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G3 (Bethesda). 2019 Mar 7;9(3):625-634. doi: 10.1534/g3.118.200865.

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

Author information

1
Department of Biology, Utah State University, Logan, UT 84322 karen.kapheim@usu.edu.
2
Smithsonian Tropical Research Institute, Panama City, Republic of Panama.
3
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
4
China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China.
5
Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark.
6
The Francis Crick Institute, London NW1 1AT, United Kingdom.
7
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL.
8
Department of Entomology, Purdue University, W. Lafayette, IN, 47907.
9
Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, 70013 Vassilika Vouton, Heraklion, Greece.
10
Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
11
Department of Biology, York University, Toronto, Ontario, M3J 1P3, Canada.
12
Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
13
Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
14
Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany.

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.

KEYWORDS:

alternative pollinators; population genetics; sociogenomics; solitary bee; transposable elements

PMID:
30642875
PMCID:
PMC6404593
DOI:
10.1534/g3.118.200865
[Indexed for MEDLINE]
Free PMC Article

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