Kapheim Karen M, Pan Hailin, Li Cai, Blatti Charles, Harpur Brock A, Ioannidis Panagiotis, Jones Beryl M, Kent Clement F, Ruzzante Livio, Sloofman Laura, Stolle Eckart, Waterhouse Robert M, Zayed Amro, Zhang Guojie, Wcislo William T
Department of Biology, Utah State University, Logan, UT 84322
Smithsonian Tropical Research Institute, Panama City, Republic of Panama.
G3 (Bethesda). 2019 Mar 7;9(3):625-634. doi: 10.1534/g3.118.200865.
Alkali bees () are solitary relatives of the halictine bees, which have become an important model for the evolution of social behavior, but for which few solitary comparisons exist. These ground-nesting bees defend their developing offspring against pathogens and predators, and thus exhibit some of the key traits that preceded insect sociality. Alkali bees are also efficient native pollinators of alfalfa seed, which is a crop of major economic value in the United States. We sequenced, assembled, and annotated a high-quality draft genome of 299.6 Mbp for this species. Repetitive content makes up more than one-third of this genome, and previously uncharacterized transposable elements are the most abundant type of repetitive DNA. We predicted 10,847 protein coding genes, and identify 479 of these undergoing positive directional selection with the use of population genetic analysis based on low-coverage whole genome sequencing of 19 individuals. We found evidence of recent population bottlenecks, but no significant evidence of population structure. We also identify 45 genes enriched for protein translation and folding, transcriptional regulation, and triglyceride metabolism evolving slower in alkali bees compared to other halictid bees. These resources will be useful for future studies of bee comparative genomics and pollinator health research.
碱蜂（）是隧蜂科蜜蜂的独居近亲，隧蜂科蜜蜂已成为社会行为进化的重要模型，但针对独居隧蜂科蜜蜂的比较研究却很少。这些地穴筑巢的蜜蜂会保护其发育中的后代免受病原体和捕食者的侵害，因此展现出了昆虫社会性出现之前的一些关键特征。碱蜂也是紫花苜蓿种子高效的本土传粉者，紫花苜蓿是美国具有重大经济价值的一种作物。我们对该物种进行了测序、组装和注释，获得了一个高质量的299.6兆碱基对的基因组草图。重复序列占该基因组的三分之一以上，此前未被表征的转座元件是最丰富的重复DNA类型。我们预测了10847个蛋白质编码基因，并通过对19个个体进行低覆盖度全基因组测序，利用群体遗传学分析确定其中479个基因正经历正向选择。我们发现了近期种群瓶颈的证据，但没有明显的种群结构证据。我们还确定了45个在蛋白质翻译与折叠、转录调控以及甘油三酯代谢方面富集的基因，与其他隧蜂科蜜蜂相比，这些基因在碱蜂中的进化速度较慢。这些资源将有助于未来蜜蜂比较基因组学和传粉者健康研究。
