabolisms of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant LRs formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. This study provides new insights into the mechanisms associated with nitrogen-auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

scholarly journals Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus

2020 ◽  
Vol 21 (4) ◽  
pp. 1337 ◽  
Author(s):  
Weida Lin ◽  
Yueling Li ◽  
Qiuwei Lu ◽  
Hongfei Lu ◽  
Junmin Li
Keyword(s):  
Transcription Factors ◽  
Candidate Genes ◽  
Phenolic Acid ◽  
Developmental Stages ◽  
Ultra Performance Liquid Chromatography ◽  
Differentially Expressed ◽  
Regulation Mechanism ◽  
Acid Biosynthesis ◽  
Cyclocarya Paliurus ◽  
Helix Loop Helix

To assess changes of metabolite content and regulation mechanism of the phenolic acid biosynthesis pathway at different developmental stages of leaves, this study performed a combined metabolome and transcriptome analysis of Cyclocarya paliurus leaves at different developmental stages. Metabolite and transcript profiling were conducted by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. Transcriptome identification showed that 58 genes were involved in the biosynthesis of phenolic acid. Among them, 10 differentially expressed genes were detected between every two developmental stages. Identification and quantification of metabolites indicated that 14 metabolites were located in the phenolic acid biosynthetic pathway. Among them, eight differentially accumulated metabolites were detected between every two developmental stages. Association analysis between metabolome and transcriptome showed that six differentially expressed structural genes were significantly positively correlated with metabolite accumulation and showed similar expression trends. A total of 128 transcription factors were identified that may be involved in the regulation of phenolic acid biosynthesis; these include 12 MYBs and 10 basic helix–loop–helix (bHLH) transcription factors. A regulatory network of the phenolic acid biosynthesis was established to visualize differentially expressed candidate genes that are involved in the accumulation of metabolites with significant differences. The results of this study contribute to the further understanding of phenolic acid biosynthesis during the development of leaves of C. paliurus.

scholarly journals The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach

Planta ◽  
2020 ◽  
Vol 252 (2) ◽  
Author(s):  
Izabela Sierocka ◽  
Sylwia Alaba ◽  
Artur Jarmolowski ◽  
Wojciech M. Karlowski ◽  
Zofia Szweykowska-Kulinska
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Male And Female ◽  
Pellia Endiviifolia

scholarly journals Identification of regulatory networks and hub genes controlling mammary gland development and lactation in dairy goats during the late lactation, dry period, and late gestation stages

2020 ◽  
Author(s):  
Rong Xuan ◽  
Tianle Chao ◽  
Xiaodong Zhao ◽  
Aili Wang ◽  
Yunpeng Chu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Mammary Gland ◽  
Differentially Expressed Genes ◽  
Mammary Gland Development ◽  
Late Gestation ◽  
Differentially Expressed ◽  
Dry Period ◽  
Mammary Gland Tissue ◽  
Three Stages ◽  
Gland Development

Abstract Background From the late lactation to late gestation stages, the mammary gland tissue of goats undergoes a process from involution to remodeling and then to high differentiation of mammary gland tissue. From the perspective of lactation, this is a continuous development process of the goat mammary gland from the termination of lactation to the restoration of lactation. We performed transcriptome sequencing on goat mammary gland tissues at three mammary gland developmental stages to screen for differentially expressed genes that affect mammary gland development and the physiological process of lactation and mapped their expression profiles in three stages. The objective of this study is to reveal the expression characteristics of these genes and their potential function during mammary gland development and lactation. Results We identified 1,381 differentially expressed genes in the mammary gland during three stages and found that the expression level of genes encoding casein, such as alpha-s1-casein (CSN1S1), alpha-s2-casein (CSN1S2), beta-casein (CSN2), and kappa-casein (CSN3), and alpha-lactalbumin (LALBA) were higher in mammary gland tissues during the late lactation stage and late gestation stage than those during the dry period. In addition, we constructed six functional networks related to differentially expressed genes and found that these genes are closely related to mammary gland growth and development, apoptosis, immunity, substance transport, biosynthesis, and metabolism. Finally, we identified 35 differentially expressed transcription factors, which were classified into 16 families, and predicted that transcription factors of the basic leucine zipper domain (bZIP) family and basic helix-loop-helix (bHLH) family regulated the expression levels of genes related to mammary gland development and lactation. Conclusions Among the late lactation, dry period, and late gestation stages, there are differences in the expression levels of genes related to mammary gland growth and development, apoptosis, immunity, basic substance transport, biosynthesis, and metabolism in mammary gland tissues. Some genes in the same family or with similar functions have similar expression patterns. These differentially expressed genes or transcription factors work synergistically to participate in the regulation of mammary gland development and the physiological process of lactation.

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