scholarly journals Genome-wide survey and expression analysis of NIN-like Protein (NLP) genes reveals its potential roles in the response to nitrate signaling in tomato

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mengyuan Liu ◽  
Xiaona Zhi ◽  
Yi Wang ◽  
Yang Wang
Keyword(s):  
Expression Analysis ◽  
Nitrate Uptake ◽  
Inorganic Nitrogen ◽  
Expression Patterns ◽  
Nitrogen Deficiency ◽  
Comparative Genomic ◽  
Tomato Genome ◽  
Inorganic Nitrogen Source ◽  
Genome Wide ◽  
Nitrate Signaling

Abstract Background Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference for nitrate as an inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. Results In this study, genome-wide analysis identified six NLP members in tomato genome. These members were clustered into three clades in a phylogenetic tree. Comparative genomic analysis showed that SlNLP genes exhibited collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in the tomato genome. Tissue-specific expression analysis showed that one of the close homologs of AtNLP6/7, SlNLP3, was strongly expressed in roots during both the seedling and flowering stages, that SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves and that SlNLP6 was expressed at high levels in fruits. Furthermore, the nitrate uptake in tomato roots and the expression patterns of SlNLP genes were measured under nitrogen deficiency and nitrate resupply conditions. Four SlNLPs, SlNLP1, SlNLP2, SlNLP4 and SlNLP6, were upregulated after nitrogen starvation. And SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions These results provide significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.

scholarly journals Title: Genome-Wide Survey and Expression Analysis of NIN-Like Protein (NLP) Genes Reveals Its Potential Roles in the Response to Nutrition Deficiency in Tomato

2021 ◽  
Author(s):  
Mengyuan Liu ◽  
Xiaona Zhi ◽  
Yi Wang ◽  
Yang Wang
Keyword(s):  
Expression Analysis ◽  
Nitrate Uptake ◽  
Molecular Mechanisms ◽  
Inorganic Nitrogen ◽  
Expression Patterns ◽  
Potassium Deficiency ◽  
Comparative Genomic ◽  
Tomato Genome ◽  
Inorganic Nitrogen Source ◽  
Genome Wide

Abstract Background: Tomato (Solanum lycopersicum) is one of the most important horticultural crops, with a marked preference of nitrate as inorganic nitrogen source. The molecular mechanisms of nitrate uptake and assimilation are poorly understood in tomato. NIN-Like Proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in nitrate signaling. Results: In this study, genome-wide analysis revealed six NLP members in tomato genome. They were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that SlNLP genes had collinear relationships to NLPs in Arabidopsis, canola, maize and rice, and that the expansion of the SlNLP family mainly resulted from segmental duplications in tomato genome. Tissue-specific expression analysis showed that the close homologues of AtNLP6/7, SlNLP3, was strongly expressed in roots during both seedling and flowering stages; SlNLP4 and SlNLP6 exhibited preferential expression in stems and leaves; and SlNLP6 were expressed in high levels in fruits. Further, the nitrate uptake in tomato roots and expression patterns of SlNLP genes were measured under nitrogen/phosphate/potassium deficiency and nitrate resupply conditions. The transcript abundance of SlNLP3 decreased to 70% under phosphate/potassium deficiency. Most of SlNLPs were up-regulated after nitrogen starvation. SlNLP1 and SlNLP5 were induced rapidly and temporally by nitrate. Conclusions: These results provided significant insights into the potential diverse functions of SlNLPs to regulate nitrate uptake.

Roles of low pH, carbon and inorganic nitrogen source use in chlamydospore formation by Fusarium solani

1976 ◽  
Vol 22 (9) ◽  
pp. 1381-1389 ◽  
Author(s):  
Gary J. Griffin
Keyword(s):  
Fusarium Solani ◽  
Inorganic Nitrogen ◽  
Nitrogen Deficiency ◽  
Low Ph ◽  
Inorganic Nitrogen Source ◽  
Chlamydospore Formation ◽  
Sudan Iii ◽  
Source Use ◽  
Germ Tubes ◽  
Citrate Phosphate

Citrate and malate were poorer sources of exogenous carbon than several hexose, pentose, or disaccharide sugars for supporting macroconidial germination by Fusarium solani at high conidial density (1 × 105 conidia/ml). Only citrate, however, failed to block chlamydospore morphogenesis to a degree comparable to glucose or other readily used sugars. Mostly immature chlamydospores were formed in the presence of citrate. At low conidial density (5 × 103 conidia/ml), exogenous carbon-independent macroconidial germination and subsequent rapid chlamydospore formation on germ tubes was not inhibited by ammonium or nitrate nitrogen. The citrate–phosphate buffered, low pH (4.0) medium of Cochrane induced more immature chlamydospore formation by F. solani than a pH 6.0 medium, but few mature chlamydospores were formed in either medium. Condensation of hyphal cytoplasm into developing chlamydospores, a character typical of chlamydospore formation, did not occur extensively and macroconidia, hyphae, and immature chlamydospores stained deeply with Sudan III, suggesting lipid biosynthesis. This inhibition of chlamydospore maturation may be due partly to nitrogen deficiency imposed by the high C: N ratio of the medium and to the presence of citrate. Only vesiculate hyphal cells were formed by F. solani f. sp. phaseoli in both media.Field soils to which the clone of F. solani used is indigenous had mean pH values ranging from 5.2 to 6.0.

Identification and expression analysis of chloroplast ribonucleoproteins (cpRNPs) in Arabidopsis and rice

Genome ◽  
2020 ◽  
Author(s):  
Jiawen Wu ◽  
Huimin Liu ◽  
Shan Lu ◽  
Jian Hua ◽  
Baohong Zou
Keyword(s):  
Expression Analysis ◽  
Stress Responses ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Stability Control ◽  
Rna Recognition Motif ◽  
Chloroplast Targeting ◽  
Genome Wide ◽  
A Genome ◽  
Targeting Signal

Chloroplast ribonucleoproteins (cpRNPs) are implicated in splicing, editing and stability control of chloroplast RNAs as well as in regulating development and stress tolerance. To facilitate a comprehensive understanding of their functions, we carried out a genome-wide identification, curation, and phylogenetic analysis of cpRNP genes in Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Ten cpRNP genes were identified in each of Arabidopsis and rice genomes based on the presence of two RRM (RNA recognition motif) domains and an N-terminal chloroplast targeting signal peptide in the predicted proteins. These proteins are localized to chloroplasts. Gene expression analysis revealed that cpRNPs have differential tissue expression patterns and some cpRNPs are induced by abiotic stresses such as cold, heat and drought. Taken together, our study provides a comprehensive annotation of the cpRNP gene family and their expression patterns in Arabidopsis and rice which will facilitate further studies on their roles in plant growth and stress responses.

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those induced by salt, drought, hot and cold) to varying degrees.

scholarly journals The Sugar Transporter Inventory of Tomato: Genome-Wide Identification and Expression Analysis

2014 ◽  
Vol 55 (6) ◽  
pp. 1123-1141 ◽  
Author(s):  
Stefan Reuscher ◽  
Masahito Akiyama ◽  
Tomohide Yasuda ◽  
Haruko Makino ◽  
Koh Aoki ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Sugar Transporter ◽  
Tomato Genome ◽  
Genome Wide

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those genes induced by salt, drought, hot and cold) to varying degrees.

scholarly journals Genome-wide identification and expression analysis of PUB genes in cotton

2020 ◽  
Author(s):  
Xuke Lu ◽  
Na Shu ◽  
Delong Wang ◽  
Junjuan Wang ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Homologous Gene ◽  
Segmental Duplications ◽  
Gene Pairs ◽  
Genome Wide ◽  
Cotton Species ◽  
Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and a necessity when studying the mechanisms of stress- tolerance in cotton.Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely localized in cells, but primarily in the nucleus. The PUBs in cotton were classified into six subfamilies (A-F) on the basis of phylogenetic analysis, which was testified by the analysis of conserved motifs and exon-intron structures. Chromosomal localization analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment analysis, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs in A2 and D5 were found; however no tandem duplications in A2 or D5 were found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, At sub-genome and Dt sub-genome of G. hirsutum, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reported the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in the response to abiotic stresses (including salt, drought, hot and cold) to varying degrees.

Abstract 16341: Application of Genomic Markers to Predict Outcome in Patients Receiving Left Ventricular Assist Device (LVAD) Therapy

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Ramesh Mazhari ◽  
Ian Toma ◽  
Nahal Konjedi ◽  
Claire Murphy ◽  
Farzad Moussavi ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Expression Patterns ◽  
Left Ventricular ◽  
Micro Rna ◽  
Rna Expression ◽  
Blood Samples ◽  
Mechanical Unloading ◽  
Genome Wide ◽  
Lv Remodeling ◽  
Highly Correlated

Introduction: LVADs are now used as a bridge to heart transplantation, or destination therapy in patients with advanced heart failure. LVAD therapy reverses left ventricular (LV) remodeling and improves survival in 50% of patients. Hypothesis: We hypothesize that patients with poor prognosis after LVAD therapy will have a different genomic profile as compared to patients with higher survival rate. We propose to use genome-wide expression analysis to determine the mRNA and microRNA profiling of LV tissue and peripheral blood and identify probes that predicts outcome in patients receiving LVAD therapy. Methods: Genome-wide RNA expression profiling of the LV apex core tissue, and blood samples of patients receiving LVAD were performed using Illumina HumanHT-12 v4 Expression BeadChip, to study the expression of 47000 mRNA and micro-RNA transcripts. Follow up echocardiographic parameters were used to determine the patients’ clinical response to LVAD therapy. We proposed that ≥10% reduction in LV end-diastolic diameter (LVEDD) at 3 months is considered a responder to LVAD therapy. The results of the gene expression analysis were integrated with clinical outcomes to identify RNA expression patterns that differentiate LVAD responders from non-responders. Results: The percent change in LVEDD at 3 months ranged from +12 to -44 (mean -12±0.21), and 45% of the patients were responders to LVAD therapy (n=35). We used GeneSpring GX12 to identify the differentially expressed transcripts, and filtered the probes by their correlation to % change in LVEDD as a continuous numerical measurement with correlation stringency of 0.85 <= r < =1.0. A total of 277 probes from LV samples were highly correlated with % change in LVEDD. The candidate mRNA, ncRNA, and microRNA transcripts (e.g. SOD1, 2, GPX1-4,TGF-β1, EGFR, AMPK, SRC) were categorized in 3 functional groups of oxidative stress, tissue fibrosis, and cellular energy depletion pathways using pathway studio. Profiling of blood samples did not reveal highly correlated probes. Conclusions: The myocardial transcriptome can predict the outcome in patients receiving LVAD therapy. The genetic markers, predictive of LV recovery after mechanical unloading, can help build new hypotheses for candidate pathways of LV remodeling.

scholarly journals Enhanced NRT1.1/NPF6.3 expression in shoots improves growth under nitrogen deficiency stress in Arabidopsis

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yasuhito Sakuraba ◽  
Chaganzhana ◽  
Atsushi Mabuchi ◽  
Koh Iba ◽  
Shuichi Yanagisawa
Keyword(s):  
Plant Growth ◽  
Nitrate Uptake ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Breeding Programs ◽  
Promoter Sequences ◽  
Genome Wide ◽  
A Genome ◽  
N Deficiency ◽  
Low Nitrogen

AbstractIdentification of genes and their alleles capable of improving plant growth under low nitrogen (N) conditions is key for developing sustainable agriculture. Here, we show that a genome-wide association study using Arabidopsis thaliana accessions suggested an association between different magnitudes of N deficiency responses and diversity in NRT1.1/NPF6.3 that encodes a dual-affinity nitrate transporter involved in nitrate uptake by roots. Various analyses using accessions exhibiting reduced N deficiency responses revealed that enhanced NRT1.1 expression in shoots rather than in roots is responsible for better growth of Arabidopsis seedlings under N deficient conditions. Furthermore, polymorphisms that increased NRT1.1 promoter activity were identified in the NRT1.1 promoter sequences of the accessions analyzed. Hence, our data indicated that polymorphism-dependent activation of the NRT1.1 promoter in shoots could serve as a tool in molecular breeding programs for improving plant growth in low N environments.

scholarly journals Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Xiaoxuan Hu ◽  
Chenyu Hao ◽  
Zong-Ming Cheng ◽  
Yan Zhong
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Expression Analysis ◽  
Gene Pair ◽  
Expression Patterns ◽  
Protein Motifs ◽  
Genome Wide ◽  
Copper Zinc ◽  
Essential Enzyme ◽  
Sod Gene Family

Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs. Additionally, many cis-elements related to different stresses were found in the promoters of the 10 VvSOD genes. Syntenic analysis revealed that VvMSD1 and VvMSD2 were derived from segmental duplication, and VvCSD4 and VvCSD5 belong to a pair of tandemly duplicated genes. Gene expression analysis based on microarray data showed that the 10 VvSOD genes were expressed in all the tested tissues. Interestingly, the segmentally duplicated gene pair (VvMSD1 and VvMSD2) exhibited differential expression patterns in various organs. In contrast, the tandemly duplicated gene pair (VvCSD4 and VvCSD5) displayed similar expression patterns in the tested organs. Our results provide a basis for further functional research on the SOD gene family in grapevine.

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