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Xiaodong Chen

Publications and source records attributed to Xiaodong Chen.

2 recordsLinked to original sources
PubMed2026

A spatiotemporal resolution to genetic redundancy: MIR164 diversification coordinates development and metabolism in Brassica.

Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.

MicroRNAs↗
PubMed2025

Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.

BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation. RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production. CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.

Rumen↗