scholarly journals A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean

2020 ◽  
Vol 21 (15) ◽  
pp. 5191
Author(s):  
Luming Yao ◽  
Biyun Yang ◽  
Xiaohong Ma ◽  
Shuangshuang Wang ◽  
Zhe Guan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Expression Patterns ◽  
Aphis Glycines ◽  
Limiting Factors ◽  
Small Subset ◽  
Transcriptional Responses ◽  
Callose Deposition ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome

Soybean aphid (Aphis glycines Matsumura) is one of the major limiting factors in soybean production. The mechanism of aphid resistance in soybean remains enigmatic as little information is available about the different mechanisms of antibiosis and antixenosis. Here, we used genome-wide gene expression profiling of aphid susceptible, antibiotic, and antixenotic genotypes to investigate the underlying aphid–plant interaction mechanisms. The high expression correlation between infested and non-infested genotypes indicated that the response to aphid was controlled by a small subset of genes. Plant response to aphid infestation was faster in antibiotic genotype and the interaction in antixenotic genotype was moderation. The expression patterns of transcription factor genes in susceptible and antixenotic genotypes clustered together and were distant from those of antibiotic genotypes. Among them APETALA 2/ethylene response factors (AP2/ERF), v-myb avian myeloblastosis viral oncogene homolog (MYB), and the transcription factor contained conserved WRKYGQK domain (WRKY) were proposed to play dominant roles. The jasmonic acid-responsive pathway was dominant in aphid–soybean interaction, and salicylic acid pathway played an important role in antibiotic genotype. Callose deposition was more rapid and efficient in antibiotic genotype, while reactive oxygen species were not involved in the response to aphid attack in resistant genotypes. Our study helps to uncover important genes associated with aphid-attack response in soybean genotypes expressing antibiosis and antixenosis.

scholarly journals Permissive epigenetic landscape facilitates distinct transcriptional signatures of activating transcription factor 6 in the liver

2021 ◽  
Author(s):  
Anjana Ramdas Nair ◽  
Priyanka Lakhiani ◽  
Chi Zhang ◽  
Filippo Macchi ◽  
Kirsten C. Sadler
Keyword(s):  
Transcription Factor ◽  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Response ◽  
Differentially Expressed ◽  
Small Subset ◽  
Gene Promoters ◽  
Transcriptional Responses ◽  
Functional Studies ◽  
Activating Transcription Factor

ABSTRACTProteostatic stress initiates a transcriptional response that is unique to the stress condition, yet the regulatory mechanisms underlying the distinct gene expression patterns observed in stressed cells remains unknown. Using a functional genomic approach, we investigated how activating transcription factor 6 (ATF6), a key transcription factor in the unfolded protein response (UPR), regulates target genes. We first designed a computational strategy to define Atf6 target genes based on the evolutionary conservation of predicted ATF6 binding in gene promoters, identifying 652 conserved putative Atf6 target (CPAT) genes. CPATs were overrepresented for genes functioning in the UPR, however, the majority functioned in cellular processes unrelated to proteostasis, including small molecule metabolism and development. Functional studies of stress-independent and toxicant based Atf6 activation in zebrafish livers showed that the pattern of CPAT expression in response to Atf6 overexpression, alcohol and arsenic was unique. Only 34 CPATs were differentially expressed in all conditions, indicating that Atf6 is sufficient to regulate a small subset of CPATs. Blocking Atf6 using Ceapins in zebrafish demonstrated that Atf6 is necessary for activation of these genes in response to arsenic. We investigated CPAT during physiologically mediated hepatocyte stress using liver regeneration in mice as a model. Over half of all CPATs were differentially expressed during this process. This was attributed to the permissive chromatin environment in quiescent livers on the promoters of these genes, characterized by the absence of H3K27me3 and enrichment of H3K4me3. Taken together, these data uncover a complex transcriptional response to Atf6 activation and implicate a permissive epigenome as a mechanism by which distinct transcriptional responses are regulated by Atf6.

scholarly journals Single-cell transcriptome atlas of Drosophila gastrula 2.0

2021 ◽  
Author(s):  
Shunta Sakaguchi ◽  
Yasushi Okochi ◽  
Chiharu Tanegashima ◽  
Osamu Nishimura ◽  
Tadashi Uemura ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Mrna Level ◽  
Gene Expression Profiles ◽  
Genome Wide ◽  
A Genome ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing both accurate spatial and lineage information is still lacking. Here, we report a new single-cell transcriptome atlas of Drosophila gastrulae, divided into 65 transcriptomically distinct clusters. We found that the expression profiles of plasma-membrane-related genes, but not those of transcription factor genes, represented each germ layer, supporting the nonequivalent contribution of each transcription factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstructed the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation.

scholarly journals Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10617
Author(s):  
Jie Li ◽  
Xinhao Liu ◽  
Qingmei Wang ◽  
Junyan Sun ◽  
Dexian He
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Seed Formation ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome ◽  
Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

scholarly journals Crosstalk in oxygen homeostasis networks: SKN-1/NRF inhibits the HIF-1 hypoxia-inducible factor in Caenorhabditis elegans

2021 ◽  
Author(s):  
Dingxia Feng ◽  
Zhiwei Zhai ◽  
Zhiyong Shao ◽  
Yi Zhang ◽  
Jo Anne Powell-Coffman
Keyword(s):  
Oxidative Stress ◽  
Hypoxia Inducible Factor ◽  
Regulatory Sequences ◽  
Low Oxygen ◽  
Transcriptional Responses ◽  
C Elegans ◽  
Protein Levels ◽  
Oxygen Homeostasis ◽  
Genome Wide ◽  
A Genome

AbstractDuring development, homeostasis, and disease, organisms must balance responses that allow adaptation to low oxygen (hypoxia) with those that protect cells from oxidative stress. The evolutionarily conserved hypoxia-inducible factors are central to these processes, as they orchestrate transcriptional responses to oxygen deprivation. Here, we employ genetic strategies in C. elegans to identify stress-responsive genes and pathways that modulate the HIF-1 hypoxia-inducible factor and facilitate oxygen homeostasis. Through a genome-wide RNAi screen, we show that RNAi-mediated mitochondrial or proteasomal dysfunction increases the expression of hypoxia-responsive reporter Pnhr-57:GFP in C. elegans. Interestingly, only a subset of these effects requires hif-1. Of particular importance, we found that skn-1 RNAi increases the expression of hypoxia-responsive reporter Pnhr-57:GFP and elevates HIF-1 protein levels. The SKN-1/NRF transcription factor has been shown to promote oxidative stress resistance. We present evidence that the crosstalk between HIF-1 and SKN-1 is mediated by EGL-9, the prolyl hydroxylase that targets HIF-1 for oxygen-dependent degradation. Treatment that induces SKN-1, such as heat, increases expression of a Pegl-9:GFP reporter, and this effect requires skn-1 function and a putative SKN-1 binding site in egl-9 regulatory sequences. Collectively, these data support a model in which SKN-1 promotes egl-9 transcription, thereby inhibiting HIF-1. We propose that this interaction enables animals to adapt quickly to changes in cellular oxygenation and to better survive accompanying oxidative stress.

scholarly journals Big fish, little fish: a multi-omics investigation of growth traits in silver trevally (Pseudocaranx georgianus – araara)

2021 ◽  
Author(s):  
◽  
Noémie Valenza-Troubat
Keyword(s):  
New Zealand ◽  
Linkage Mapping ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Growth Traits ◽  
Expression Patterns ◽  
Linkage Groups ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome

<p><b>Understanding the relationship between DNA sequence variation and the diversity of observable traits across the tree of life is a central research theme in biology. In all organisms, most traits vary continuously between individuals. Explaining the genetic basis of this quantitative variation requires disentangling genetic from non-genetic factors, as well as their interactions. The identification of causal genetic variants yields fundamental insights into how evolution creates diversity across the tree of life. Ultimately, this information can be used for medical, environmental and agricultural applications. Aquaculture is an industry that is experiencing significant global growth and is benefiting from the advances of genomic research. Genomic information helps to improve complex commercial phenotypes such as growth traits, which are easily quantified visually, but influenced by polygenes and multiple environmental factors, such as temperature. In the context of a global food crisis and environmental change, there is an urgent need not only to understand which genetic variants are potential candidates for selection gains, but also how the architecture of these traits are composed (e.g. monogenes, polygenes) and how they are influenced by and interact with the environment. The overall goal of this thesis research was to generate a genome-wide multi-omics dataset matched with exhaustive phenotypic information derived from a F0-F1 pedigree to investigate the quantitative genetic basis of growth in the New Zealand silver trevally (Pseudocaranx georgianus). These data were used to identify genomic regions that co-segregate with growth traits, and to describe the regulation of the genes involved in response to temperature fluctuations. The findings of this research helped gain fundamental insights into the genotype–phenotype map in an important teleost species and understand its ability to dynamically respond to temperature variations. This will ultimately support the establishment of a genomics-informed New Zealand aquaculture breeding programme. </b></p> <p>Chapter 1 of this thesis provides an overview of how genes interact with the environment to produce various growth phenotypes and how an understanding of this is important in aquaculture. This first chapter provides the deeper context for the research in subsequent data chapters. </p> <p>Chapter 2 describes the study population, the collection of phenotypic and genotypic data, and a first description of the genetic parameters of growth traits in trevally. A combination of Whole Genome Sequencing (WGS) and Genotyping-By-Sequencing (GBS) techniques were used to generate 60 thousand Single Nucleotide Polymorphism (SNP) markers for individuals in a two-generation pedigree. Together with phenotypic data, the genotyping data were used to reconstruct the pedigree, measure inbreeding levels, and estimate heritability for 10 growth traits. Parents were identified for 63% of the offspring and successful pedigree reconstruction indicated highly uneven contributions of each parent, and between the sexes, to the subsequent generation. The average inbreeding levels did not change between generations, but were significantly different between families. Growth patterns were found to be similar to that of other carangids and subject to seasonal variations. Heritability as well as genetic and phenotypic correlations were estimated using both a pedigree and a genomic relatedness matrix. All growth trait heritability estimates and correlations were found to be consistently high and positively correlated to each other. </p> <p>In Chapter 3, genotypic and phenotypic data were used to carry out linkage mapping and a genome-wide association study (GWAS) to map quantitative trait loci (QTLs) associated with growth differences in the F1 population. A linkage map was generated using the largest family, which allowed to scan for rare variants associated with the traits. The linkage map reported in this thesis is the first one for the Pseudocaranx genus and one of the densest for the carangid family. It included 19,861 SNPs contained in 24 linkage groups, which correspond to the 24 trevally chromosomes. Eight significant QTLs associated with height, length and weight were discovered on three linkage groups. Using GWAS, 113 SNPs associated with nine traits were identified and 29 genetic growth hot spots were uncovered. Two of the GWAS markers co-located with the QTLs discovered with the linkage mapping analysis. This demonstrates that combining QTL mapping and GWAS represents a powerful approach for the identification and validation of loci controlling complex phenotypes, such as growth, and provides important insights into the genetic architecture of these traits. </p> <p>Chapter 4, the last data chapter, investigates plasticity in gene expression patterns and growth of juvenile trevally, in response to different temperatures. Temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and the gene expression patterns of the pituitary gland and the liver were compared across treatments in a subset of 100 individuals, using RNA sequencing. Results showed that growth increased 50% more in the warmer compared with the colder condition, suggesting that temperature has a large impact on the metabolic activity associated with growth. We were able to annotate 27,887 gene models and found 39 differentially expressed genes (DEGs) in the pituitary, and 238 in the liver. Of these, 6 DEGs showed a common expression pattern between the tissues. Annotated blast matches of all DEGs revealed genes linked to major pathways affecting metabolism and reproduction. Our results indicate that native New Zealand trevally exhibit predictable plastic regulatory responses to temperature stress and the genes identified provide excellent for selective breeding objectives and studied how populations may adapt to increasing temperatures.</p> <p>Finally, Chapter 5 discusses the implications, future directions, and application of this research for trevally and other breeding programmes. It more broadly highlights the insights that were gained on the genetic architecture of growth, and the role of temperature in interacting and modulating genes involved in plastic growth responses.</p>

scholarly journals Genome-Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Eric G. Matson ◽  
Adam Z. Rosenthal ◽  
Xinning Zhang ◽  
Jared R. Leadbetter
Keyword(s):  
Protein Synthesis ◽  
Large Body ◽  
Transcriptional Responses ◽  
Translational Coupling ◽  
Genome Wide ◽  
A Genome ◽  
Protein Encoding ◽  
Termite Gut ◽  
Inhibiting Protein ◽  
Encoding Genes

ABSTRACTWhen prokaryotic cells acquire mutations, encounter translation-inhibiting substances, or experience adverse environmental conditions that limit their ability to synthesize proteins, transcription can become uncoupled from translation. Such uncoupling is known to suppress transcription of protein-encoding genes in bacteria. Here we show that the trace element selenium controls transcription of the gene for the selenocysteine-utilizing enzyme formate dehydrogenase (fdhFSec) through a translation-coupled mechanism in the termite gut symbiontTreponema primitia, a member of the bacterial phylumSpirochaetes. We also evaluated changes in genome-wide transcriptional patterns caused by selenium limitation and by generally uncoupling translation from transcription via antibiotic-mediated inhibition of protein synthesis. We observed that inhibiting protein synthesis inT. primitiainfluences transcriptional patterns in unexpected ways. In addition to suppressing transcription of certain genes, the expected consequence of inhibiting protein synthesis, we found numerous examples in which transcription of genes and operons is truncated far downstream from putative promoters, is unchanged, or is even stimulated overall. These results indicate that gene regulation in bacteria allows for specific post-initiation transcriptional responses during periods of limited protein synthesis, which may depend both on translational coupling and on unclassified intrinsic elements of protein-encoding genes.IMPORTANCEA large body of literature demonstrates that the coupling of transcription and translation is a general and essential method by which bacteria regulate gene expression levels. However, the potential role of noncanonical amino acids in regulating transcriptional output via translational control remains, for the most part, undefined. Furthermore, the genome-wide transcriptional state in response to translational decoupling is not well quantified. The results presented here suggest that the noncanonical amino acid selenocysteine is able to tune transcription of an important metabolic gene via translational coupling. Furthermore, a genome-wide analysis reveals that transcriptional decoupling produces a wide-ranging effect and that this effect is not uniform. These results exemplify how growth conditions that impact translational processivity can rapidly feed back on transcriptional productivity of prespecified groups of genes, providing bacteria with an efficient response to environmental changes.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

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