Browsing by Author "Sun, Cheng"
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- Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral TraitsSun, Cheng; Huang, Jiaxing; Wang, Yun; Zhao, Xiaomeng; Su, Long; Thomas, Gregg W. C.; Zhao, Mengya; Zhang, Xingtan; Jungreis, Irwin; Kellis, Manolis; Vicario, Saverio; Sharakhov, Igor V.; Bondarenko, Semen M.; Hasselmann, Martin; Kim, Chang N.; Paten, Benedict; Penso-Dolfin, Luca; Wang, Li; Chang, Yuxiao; Gao, Qiang; Ma, Ling; Ma, Lina; Zhang, Zhang; Zhang, Hongbo; Zhang, Huahao; Ruzzante, Livio; Robertson, Hugh M.; Zhu, Yihui; Liu, Yanjie; Yang, Huipeng; Ding, Lele; Wang, Quangui; Ma, Dongna; Xu, Weilin; Liang, Cheng; Itgen, Michael W.; Mee, Lauren; Cao, Gang; Zhang, Ze; Sadd, Ben M.; Hahn, Matthew W.; Schaack, Sarah; Barribeau, Seth M.; Williams, Paul H.; Waterhouse, Robert M.; Mueller, Rachel Lockridge (Oxford University Press, 2021-02-01)Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage, and global climate change, as interconnected causes. These threats to bumblebee diversity make our reliance on a handful of well-studied species for agricultural pollination particularly precarious. To broadly sample bumblebee genomic and phenotypic diversity, we de novo sequenced and assembled the genomes of 17 species, representing all 15 subgenera, producing the first genus-wide quantification of genetic and genomic variation potentially underlying key ecological and behavioral traits. The species phylogeny resolves subgenera relationships, whereas incomplete lineage sorting likely drives high levels of gene tree discordance. Five chromosome-level assemblies show a stable 18-chromosome karyotype, with major rearrangements creating 25 chromosomes in social parasites. Differential transposable element activity drives changes in genome sizes, with putative domestications of repetitive sequences influencing gene coding and regulatory potential. Dynamically evolving gene families and signatures of positive selection point to genus-wide variation in processes linked to foraging, diet and metabolism, immunity and detoxification, as well as adaptations for life at high altitudes. Our study reveals how bumblebee genes and genomes have evolved across the Bombus phylogeny and identifies variations potentially linked to key ecological and behavioral traits of these important pollinators.
- Theoretical prediction and atomic kinetic Monte Carlo simulations of void superlattice self-organization under irradiationGao, Yipeng; Zhang, Yongfeng; Schwen, Daniel; Jiang, Chao; Sun, Cheng; Gan, Jian; Bai, Xianming (Springer Nature, 2018-04-26)Nano-structured superlattices may have novel physical properties and irradiation is a powerful mean to drive their self-organization. However, the formation mechanism of superlattice under irradiation is still open for debate. Here we use atomic kinetic Monte Carlo simulations in conjunction with a theoretical analysis to understand and predict the self-organization of nano-void superlattices under irradiation, which have been observed in various types of materials for more than 40 years but yet to be well understood. The superlattice is found to be a result of spontaneous precipitation of voids from the matrix, a process similar to phase separation in regular solid solution, with the symmetry dictated by anisotropic materials properties such as one-dimensional interstitial atom diffusion. This discovery challenges the widely accepted empirical rule of the coherency between the superlattice and host matrix crystal lattice. The atomic scale perspective has enabled a new theoretical analysis to successfully predict the superlattice parameters, which are in good agreement with independent experiments. The theory developed in this work can provide guidelines for designing target experiments to tailor desired microstructure under irradiation. It may also be generalized for situations beyond irradiation, such as spontaneous phase separation with reaction.