The gingiva is a key oral barrier that protects oral tissues from various stimuli.A loss of gingival tissue homeostasis causes periodontitis,one of the most prevalent inflammatory diseases in humans.The human gingiva ...The gingiva is a key oral barrier that protects oral tissues from various stimuli.A loss of gingival tissue homeostasis causes periodontitis,one of the most prevalent inflammatory diseases in humans.The human gingiva exists as a complex cell network comprising specialized structures.To understand the tissue-specific pathophysiology of the gingiva,we applied a recently developed spatial enhanced resolution omics-sequencing(Stereo-seq)technique to obtain a spatial transcriptome(ST)atlas of the gingiva in healthy individuals and periodontitis patients.By utilizing Stereo-seq,we identified the major cell types present in the gingiva,which included epithelial cells,fibroblasts,endothelial cells,and immune cells,as well as subgroups of epithelial cells and immune cells.We further observed that inflammation-related signalling pathways,such as the JAK-STAT and NF-κB signalling pathways,were significantly upregulated in the endothelial cells of the gingiva of periodontitis patients compared with those of healthy individuals.Additionally,we characterized the spatial distribution of periodontitis risk genes in the gingiva and found that the expression of IFI16 was significantly increased in endothelial cells of inflamed gingiva.In conclusion,our Stereo-seq findings may facilitate the development of innovative therapeutic strategies for periodontitis by mapping periodontitis-relevant genes and pathways and effector cells.展开更多
Pecan(Carya illinoinensis)is a tree nut crop of worldwide economic importance that is rich in healthpromoting factors.However,pecan production and nut quality are greatly challenged by environmental stresses such as t...Pecan(Carya illinoinensis)is a tree nut crop of worldwide economic importance that is rich in healthpromoting factors.However,pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases.Here,we report a high-quality,chromosome-scale genome assembly of the controlled-cross pecan cultivar‘Pawnee’constructed by integrating Nanopore sequencing and Hi-C technologies.Phylogenetic and evolutionary analyses reveal two whole-genome duplication(WGD)events and two paleo-subgenomes in pecan and walnut.Time estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from bayberry.The two paleo-subgenomes differ in size and protein-coding gene sets.They exhibit uneven ancient gene loss,asymmetrical distribution of transposable elements(especially LTR/Copia and LTR/Gypsy),and expansions in transcription factor families(such as the extreme pecan-specific expansion in the far-red impaired response 1 family),which are likely to reflect the long evolutionary history of species in the Juglandaceae.A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate genes.Significant changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scabsusceptible cultivars‘Excell’and‘Pawnee’.These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan.The high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.展开更多
基金supported by the National Natural Science Foundation of China(82201011,82030031,92149301 and 82270945)the Beijing Municipal Government grant(Beijing Laboratory of Oral Health,PXM2021-014226-000041)+2 种基金the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences(2019-I2M-5-038)the Science and Technology Project of Guangzhou,China(202206080009)the Postdoctoral Foundation of China(2021M703695 and 2021TQ0308)。
文摘The gingiva is a key oral barrier that protects oral tissues from various stimuli.A loss of gingival tissue homeostasis causes periodontitis,one of the most prevalent inflammatory diseases in humans.The human gingiva exists as a complex cell network comprising specialized structures.To understand the tissue-specific pathophysiology of the gingiva,we applied a recently developed spatial enhanced resolution omics-sequencing(Stereo-seq)technique to obtain a spatial transcriptome(ST)atlas of the gingiva in healthy individuals and periodontitis patients.By utilizing Stereo-seq,we identified the major cell types present in the gingiva,which included epithelial cells,fibroblasts,endothelial cells,and immune cells,as well as subgroups of epithelial cells and immune cells.We further observed that inflammation-related signalling pathways,such as the JAK-STAT and NF-κB signalling pathways,were significantly upregulated in the endothelial cells of the gingiva of periodontitis patients compared with those of healthy individuals.Additionally,we characterized the spatial distribution of periodontitis risk genes in the gingiva and found that the expression of IFI16 was significantly increased in endothelial cells of inflamed gingiva.In conclusion,our Stereo-seq findings may facilitate the development of innovative therapeutic strategies for periodontitis by mapping periodontitis-relevant genes and pathways and effector cells.
基金This work was supported by grants from the Natural Science Foundation of Zhejiang Province,China(grant no.Z20C160001)the State Key Laboratory of Subtropical Silviculture at Zhejiang A&F University(grant no.ZY20180202)the Research and Development Fund of Zhejiang A&F University(grant no.2018FR002).
文摘Pecan(Carya illinoinensis)is a tree nut crop of worldwide economic importance that is rich in healthpromoting factors.However,pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases.Here,we report a high-quality,chromosome-scale genome assembly of the controlled-cross pecan cultivar‘Pawnee’constructed by integrating Nanopore sequencing and Hi-C technologies.Phylogenetic and evolutionary analyses reveal two whole-genome duplication(WGD)events and two paleo-subgenomes in pecan and walnut.Time estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from bayberry.The two paleo-subgenomes differ in size and protein-coding gene sets.They exhibit uneven ancient gene loss,asymmetrical distribution of transposable elements(especially LTR/Copia and LTR/Gypsy),and expansions in transcription factor families(such as the extreme pecan-specific expansion in the far-red impaired response 1 family),which are likely to reflect the long evolutionary history of species in the Juglandaceae.A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate genes.Significant changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scabsusceptible cultivars‘Excell’and‘Pawnee’.These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan.The high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.
