On the probability of reaching high peaks in fitness landscapes by adaptive walks Molecular Biology and Evolution 2025 Yang Li and Jianzhi Zhang

• The probability of reaching high peaks (P_HP) varies widely across empirical and theoretical fitness landscapes.
• Landscape ruggedness strongly influences (P_HP), with smoother landscapes allowing easier access to high peaks.
• Higher peaks generally have larger basins, but this correlation alone does not ensure high (P_HP).
• Empirical landscapes do not consistently exhibit higher-than-expected (P_HP) compared to RMF landscapes.

Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved Genome Research 2025 Yang Li and Jianzhi Zhang

• Gene knockout effects often include byproducts and do not reflect true function.
• Orthologous gene deletions in different yeasts show distinct transcriptomic and proteomic changes.
• Expression levels are stable, but deletion effects vary due to genetic background.
• Most gene deletion effects do not reveal real gene function.

FoxO and rotund form a binding complex governing wing polyphenism in planthoppers iScience 2023 Chen, S.-J., Zhang, J.-L., Ma, W.-J., Wu, H.-J., Yang Li, Shen, X.-X. Xu, H.-J. F

• Rotund is differentially expressed between long-winged and short-winged BPHs.
• Knockdown of rotund reverses long wings into intermediate wings.
• Binding to the TF FoxO inhibits the rotund activity.

How has HGT shaped the evolution of insect genomes? Environmental Microbiology 2023 Chao, L., Yang Li, Chen, Y., Chen, X.-x., Huang, J., Rokas, A. Shen, X.-X.

• Insects are incredibly diverse and essential to ecosystems.
• Horizontal gene transfer (HGT) is important in prokaryotic evolution, and recent studies show it also plays a role in insect evolution.
• Although genomic data has revealed many HGT events in insects, the full extent of its influence and the mechanisms behind it remain unclear.

HGT is widespread in insects and contributes to male courtship in lepidopterans Cell 2022 Yang Li, Liu, Z., Liu, C., Shi, Z., Pang, L., Chen, C., Chen, Y., Pan, R., Zhou, W., Chen, X.-x., Rokas, A., Huang, J. Shen, X.-X.

• Genome-scale screening of HGT in 218 insect genomes.
• Intron gains from native insect genomes were likely involved in HGT adaptation.
• Lepidopterans acquired, on average, the highest number of HGT-acquired genes.
• HGT-acquired gene enhances male courtship behavior in lepidopterans.

BmNPV-induced hormone metabolic disorder in silkworm leads to enhanced locomotory behavior Developmental & Comparative Immunology 2021 Yang Li, Zhang, J., Zhao, S. Wu, X.

• BmNPV triggers the heat-shock response, resulting in severe brain pathology.
• BmNPV infection changed the host endogenous hormone homeostasis.
• 20E and dopamine counteractively regulate ELA behavior induced by BmNPV.
• Dopamine may promote dopaminergic signal systems to trigger this aberrant hyperactivity.

Bombyx mori nucleopolyhedrovirus Bm46 is essential for efficient production of infectious BV and nucleocapsid morphogenesis Virus Research 2020 Yang Li, Zhang, J., Kong, X., Chen, N., Zeng, X. Wu, X.

• Bm46 is not a core gene in baculovirus, but plays a pivotal role during the late infection.
• The deletion of Bm46 resulted in a decreased BV production but did not affect viral DNA replication.
• Bm46 is required for the proper assembly and morphogenesis of nucleocapsid.
• In Bm46KO-infected cells, VP39 mislocalized into filaments and cables punctate in RZ.

Bombyx mori nucleopolyhedrovirus F-like protein Bm14 is a factor for viral-induced cytopathic effects via regulating oxidative phosphorylation and cellular ROS levels Virology 2020 Kong, X., Xu, W., Chen, N., Yang Li, Shen, Y. Wu, X.

• BmNPV infection induces cell detachment and morphological changes.
• Bm14 is a viral factor involved in BmNPV infection induced CPEs.
• Bm14 deletion activates cellular oxidative phosphorylation pathway and suppresses ROS levels.
• The novel role of F-like protein in accelerating baculovirus infection via exerting cytopathogenic function.

Identification of A functional region in Bombyx mori nucleopolyhedrovirus VP39 that is essential for nuclear actin polymerization Virology 2020 Zhang, J., Yang Li, Zhao, S. Wu, X.

• Nuclear actin polymerization is crucial for the assembly of baculovirus nucleocapsid, but the virus-mediated mechanism remains unclear.
• VP39, the major protein in the baculovirus capsid, interacts with cellular actin and mediates actin polymerization. Its role in nuclear actin polymerization was previously uncertain.
• Deletion of vp39 abolished nuclear actin polymerization, which was restored upon vp39 repair, highlighting VP39’s essential role in this process.
• Mutant analysis and intracellular localization studies identified that amino acids 192–286 in the C-terminal region of VP39 are crucial for nuclear actin polymerization.

Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection Plos Pathogens 2020 Kong, X., Wei, G., Chen, N., Zhao, S., Shen, Y., Zhang, J., Yang Li, Zeng, X. Wu, X.

• The study examines how Bombyx mori nucleopolyhedrovirus (BmNPV) infection impacts host chromatin architecture.
• BmNPV infection leads to progressive chromatin remodeling, resulting in a more open chromatin structure and the marginalization of the host genome, accompanied by nucleosome disassembly.
• In uninfected cells, chromatin accessibility is regulated by euchromatic modifications, whereas BmNPV infection induces accessible regions associated with facultative heterochromatic modifications.
• The findings provide new insights into how DNA viruses alter host chromatin organization and epigenomic regulation.