2025 Summer Undergraduate Research Program (SURP) symposium
Location
Dr. Ken Budke Family Auditorium, Schindler Education Center, University of Nothern Iowa
Presentation Type
Open Access Poster Presentation
Document Type
poster
Abstract
Bumblebee populations are a key source of pollination in many local prairies across Iowa, and genetic diversity among these populations is essential to their health. In order to study the variation, it needs to be examined at the genomic level. However, the current method for bumblebee DNA extraction is lethal, and involves removing tissue from the thorax of captured bees. To find a non-lethal method, procedures were adapted from reference literature that used tarsal clippings of bees rather than capturing and freezing the entire bee. DNA was extracted from 18 previously captured Bombus impatiens individuals, among which four bees were extracted via both thorax and tarsal methods. This tarsal clip method showed a lower initial concentration via electrophoresis gel after extraction. The Collibri Whole Genome Kit protocol was modified to targeted DNA fragment size and used to prepare bumblebee DNA for sequencing. The Collibri prep fragmented, indexed, and amplified the DNA. The samples were then quantified and resulted in concentrations above 2.0 ng/uL, the standard. A total of 24 libraries were completed using the refined protocol, and were sequenced at the University of Iowa with 2x150 bp runs. Compared to completed thorax libraries, the small amount of input DNA from tarsal clippings yielded libraries with similar final DNA concentrations and sequencing depth. Both Qubit and bioanalyzer data show a viable concentration and peak around 500-600 bp. Ugene software was used for sequence alignment, SNP data analysis, and further studies on genetic diversity.
Keywords: Bombus impatiens, tarsal clip, DNA sequence, tissue extraction, bioinformatic analysis
Start Date
1-8-2025 11:00 AM
End Date
1-8-2025 1:30 PM
Event Host
Summer Undergraduate Research Program, University of Northern Iowa
Faculty Advisor
Ai Wen
Department
Department of Biology
Copyright
©2025 Halle Hoefing and Ai Wen
File Format
application/pdf
Recommended Citation
Hoefing, Halle and Wen, Ai, "Whole Genome Sequencing of Bumblebees with Varied Tissue Quantity, Extraction Methods, and Bioinformatic Inquiries" (2025). Summer Undergraduate Research Program (SURP) Symposium. 6.
https://scholarworks.uni.edu/surp/2025/all/6
Whole Genome Sequencing of Bumblebees with Varied Tissue Quantity, Extraction Methods, and Bioinformatic Inquiries
Dr. Ken Budke Family Auditorium, Schindler Education Center, University of Nothern Iowa
Bumblebee populations are a key source of pollination in many local prairies across Iowa, and genetic diversity among these populations is essential to their health. In order to study the variation, it needs to be examined at the genomic level. However, the current method for bumblebee DNA extraction is lethal, and involves removing tissue from the thorax of captured bees. To find a non-lethal method, procedures were adapted from reference literature that used tarsal clippings of bees rather than capturing and freezing the entire bee. DNA was extracted from 18 previously captured Bombus impatiens individuals, among which four bees were extracted via both thorax and tarsal methods. This tarsal clip method showed a lower initial concentration via electrophoresis gel after extraction. The Collibri Whole Genome Kit protocol was modified to targeted DNA fragment size and used to prepare bumblebee DNA for sequencing. The Collibri prep fragmented, indexed, and amplified the DNA. The samples were then quantified and resulted in concentrations above 2.0 ng/uL, the standard. A total of 24 libraries were completed using the refined protocol, and were sequenced at the University of Iowa with 2x150 bp runs. Compared to completed thorax libraries, the small amount of input DNA from tarsal clippings yielded libraries with similar final DNA concentrations and sequencing depth. Both Qubit and bioanalyzer data show a viable concentration and peak around 500-600 bp. Ugene software was used for sequence alignment, SNP data analysis, and further studies on genetic diversity.
Keywords: Bombus impatiens, tarsal clip, DNA sequence, tissue extraction, bioinformatic analysis
