Sun 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
Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.
School of Life Sciences, Chongqing University, Chongqing, China.
Mol Biol Evol. 2021 Jan 23;38(2):486-501. doi: 10.1093/molbev/msaa240.
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.
熊蜂是自然生态系统和农业食品生产中全球重要的传粉者，种类多样。它们具有群居和独居的生命周期阶段，还有一些社会性寄生种类，是理解社会进化、行为和生态的特别有趣的模型。许多物种数量下降的报告指出，病原体传播、栖息地丧失、农药使用和全球气候变化是相互关联的原因。这些对熊蜂多样性的威胁使我们在农业授粉方面对少数经过充分研究的物种的依赖尤其不稳定。为了广泛采样熊蜂的基因组和表型多样性，我们对代表所有15个亚属的17个物种的基因组进行了从头测序和组装，首次对可能构成关键生态和行为特征基础的遗传和基因组变异进行了全属范围的量化。物种系统发育解析了亚属关系，而不完全谱系分选可能导致高水平的基因树不一致。五个染色体水平的组装显示出稳定的18条染色体核型，主要重排在社会性寄生种类中产生了25条染色体。转座元件活性的差异驱动了基因组大小的变化，重复序列的假定驯化影响了基因编码和调控潜力。动态进化的基因家族和正选择特征表明，在与觅食、饮食和代谢、免疫和解毒以及高海拔生活适应相关的过程中存在全属范围的变异。我们的研究揭示了熊蜂基因和基因组在熊蜂系统发育中的进化方式，并确定了可能与这些重要传粉者的关键生态和行为特征相关的变异。
