Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi)

Authors

Karen M. Kapheim, Utah State UniversityFollow
Hailin Pan, Chinese Academy of Sciences
Cai Li, The Francis Crick Institute
Charles Blatti Ill, Carl R. Woese Institute of Genomic Biology
Brock A. Harpur, Purdue University
Panagiotis Ioannidis, Institute of Molecular Biology and Biotechnology
Beryl M. Jones, University of Illinois at Urbana-Champaign
Clement F. Kent, York University
Livio Ruzzante, Swiss Institute of Bioinformatics
Laura Sloofman, Carl R. Woese Institute of Genomic Biology
Eckart Stolle, Martin-Luther-University Halle-Wittenberg
Robert M. Waterhouse, Swiss Institute of Bioinformatics
Amro Zayed, York University
Guojie Zhang, Chinese Academy of Sciences
William T. Wcislo, Smithsonian Tropical Research Institute

Document Type

Article

Journal/Book Title/Conference

G3: Genes, Genomes, Genetics

Volume

9

Issue

3

Publisher

Scientific Society Publisher Alliance

Publication Date

3-1-2019

Award Number

USDA, National Institute of Food and Agriculture (NIFA) 2018-67014-27542

Funder

USDA, National Institute of Food and Agriculture (NIFA)

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

First Page

625

Last Page

634

Related Content

Kapheim, Karen M., et al. (2018) "Supplemental Material for Kapheim et al., 2018". GSA, doi:10.25387/g3.7296281.v1.

Abstract

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.

Recommended Citation

Kapheim, Karen M., et al. "Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi)." G3: Genes, Genomes, Genetics, 2019 vol. 9, no. 3, pp. 625-634. https://doi.org/10.1534/g3.118.200865