Dataset Information

Age group DNA methylation differences in lemon sharks (Negaprion brevirostris): Implications for future age estimation tools.

ABSTRACT: Age information is often non-existent for most shark populations due to a lack of measurable physiological and morphological traits that can be used to estimate age. Recently, epigenetic clocks have been found to accurately estimate age for mammals, birds, and fish. However, since these clocks rely, among other things, on the availability of reference genomes, their application is hampered in non-traditional model organisms lacking such molecular resources. The technique known as Methyl-Sensitive Amplified Polymorphism (MSAP) has emerged as a valid alternative for studying DNA methylation biomarkers when reference genome information is missing, and large numbers of samples need to be processed. Accordingly, the MSAP technique was used in the present study to characterize global DNA methylation patterns in lemon sharks from three different age groups (juveniles, subadults, and adults). The obtained results reveal that, while MSAP analyses lack enough resolution as a standalone approach to infer age in these organisms, the global DNA methylation patterns observed using this technique displayed significant differences between age groups. Overall, these results confer that DNA methylation does change with age in sharks like what has been seen for other vertebrates and that MSAP could be useful as part of an epigenetics pipeline to infer the broad range of ages found in large samples sizes.

SUBMITTER: Beal AP

PROVIDER: S-EPMC9425014 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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Age group DNA methylation differences in lemon sharks (<i>Negaprion brevirostris</i>): Implications for future age estimation tools.

Beal Andria Paige AP Hackerott Serena S Feldheim Kevin K Gruber Samuel H SH Eirin-Lopez Jose M JM

Ecology and evolution 20220829 8

Age information is often non-existent for most shark populations due to a lack of measurable physiological and morphological traits that can be used to estimate age. Recently, epigenetic clocks have been found to accurately estimate age for mammals, birds, and fish. However, since these clocks rely, among other things, on the availability of reference genomes, their application is hampered in non-traditional model organisms lacking such molecular resources. The technique known as Methyl-Sensitiv ...[more]

PMID: 36052296

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Project description:Skin mucus in fish is the first barrier between the organism and the environment but the role of skin mucus in protecting fish against pathogens is not well understood. During copulation in sharks, the male bites the female generating wounds, which are then highly likely to become infected by opportunistic bacteria from the water or from the male shark's mouth. Describing the microbial component of epithelial mucus may allow future understanding of this first line of defense in sharks. In this study, we analyzed mucus and skin samples obtained from 19 individuals of two shark species and a stingray: the nurse shark (Ginglymostoma cirratum), the lemon shark (Negaprion brevirostris) and the southern stingray (Hypanus americanus). Total DNA was extracted from all samples, and the bacterial 16S rRNA gene (region V3-V4) was amplified and sequenced on the Ion Torrent Platform. Bacterial diversity (order) was higher in skin and mucus than in water. Order composition was more similar between the two shark species. Alpha-diversities (Shannon and Simpson) for OTUs (clusters of sequences defined by a 97% identity threshold for the16S rRNA gene) were high and there were non-significant differences between elasmobranch species or types of samples. We found orders of potentially pathogenic bacteria in water samples collected from the area where the animals were found, such as Pasteurellales (i.e., genus Pasteurella spp. and Haemophilus spp.) and Oceanospirillales (i.e., genus Halomonas spp.) but these were not found in the skin or mucus samples from any species. Some bacterial orders, such as Flavobacteriales, Vibrionales (i.e., genus Pseudoalteromonas), Lactobacillales and Bacillales were found only in mucus and skin samples. However, in a co-occurrence analyses, no significant relationship was found among these orders (strength less than 0.6, p-value > 0.01) but significant relationships were found among the order Trembayales, Fusobacteriales, and some previously described marine environmental Bacteria and Archaea, including Elusimicrobiales, Thermoproteales, Deinococcales and Desulfarculales. This is the first study focusing on elasmobranch microbial communities. The functional role and the benefits of these bacteria still needs understanding as well as the potential changes to microbial communities as a result of changing environmental conditions.

Dataset Information

Age group DNA methylation differences in lemon sharks (Negaprion brevirostris): Implications for future age estimation tools.

Publications

Age group DNA methylation differences in lemon sharks (<i>Negaprion brevirostris</i>): Implications for future age estimation tools.

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