Biomedical subjects

Yibo Hu

Publications and source records attributed to Yibo Hu.

3 recordsLinked to original sources

PubMed2026

Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation.

Uncovering the key genetic basis of complex phenotypic convergence in distantly related species has been a long-standing focus in evolutionary biology and genetics, and the convergent evolution of gliding in mammals offers a valuable opportunity to address this question. Here, we investigated the genomic basis of convergent evolution of gliding in mammals by analyzing both protein-coding genes and conserved non-coding elements (CNEs). We first de novo assembled and annotated two chromosome-level genomes of gliding mammals, the red and white giant flying squirrel (Petaurista alborufus) and sugar gliders (Petaurus breviceps), and conducted comprehensive comparative genomic analysis combined with another gliding mammal, the Sunda flying lemur (Galeopterus variegatus) and 14 background species. We found that the convergent evolution of protein-coding genes provided relatively limited but functionally relevant evidence linked to gliding phenotypes. By contrast, we found that gliding-accelerated CNEs (GACNEs) cluster near functionally equivalent genes and frequently aggregate into highly diverged yet functionally convergent hotspot regions. Across the three gliding lineages, both GACNEs and hotspot GACNEs show strong convergence in their functional enrichment profiles, suggesting a broad genetic basis underlying the convergent gliding phenotype. Furthermore, we identified 72 core transcription factors underpinning the genetic basis of gliding convergence, including EMX2 and ZFHX3, potentially involved in multiple aspects of gliding adaptation. Our study highlights the role of functional convergence in regulatory regions as a key mechanism in mammalian gliding convergence, offering valuable insights and strategies for uncovering the genetic basis of complex convergent traits, thereby advancing understanding of the molecular basis of convergent traits.

Petaurista alborufus↗

PubMed2026

Natural variation in BRN1 enhances nitrogen sensitivity to improve rice nitrogen use efficiency.

Green Revolution rice varieties deliver high yields but require excessive nitrogen (N) fertilizer and show diminished N responsiveness, severely reducing nitrogen-use efficiency (NUE). To dissect the molecular basis of low N sensitivity in modern cultivars, we conducted a genome-wide association study (GWAS) for biomass response to N (BRN), a trait tightly linked to N sensitivity, using a diverse rice germplasm panel. We identified BRN1 as a key regulator of N-dependent biomass accumulation that regulates NLP3, a master transcription factor governing nitrate signaling. Under elevated N supply, the strigolactone signaling repressor D53 accumulates substantially and interacts with BRN1 to repress NLP3 transcription, thereby reducing rice N response. Notably, the high-response BRN1H allele encodes a more stable protein that alleviates D53-mediated suppression. Introgression of this allele into modern cultivars significantly enhanced N sensitivity and grain yield under both low and high N conditions. Our findings establish a D53-BRN1-NLP3 regulatory module controlling rice NUE, providing a target for rice breeding to sustain high productivity with improved resource sustainability.

Oryza↗

PubMed2025

Mitochondrial Impostors: Prevalence and Impacts of NUMTs on Genetic and Evolutionary Studies in Carnivora.

Nuclear mitochondrial pseudogenes are mitochondria-derived DNA sequences integrated into the nuclear genome, which can introduce errors in species identification, phylogenetic inference, and population genetics. Although nuclear mitochondrial pseudogene contamination has been reported in some Carnivora species, a systematic investigation into the prevalence and impacts of nuclear mitochondrial pseudogenes across an order is still lacking. In this study, 22,102 mitochondrial DNA sequences of 80 Carnivora species from 14 families and 54 genera were retrieved from the public National Center for Biotechnology Information database and further analyzed. Using alignment-based methods, 158 problematic sequences/sequence groups were identified and categorized into four types: nuclear mitochondrial pseudogenes, species misidentification or mislabeling, sequence errors, and anomalous sites. Among families, Felidae exhibited the highest rate of nuclear mitochondrial pseudogene contamination, particularly in species of the genus Panthera. In contrast, no nuclear mitochondrial pseudogene contamination was detected in members of Ursidae and Ailuridae. Phylogenetic analysis revealed multiple independent origins of nuclear mitochondrial pseudogene, with some tracing back to the common ancestor of Carnivora. To mitigate nuclear mitochondrial pseudogene-related errors, rigorous sequence verification strategies, such as sequence alignment and phylogenetic validation, should be implemented. In conclusion, our findings highlight the necessity of nuclear mitochondrial pseudogene awareness in genetic and evolutionary studies of Carnivora and other taxa.

Animals↗