scholarly journals Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes

2022 ◽  
Vol 19 (1) ◽  
pp. 574
Author(s):  
Jacopo Umberto Verga ◽  
Matthew Huff ◽  
Diarmuid Owens ◽  
Bethany J. Wolf ◽  
Gary Hardiman
Keyword(s):  
Endocrine Disrupting Chemicals ◽  
Gene Families ◽  
Cellular Tissue ◽  
Adverse Outcomes ◽  
Adverse Outcome Pathway ◽  
Aquatic Life ◽  
Genomic Technologies ◽  
Genome Wide ◽  
Whole Transcriptome Sequencing ◽  
Assessment Strategies

Exposure to Endocrine Disrupting Chemicals (EDC) has been linked with several adverse outcomes. In this review, we examine EDCs that are pervasive in the environment and are of concern in the context of human, animal, and environmental health. We explore the consequences of EDC exposure on aquatic life, terrestrial animals, and humans. We focus on the exploitation of genomics technologies and in particular whole transcriptome sequencing. Genome-wide analyses using RNAseq provides snap shots of cellular, tissue and whole organism transcriptomes under normal physiological and EDC perturbed conditions. A global view of gene expression provides highly valuable information as it uncovers gene families or more specifically, pathways that are affected by EDC exposures, but also reveals those that are unaffected. Hypotheses about genes with unknown functions can also be formed by comparison of their expression levels with genes of known function. Risk assessment strategies leveraging genomic technologies and the development of toxicology databases are explored. Finally, we review how the Adverse Outcome Pathway (AOP) has exploited this high throughput data to provide a framework for toxicology studies.

scholarly journals Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Kai Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Genome Wide ◽  
Lea Gene ◽  
Late Embryogenesis ◽  
Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1510
Author(s):  
Salvatore Mastrangelo ◽  
Rosalia Di Gerlando ◽  
Maria Teresa Sardina ◽  
Anna Maria Sutera ◽  
Angelo Moscarelli ◽  
...  
Keyword(s):  
Conservation Status ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Local Populations ◽  
Genomic Technologies ◽  
Fitness Traits ◽  
Genome Wide ◽  
Breeding Schemes ◽  
Genomic Inbreeding

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

scholarly journals Genome-wide identification and expression profiling of thes MAPK, MAPKK, and MAPKKK gene families in Ophiocordyceps sinensis

Gene ◽  
2022 ◽  
Vol 807 ◽  
pp. 145930
Author(s):  
Pan Yue ◽  
Han Zhang ◽  
Xinxin Tong ◽  
Ting Peng ◽  
Pan Tang ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Gene Families ◽  
Ophiocordyceps Sinensis ◽  
Genome Wide

scholarly journals Potential Application of Genomic Technologies in Breeding for Fungal and Oomycete Disease Resistance in Pea

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1260
Author(s):  
Ambuj B. Jha ◽  
Krishna K. Gali ◽  
Zobayer Alam ◽  
V. B. Reddy Lachagari ◽  
Thomas D. Warkentin
Keyword(s):  
Disease Resistance ◽  
Genome Sequence ◽  
Potential Application ◽  
Ascochyta Blight ◽  
Gene Families ◽  
Snp Markers ◽  
Growth And Yield ◽  
Current Status ◽  
Genomic Technologies ◽  
Sequencing Platforms

Growth and yield of pea crops are severely affected by various fungal diseases, including root rot, Ascochyta blight, powdery mildew, and rust, in different parts of the world. Conventional breeding methods have led to enhancement of host plant resistance against these diseases in adapted cultivars, which is the primary option to minimize the yield losses. To support the breeding programs for marker-assisted selection, several successful attempts have been made to detect the genetic loci associated with disease resistance, based on SSR and SNP markers. In recent years, advances in next-generation sequencing platforms, and resulting improvements in high-throughput and economical genotyping methods, have been used to make rapid progress in identification of these loci. The first reference genome sequence of pea was published in 2019 and provides insights on the distribution and architecture of gene families associated with disease resistance. Furthermore, the genome sequence is a resource for anchoring genetic linkage maps, markers identified in multiple studies, identification of candidate genes, and functional genomics studies. The available pea genomic resources and the potential application of genomic technologies for development of disease-resistant cultivars with improved agronomic profile will be discussed, along with the current status of the arising improved pea germplasm.

Genome-wide identification of polar auxin transporter gene families reveals a possible new polar auxin flow in inverted cuttings of Populus yunnanensis

Gene ◽  
2020 ◽  
pp. 145349
Author(s):  
An-Pei Zhou ◽  
Yuan-Yuan Zhong ◽  
Si-Qi Li ◽  
Xuan Fei ◽  
Pei-Hua Gan ◽  
...  
Keyword(s):  
Gene Families ◽  
Transporter Gene ◽  
Genome Wide ◽  
Auxin Transporter

Quantification of Plant Sterols in Pulp and Paper Mill Effluents

2008 ◽  
Vol 43 (2-3) ◽  
pp. 173-181 ◽  
Author(s):  
Zahid Mahmood-Khan ◽  
Eric R. Hall
Keyword(s):  
Endocrine Disrupting Chemicals ◽  
Complex Mixture ◽  
Paper Mill ◽  
Pulp And Paper ◽  
Plant Sterols ◽  
Pulp And Paper Mill ◽  
Modified Technique ◽  
Butyl Ether ◽  
Aquatic Life ◽  
Paper Mill Effluents

Abstract Pulp and paper mill effluents (PPMEs) may contain high levels of otherwise naturally occurring organic pollutants such as plant sterols, which are suspected endocrine disrupting chemicals. Exposure to such chemicals may cause various physiological and morphological abnormalities that have been reported in the fish and other aquatic life inhabiting PPME receiving waters. Plant sterols, or phytosterols, form a constituent of wood extractives that may be released into the effluents during the pulping and paper making processes. Isolation and analysis of sterols from the complex mixture of PPMEs is challenging and standard analytical protocols do not exist. The need for having a reliable method for analyzing a particular environmental contaminant such as plant sterols cannot be overemphasized. In the present study a technique was modified for reliable analysis of PPME sterols. The technique involves liquid-liquid extractions using methyl-t-butyl ether and trimethyl-silylation derivatizations of the extracted sterols. Identification and quantification of the PPME sterols were accomplished by gas chromatography and mass spectrometry. Analytical problems were resolved by conducting multiple extractions, drying the sterol extracts, and redissolving and silylating the extracts at an increased derivatization temperature of 70°C. This shortened the suggested incubation period from 12 to 4 h. The modified technique offered improved method sensitivity and reproducibility, and successfully quantified campesterol, β-sitosterol, β-sitostanol, stigmasterol, stigmastanol, cholesterol, and ergosterol in PPMEs. Primary and secondary treated PPMEs analyses suggested 800 ± 190 µg/L total sterols in primary effluents, and 211 ± 90 µg/L in biologically treated final effluents. β-Sitosterol, β-sitostanol, and campesterol alone accounted for about 80% of the total sterols. A general comparison of the sterols in primary and secondary effluents suggested about 73% removal across the secondary treatment systems sampled.

scholarly journals Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1867
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Jiatong Wei ◽  
Kewei Cai ◽  
Hongzhi Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Cold Stress ◽  
Gene Family ◽  
Gene Families ◽  
Regulatory Function ◽  
Wrky Gene ◽  
Wrky Transcription Factors ◽  
Biotic Stresses ◽  
Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

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