Genome‐wide identification studies – A primer to explore new genes in plant species

Safder, Imran; Shao, Gaoneng; Sheng, Zhonghua; Hu, Peisong; Tang, Shengxiang

doi:10.1111/plb.13340

Cited by 7 publications

(4 citation statements)

References 96 publications

(217 reference statements)

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Section: Methodsmentioning

confidence: 99%

“…Microbial community was identified by searching the clustered proteins in the Unified Human Gastrointestinal Genome (UHGG) (version 2.0) database using Blastp and an E-value threshold of 1 × 10 −10 . 30 The microorganisms screened by the UHGG database will be used for subsequent microbiome analysis. 31 Eggnog-mapper (v.2.1.7) was used to implement function annotations of metagenomic reads for COG (Cluster of Orthologous Groups), CAZy (Carbohydrate-Active Enzymes), and KEGG (Kyoto Encyclopedia of Genes and Genomes).…”

Section: Metagenomic Data Analysismentioning

confidence: 99%

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Associations between Wastewater Microbiome and Population Smoking Rate Identified Using Wastewater-Based Epidemiology

Wu,

Zhang,

Chen

et al. 2023

Environ. Health

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Tobacco use is known to cause health damage, partly by changing the mouth, respiratory tract, and gut-related microbiomes. This study aims to identify the associations between the human microbiome detected in domestic wastewater and the population smoking rate. Metagenomic sequencing and a biomarker discovery algorithm were employed to identify microorganisms as potential microbial biomarkers of smoking through wastewater-based epidemiology. Wastewater samples were collected from selected catchments with low and high smoking rates, i.e., 11.2 ± 1.5% and 17.0 ± 1.6%, respectively. Using the linear discriminant analysis effect size (LEfSe) method, Neisseria, Desulfovibrio, Megamonas, Blautia, Fusicatenibacter, Granulicatella and Enterococcus were suggested as potential biomarker microorganisms. A higher abundance of pathogens, including Neisseria, Eikenella and Haemophilus, was associated with the high smoking rate, likely because of their colonization in smoking-disturbed human guts. The identified potential microbial biomarkers reflect the change of the human gut microbiome due to the long-term smoking behavior. The metagenomic analysis also indicates that smoking upregulates microbial gene expression of genetic information processing, environmental information processing, and cell wall peptidoglycan cleavage, while it downregulates amino acid, lipid, and galactose metabolisms. The findings demonstrate the potential of microbial biomarkers for the surveillance of smoking through a wastewaterbased epidemiology approach.

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Section: Methodsmentioning

confidence: 99%

Section: Metagenomic Data Analysismentioning

confidence: 99%

Associations between Wastewater Microbiome and Population Smoking Rate Identified Using Wastewater-Based Epidemiology

Wu,

Zhang,

Chen

et al. 2023

Environ. Health

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“…The genome-wide identification and characterization of gene families will provide the following parameters: chromosomal distribution, number of introns and exons, phylogenetic relationship, gene duplication, expression profiles and so forth that can be used for tomato crop improvement [ 27 ]. A genome-wide characterization of the E2F/DP gene family has been performed in a few plant species.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.)

Divya,

Robin,

Cho

et al. 2024

BMC Plant Biol

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Background E2F/DP (Eukaryotic 2 transcription factor/dimerization partner) family proteins play an essential function in the cell cycle development of higher organisms. E2F/DP family genes have been reported only in a few plant species. However, comprehensive genome-wide characterization analysis of the E2F/DP gene family of Solanum lycopersicum has not been reported so far. Results This study identified eight nonredundant SlE2F/DP genes that were classified into seven groups in the phylogenetic analysis. All eight genes had a single E2F-TDP domain and few genes had additional domains. Two segmental duplication gene pairs were observed within tomato, in addition to cis-regulatory elements, miRNA target sites and phosphorylation sites which play an important role in plant development and stress response in tomato. To explore the three-dimensional (3D) models and gene ontology (GO) annotations of SlE2F/DP proteins, we pointed to their putative transporter activity and their interaction with several putative ligands. The localization of SlE2F/DP-GFP fused proteins in the nucleus and endoplasmic reticulum suggested that they may act in other biological functions. Expression studies revealed the differential expression pattern of most of the SlE2F/DP genes in various organs. Moreover, the expression of E2F/DP genes against abiotic stress, particularly SlE2F/DP2 and/or SlE2F/DP7, was upregulated in response to heat, salt, cold and ABA treatment. Furthermore, the co-expression analysis of SlE2F/DP genes with multiple metabolic pathways was co-expressed with defence genes, transcription factors and so on, suggested their crucial role in various biological processes. Conclusions Overall, our findings provide a way to understand the structure and function of SlE2F/DP genes; it might be helpful to improve fruit development and tolerance against abiotic stress through marker-assisted selection or transgenic approaches.

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“…In plants, BAG protein family can be classified into two groups according to their structural characteristics through genome-wide alignment and conservative domain identification ( Safder et al., 2022 ). The first group has a ubiquitin-like (UBL) domain at the N-terminal end, similar to the structural composition of animal BAG1.…”

Section: Introductionmentioning

confidence: 99%

Functional insights of plant bcl-2–associated ahanogene (BAG) proteins: Multi-taskers in diverse cellular signal transduction pathways

et al. 2023

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Bcl-2-associated athanogene (BAG) gene family is a highly conserved molecular chaperone cofactor in evolution from yeast to humans and plants playing important roles in a variety of signal pathways. Plant BAG proteins have special structures, especially those containing CaM-binding IQ motifs which are unique to plants. While early studies focused more on the structure and physiological function of plant BAGs, recent studies have revealed many novel functional mechanisms involved in multiple cellular processes. How to achieve signal specificity has become an interesting topic of plant BAG research. In this review, we have provided a historic view of plant BAG research and summarized recent advances in the establishment of BAG as essential components in normal plant growth, environmental stress response, and plant immunity. Based on the relationship between BAG proteins and their newly interacting proteins, this review highlights the functional mechanisms of various cellular signals mediated by plant BAGs. Future work needs to focus on the post-translational modification of BAG proteins, and on understanding how specificity is achieved among BAG signaling pathways.

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Genome‐wide identification studies – A primer to explore new genes in plant species

Cited by 7 publications

References 96 publications

Associations between Wastewater Microbiome and Population Smoking Rate Identified Using Wastewater-Based Epidemiology

Associations between Wastewater Microbiome and Population Smoking Rate Identified Using Wastewater-Based Epidemiology

Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.)

Functional insights of plant bcl-2–associated ahanogene (BAG) proteins: Multi-taskers in diverse cellular signal transduction pathways

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