Molecular-level effects of acupuncture on depression: a genome-wide transcriptome analysis of pituitary gland in rats exposed to chronic restraint stress

Abstract Background Rice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The development and use of resistant rice varieties or genes is currently the most effective strategy to control BLB. Results Here, we used 259 rice accessions, which are genotyped with 2 888 332 high-confidence single nucleotide polymorphisms (SNPs). Combining resistance variation data of 259 rice lines for two Xoo races observed in 2 years, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) conferring plant resistance against BLB. The expression levels of genes, which contains in GWAS results were also identified between the resistant and susceptible rice lines by transcriptome analysis at four time points after pathogen inoculation. From that 109 candidate resistance genes showing significant differential expression between resistant and susceptible rice lines were uncovered. Furthermore, the haplotype block structure analysis predicted 58 candidate genes for BLB resistance based on Chr. 7_707158 with a minimum P-value (–log 10 P = 9.72). Among them, two NLR protein-encoding genes, LOC_Os07g02560 and LOC_Os07g02570, exhibited significantly high expression in the resistant line, but had low expression in the susceptible line of rice. Conclusions Together, our results reveal novel BLB resistance gene resources, and provide important genetic basis for BLB resistance breeding of rice crops.

Download Full-text

Antidepressant Mechanism Research of Acupuncture: Insights from a Genome-Wide Transcriptome Analysis of Frontal Cortex in Rats with Chronic Restraint Stress

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2017/1676808 ◽

2017 ◽

Vol 2017 ◽

pp. 1-13 ◽

Cited By ~ 9

Author(s):

Yu Wang ◽

Huili Jiang ◽

Hong Meng ◽

Jing Li ◽

XinJing Yang ◽

...

Keyword(s):

Frontal Cortex ◽

Signaling Pathway ◽

Restraint Stress ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Chronic Restraint Stress ◽

Rna Seq ◽

Toll Like Receptor ◽

Genome Wide ◽

Receptor Signaling Pathway

Major depressive disorder (MDD) is a chronic disease that adversely affects mood and cognition. In this study, we randomly divided the rats into control group (C), model group (M), fluoxetine group (F), and acupuncture group (A), used open-field test to ascertain whether acupuncture affects chronic restraint stress (CRS) induced depression-like behaviors of rats, and explored the antidepressant mechanism of acupuncture at the molecular level of transcriptome in the frontal cortex of CRS rats by RNA-sequencing (RNA-seq). According to differentially expressed genes (DEG) analysis, we identified 134, 46, and 89 response genes differentially expressed in C versus M, F versus M, and A versus M, respectively. Through Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we identified the gene sets involved in extracellular space, inflammatory response, Toll-like receptor signaling pathway, chemokine signaling pathway, and TNF signaling pathway. In this study, RNA-seq technology was used to investigate the frontal cortex genome-wide transcriptomes in depression rats under CRS, which suggested that the antidepressant effect of acupuncture is effective and has a multitarget characteristic, which may be related to amino acid metabolism and inflammatory pathways, especially the Toll-like receptor signaling pathway, TNF signaling pathway, and NF-kappa B signaling pathway.

Download Full-text

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

BMC Plant Biology ◽

10.1186/s12870-021-03145-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jianping Yu ◽

Chaolei Liu ◽

Hai Lin ◽

Bin Zhang ◽

Xiaoxia Li ◽

...

Keyword(s):

Association Study ◽

Transcriptome Analysis ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Growth Responses ◽

Cd Stress ◽

New Genes ◽

Genome Wide ◽

A Genome ◽

Natural Variations

Abstract Background Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. Results In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. Conclusion The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Download Full-text

A Genome-Wide Longitudinal Transcriptome Analysis of the Aging Model Podospora anserine

PLoS ONE ◽

10.1371/journal.pone.0083109 ◽

2013 ◽

Vol 8 (12) ◽

pp. e83109 ◽

Cited By ~ 17

Author(s):

Oliver Philipp ◽

Andrea Hamann ◽

Jörg Servos ◽

Alexandra Werner ◽

Ina Koch ◽

...

Keyword(s):

Transcriptome Analysis ◽

Aging Model ◽

Genome Wide ◽

A Genome

Download Full-text

Bacillus megaterium adapts to acid stress condition through a network of genes: Insight from a genome-wide transcriptome analysis

Scientific Reports ◽

10.1038/s41598-018-34221-0 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 4

Author(s):

Gunajit Goswami ◽

Debashis Panda ◽

Ramkrishna Samanta ◽

Robin Chandra Boro ◽

Mahendra Kumar Modi ◽

...

Keyword(s):

Bacillus Megaterium ◽

Transcriptome Analysis ◽

Stress Condition ◽

Acid Stress ◽

Genome Wide ◽

A Genome

Download Full-text

Integrating a genome‐wide association study with a large‐scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice

Plant Biotechnology Journal ◽

10.1111/pbi.13051 ◽

2019 ◽

Vol 17 (7) ◽

pp. 1261-1275 ◽

Cited By ~ 13

Author(s):

Roslen Anacleto ◽

Saurabh Badoni ◽

Sabiha Parween ◽

Vito M. Butardo ◽

Gopal Misra ◽

...

Keyword(s):

Association Study ◽

Transcriptome Analysis ◽

Large Scale ◽

Genome Wide Association Study ◽

Glycaemic Index ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

Download Full-text

Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry

International Journal of Molecular Sciences ◽

10.3390/ijms222212587 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12587

Author(s):

Abinaya Manivannan ◽

Koeun Han ◽

Sun Yi Lee ◽

Hye-Eun Lee ◽

Jong Pil Hong ◽

...

Keyword(s):

Transcription Factor ◽

Transcriptome Analysis ◽

Fruit Color ◽

Regulatory Genes ◽

Ploidy Levels ◽

Anthocyanin Pathway ◽

Genome Wide ◽

A Genome ◽

The Difference ◽

Myb10 Transcription Factor

The genus Fragaria encompass fruits with diverse colors influenced by the distribution and accumulation of anthocyanin. Particularly, the fruit colors of strawberries with different ploidy levels are determined by expression and natural variations in the vital structural and regulatory genes involved in the anthocyanin pathway. Among the regulatory genes, MYB10 transcription factor is crucial for the expression of structural genes in the anthocyanin pathway. In the present study, we performed a genome wide investigation of MYB10 in the diploid and octoploid Fragaria species. Further, we identified seven quantitative trait loci (QTLs) associated with fruit color in octoploid strawberry. In addition, we predicted 20 candidate genes primarily influencing the fruit color based on the QTL results and transcriptome analysis of fruit skin and flesh tissues of light pink, red, and dark red strawberries. Moreover, the computational and transcriptome analysis of MYB10 in octoploid strawberry suggests that the difference in fruit colors could be predominantly influenced by the expression of MYB10 from the F. iinumae subgenome. The outcomes of the present endeavor will provide a platform for the understanding and tailoring of anthocyanin pathway in strawberry for the production of fruits with aesthetic colors.

Download Full-text

GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401874 ◽

2020 ◽

Vol 10 (12) ◽

pp. 4369-4372

Author(s):

Laura G. Macías ◽

Eladio Barrio ◽

Christina Toft

Keyword(s):

Phylogenetic Analysis ◽

Maximum Likelihood ◽

Positive Selection ◽

Molecular Level ◽

Variable Number ◽

Orthologous Genes ◽

Genome Wide ◽

A Genome ◽

One To One ◽

Python Package

One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package. However, it has a limitation when it comes to genome-wide studies, as it runs on a gene-by-gene basis. Furthermore, the size of such studies will depend on the number of orthologous genes the genomes have income and these are often restricted to only account for instances where a one-to-one relationship is observed between the genomes. In this work, we present GWideCodeML, a Python package, which runs a genome-wide codeml with the option of parallelization. To maximize the number of analyzed genes, the package allows for a variable number of taxa in the alignments and will automatically prune the topology to fit each of them, before running codeml.

Download Full-text