A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi

Harrison, Matthew; Sotola, V. Alex; Zalmat, Alexander; Sullivan, Kyle T.; Littrell, Bradley M.; Bonner, Timothy H.; Martin, Noland H.

doi:10.3390/genes14061197

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A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi

by

Matthew Harrison

¹,

V. Alex Sotola

^2,*

,

Alexander Zalmat

¹,

Kyle T. Sullivan

³,

Bradley M. Littrell

³,

Timothy H. Bonner

¹ and

Noland H. Martin

^1,*

¹

Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA

²

Biology Department, State University of New York at Oneonta, 108 Ravine Parkway, Oneonta, NY 13820, USA

³

BIO-WEST, Inc., 1405 United Drive, Suite 111, San Marcos, TX 78666, USA

^*

Authors to whom correspondence should be addressed.

Genes 2023, 14(6), 1197; https://doi.org/10.3390/genes14061197

Submission received: 4 May 2023 / Revised: 25 May 2023 / Accepted: 29 May 2023 / Published: 30 May 2023

(This article belongs to the Section Population and Evolutionary Genetics and Genomics)

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Abstract

Limiting harm to organisms caused by genetic sampling is an important consideration for rare species, and a number of non-destructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the unionid freshwater mussel, the Texas pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared with swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence), while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.

Keywords: non-destructive DNA sampling; DNA collection methods; Texas pigtoe; population genetic structure; genomic coverage; sequencing depth

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MDPI and ACS Style

Harrison, M.; Sotola, V.A.; Zalmat, A.; Sullivan, K.T.; Littrell, B.M.; Bonner, T.H.; Martin, N.H. A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi. Genes 2023, 14, 1197. https://doi.org/10.3390/genes14061197

AMA Style

Harrison M, Sotola VA, Zalmat A, Sullivan KT, Littrell BM, Bonner TH, Martin NH. A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi. Genes. 2023; 14(6):1197. https://doi.org/10.3390/genes14061197

Chicago/Turabian Style

Harrison, Matthew, V. Alex Sotola, Alexander Zalmat, Kyle T. Sullivan, Bradley M. Littrell, Timothy H. Bonner, and Noland H. Martin. 2023. "A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi" Genes 14, no. 6: 1197. https://doi.org/10.3390/genes14061197

APA Style

Harrison, M., Sotola, V. A., Zalmat, A., Sullivan, K. T., Littrell, B. M., Bonner, T. H., & Martin, N. H. (2023). A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi. Genes, 14(6), 1197. https://doi.org/10.3390/genes14061197

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A Comparison of Non-Destructive Visceral Swab and Tissue Biopsy Sampling Methods for Genotyping-by-Sequencing in the Freshwater Mussel Fusconaia askewi

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