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

• Published in: Genes Vol. 14; no. 6; p. 1197
• Main Authors: Harrison, Matthew, Sotola, V Alex, Zalmat, Alexander, Sullivan, Kyle T, Littrell, Bradley M, Bonner, Timothy H, Martin, Noland H
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 30.05.2023; MDPI
• Subjects: Animals; Bar codes; Biopsy; Bivalvia - genetics; Brief Report; Datasets; Deoxyribonucleic acid; DNA; DNA - genetics; DNA collection methods; Fusconaia askewi; Genomes; genomic coverage; Genotype; Genotyping; Genotyping Techniques - methods; Mollusks; non-destructive DNA sampling; Nondestructive testing; Nucleotide sequence; population genetic structure; Rare species; Sampling; Sampling techniques; sequencing depth; Texas pigtoe; Unionidae - genetics; United States > US; Texas; sequencing depth; non-destructive DNA sampling; DNA collection methods; genomic coverage; population genetic structure; Texas pigtoe
• ISSN: 2073-4425
• DOI: 10.3390/genes14061197

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 ( ). 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.