Malus sieversii (Ledeb.) M. Roem. (M. anisophylla Sumn., M. heterophylla Sumn. non valide publ., M. hissarica Kudr., M. jarmolenkoi Sumn., M. juzepczukii Vass. non valide publ., M. kirghisorum Al. Theod. et Fed., M. kudrjaschevii Sumn., M. linczevskii Poljak., M. niedzwetzkyana Dieck, M. persicifolta (M. Pop.) Sumn., M. pumila Mill. var persicifolia M. Pop., M. schischkinii Poljak., M. sieversii subsp. hissarica (Kudr.) Likhonos, M. sieversii subsp. kirghisorum (Al. Theod et Fed.) Likhonos, M. sieversii su

Azimova, Shakhnoza S.; Glushenkova, Anna I.

doi:10.1007/978-0-85729-323-7_2415

Cited by 32 publications

(30 citation statements)

References 1 publication

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“…To identify the biological function of DEGs from bulk transcriptional analysis, the common IMR DEGs were subjected to Gene Ontology (GO) (Consortium, 2017) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa et al, 2008) analysis using Metascape (http://metascape.org/gp/index. html), with significant enrichment considered at p < 0.01.…”

Section: Functional Annotation and Pathway Enrichment Analysismentioning

confidence: 99%

Transcriptomic analysis identified SLC40A1 as a key iron metabolism-related gene in airway macrophages in childhood allergic asthma

Wang

Cun

et al. 2023

Front. Cell Dev. Biol.

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Introduction: Asthma is the most common chronic condition in children, with allergic asthma being the most common phenotype, accounting for approximately 80% of cases. Growing evidence suggests that disruption of iron homeostasis and iron regulatory molecules may be associated with childhood allergic asthma. However, the underlying molecular mechanism remains unclear.Methods: Three childhood asthma gene expression datasets were analyzed to detect aberrant expression profiles of iron metabolism-related genes in the airways of children with allergic asthma. Common iron metabolism-related differentially expressed genes (DEGs) across the three datasets were identified and were subjected to functional enrichment analysis. Possible correlations between key iron metabolism-related DEGs and type 2 airway inflammatory genes were investigated. Single-cell transcriptome analysis further identified major airway cell subpopulations driving key gene expression. Key iron metabolism-related gene SLC40A1 was validated in bronchoalveolar lavage (BAL) cells from childhood asthmatics with control individuals by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and immunofluorescence. The intracellular iron content in BAL cells was assessed by Perls iron staining and the iron levels in BAL supernatant was measured by iron assay to assess airway iron metabolism status in childhood asthmatics.Results: Five common iron metabolism-related DEGs were identified, which were functionally related to iron homeostasis. Among these genes, downregulated SLC40A1 was strongly correlated with type 2 airway inflammatory markers and the gene signature of SLC40A1 could potentially be used to determine type 2-high and type 2-low subsets in childhood allergic asthmatics. Further single-cell transcriptomic analysis identified airway macrophages driving SLC40A1 expression. Immunofluorescence staining revealed colocalization of FPN (encoded by SLC40A1) and macrophage marker CD68. Down-regulation of SLC40A1 (FPN) was validated by qRT-PCR and immunofluorescence analysis. Results further indicated reduced iron levels in the BAL fluid, but increased iron accumulation in BAL cells in childhood allergic asthma patients. Furthermore, decreased expression of SLC40A1 was closely correlated with reduced iron levels in the airways of children with allergic asthma.Discussion: Overall, these findings reveal the potential role of the iron metabolism-related gene SLC40A1 in the pathogenesis of childhood allergic asthma.

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Section: Functional Annotation and Pathway Enrichment Analysismentioning

confidence: 99%

Transcriptomic analysis identified SLC40A1 as a key iron metabolism-related gene in airway macrophages in childhood allergic asthma

Wang

Cun

et al. 2023

Front. Cell Dev. Biol.

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“…All DEGs were mapped to Gene Ontology (GO) terms in the Gene Ontology database (http:// www.geneontology.org), and the output of enrichment was limited to FDR < 0.05. Pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (Kanehisa et al, 2008), and pathways with FDRcorrected p≤ 0.05 were considered significantly enriched in DEGs. The expression modules in Figure 4A were generated by STEM v1.3.7 (Ernst and Bar-Joseph, 2006) based on the FPKM values.…”

Section: Genes Expression Data Analysismentioning

confidence: 99%

Comparative transcriptome analysis of molecular mechanisms underlying adventitious root developments in Huangshan Bitter tea (Camellia gymnogyna Chang) under red light quality

Wei

Chen

et al. 2023

Front. Plant Sci.

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As the formation of adventitious roots (AR) is an important component of in vitro regeneration of tea plants, the propagation and preservation of Huangshan Bitter tea (Camellia gymnogyna Chang) cuttings have been hindered due to its lower rooting rate. As light is a crucial environmental factor that affects AR formation, this study aimed to investigate the special role of red light (RL) in the formation of AR in Huangshan Bitter tea plants, which has not been well understood. Huangshan Bitter tea plants were induced with white light (control, WL) and red light (660 nm, RL) qualities 36 days after induced treatment (DAI) to investigate dynamic AR formation and development, anatomical observation, hormones content change, and weighted gene co-expression network analysis (WGCNA) of the transcriptome. Results showed that RL promoted the rooting rate and root characteristics compared to WL. Anatomical observations demonstrated that root primordium was induced earlier by RL at the 4 DAI. RL positively affected IAA, ZT and GA3 content and negatively influenced ABA from the 4 to 16 DAI. RNA-seq and analysis of differential expression genes (DEGs) exhibited extensive variation in gene expression profiles between RL and WL. Meanwhile, the results of WGCNA and correlation analysis identified three highly correlated modules and hub genes mainly participated in 'response to hormone', 'cellular glucan metabolic progress', and 'response to auxin'. Furthermore, the proportion of transcription factors (TFs) such as ethylene response factor (ERF), myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WRKYGQK (WRKY) were the top four in DEGs. These results suggested that the AR-promoting potential of red light was due to complex hormone interactions in tea plants by regulating the expression of related genes. This study provided an important reference to shorten breeding cycles and accelerate superiority in tea plant propagation and preservation.

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“…GO terms with p-value <0.05 were considered as significantly enriched. Pathway enrichment of DEGs was performed using the KEGG database (Kanehisa et al, 2008). Then, the KOBAS software (v2.0.12) was used to test the statistical enrichment of the DEGs in the KEGG pathways (Mao et al, 2005).…”

Section: Transcriptome Data Analysismentioning

confidence: 99%

Transcriptome analysis reveals defense-related genes and pathways during dodder (Cuscuta australis) parasitism on white clover (Trifolium repens)

Zhou

Zawaira

et al. 2023

Front. Genet.

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Dodders (Cuscuta australis R. Br.) are holo-parasitic stem angiosperms with an extensive host range that have significant ecological and economic potential impact on the ecosystem and the agricultural system. However, how the host plant responds to this biotic stress remains mostly unexplored. To identify the defense-related genes and the pathways in white clover (Trifolium repens L.) induced by dodder parasitism, we performed a comparative transcriptome analysis of the leaf and root tissues from white clover with and without dodder infection by high throughput sequencing. We identified 1,329 and 3,271 differentially expressed genes (DEGs) in the leaf and root tissues, respectively. Functional enrichment analysis revealed that plant-pathogen interaction, plant hormone signal transduction, and phenylpropanoid biosynthesis pathways were significantly enriched. Eight WRKY, six AP2/ERF, four bHLH, three bZIP, three MYB, and three NAC transcription factors showed a close relationship with lignin synthesis-related genes, which defended white clover against dodder parasitism. Real-time quantitative PCR (RT-qPCR) for nine DEGs, further validated the data obtained from transcriptome sequencing. Our results provide new insights into understanding the complex regulatory network behind these parasite-host plant interactions.

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Cited by 32 publications

References 1 publication

Transcriptomic analysis identified SLC40A1 as a key iron metabolism-related gene in airway macrophages in childhood allergic asthma

Transcriptomic analysis identified SLC40A1 as a key iron metabolism-related gene in airway macrophages in childhood allergic asthma

Comparative transcriptome analysis of molecular mechanisms underlying adventitious root developments in Huangshan Bitter tea (Camellia gymnogyna Chang) under red light quality

Transcriptome analysis reveals defense-related genes and pathways during dodder (Cuscuta australis) parasitism on white clover (Trifolium repens)

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