Draft genome assembly and population genetics of an agricultural pollinator, the solitary alkali bee (Halictidae: Nomia melanderi)

Karen M. Kapheim, Hailin Pan, Cai Li, Charles Blatti, Brock A. Harpur, Panagiotis Ioannidis, Beryl M. Jones, Clement F. Kent, Livio Ruzzante, Laura Sloofman, Eckart Stolle, Robert M. Waterhouse, Amro Zayed, Guojie Zhang, William T. Wcislo

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Alkali bees (Nomia melanderi) 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.

Original languageEnglish
Pages (from-to)625-634
Number of pages10
JournalG3: Genes, Genomes, Genetics
Issue number3
StatePublished - Mar 1 2019

Bibliographical note

Funding Information:
We are grateful to M. Ingham, M. Buckley, and M. Wagoner for allowing us to collect from their bee beds. J. Dodd and Forage Genetics International provided lab space while in the field. Sequencing was performed by the Roy J. Carver Biotechnology Center at University of Illinois at Urbana-Champaign (UIUC). Computational support was provided by University of Utah Center for High Performance Computing and UIUC CNRG/Biocluster. J. Johnson (Life Sciences Studios) created the illustration in Figure 1. Funding was provided by grants from the USDA-ARS Alfalfa Pollinator Research Initiative (KMK). This research was supported by the Utah Agricultural Experiment Station, Utah State University, and approved as journal paper number 9175 (KMK) and Agriculture and Food Research Initiative competitive award no. 2018-67014-27542 from the USDA National Institute of Food and Agriculture (KMK). Additional funding was provided by a Smithsonian Institution Competitive Grants Program for Biogenomics (WTW, KMK, BMJ), Swiss National Science Foundation grant PP00P3_170664 (RMW), and general research funds from the Smithsonian Tropical Research Institute (WTW).

Publisher Copyright:
Copyright © 2019 Kapheim et al.


  • Alternative
  • Bee
  • Elements
  • Genetics
  • Pollinators
  • Population
  • Sociogenomics
  • Solitary
  • Transposable

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)


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