Development of Epigenetic Biomarkers in Aquatic Organisms

Published: June 30, 2023

Biomarkers, as measurable characteristics of normal or pathogenic processes, are used in the context human health and to monitor animal welfare ecosystem status. Epigenetic biomarkers generally stable time regardless genomic context. They show cell specificity can be detected early. These biological properties confer advantages over traditional molecular biomarkers. Genome-wide high-resolution epigenomic data now obtained at a reasonable cost because technological advances sequencing. In parallel, computational approaches such machine learning their accessibility allow for integrated analysis data. We suggest general systematic procedure epigenetic biomarker development using methods that adapted specific needs each project. Clearly defined outcome variables (e.g. phenotypic traits sex, age, growth, past exposures environmental factors) guide choice classification regression models development. describe basic concepts applying aquatic organisms provide detailed examples. Furthermore, we discuss relevant areas application organisms, hatchery-rearing, morphology, nutrition, health, influences, adaptation processes. Together, these could contribute toward developing mitigating strategies climate change-related challenges faced by aquaculture well monitoring welfare, life history traits, nutritional conditions under current artificial rearing evaluating overall impacts on broader environment.

Language: Английский

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ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactroceradorsalis

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 23, 2023

Introduction: While it has been suggested that histone modifications can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome modification patterns in invasive species, leaving the regulatory landscape of species unclear. Methods: Here, we screen genome-wide two important modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and 27 (H3K27me3), adult thorax muscles a notorious pest, Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). Results: We identified promoters featured by occupancy H3K4me3, H3K27me3 or bivalent were respectively annotated unique genes key muscle development structure maintenance. In addition, found occupied entire body genes, where average enrichment was almost constant. Transcriptomic analysis indicated H3K4me3 is associated active gene transcription, mostly transcriptional repression. Importantly, putative motifs modified distinct may possibly regulate flight activity. Discussion: These findings provide first evidence signature B. dorsalis, will be useful for future epigenetic other insect species.

Language: Английский

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Mixed Patterns of Intergenerational DNA Methylation Inheritance in Acropora

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(2)

Published: Jan. 18, 2024

Abstract For sessile organisms at high risk from climate change, phenotypic plasticity can be critical to rapid acclimation. Epigenetic markers like DNA methylation are hypothesized as mediators of plasticity; is associated with the regulation gene expression, change in response ecological cues, and a proposed basis for inheritance acquired traits. Within reef-building corals, gene-body (gbM) stressors. If coral transmissible across generations, this could potentially facilitate acclimation environmental change. We investigated heritability Acropora, stony coral. Two Acropora millepora two selago adults were crossed, producing eight offspring crosses (four hybrid, each species). used whole-genome bisulfite sequencing identify methylated loci allele-specific alignments quantify per-locus inheritance. heritable, differential (DM) between parents should equal DM paired alleles given locus. found mixture heritable nonheritable loci, portions ranging 44% 90% among crosses. gBM was more than intergenic methylation, most had consistent degree (i.e. deviation parental similar magnitude direction). Our results provide evidence that inherited but heterogenous throughout genome. Future investigations into heterogeneity its implications will important understanding potential capability intergenerational reef building corals.

Language: Английский

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Phenotypic plasticity in the monoclonal marbled crayfish is associated with very low genetic diversity but pronounced epigenetic diversity

Current Zoology, Journal Year: 2022, Volume and Issue: 69(4), P. 426 - 441

Published: Dec. 2, 2022

Clonal organisms are particularly useful to investigate the contribution of epigenetics phenotypic plasticity, because confounding effects genetic variation negligible. In last decade, apomictic parthenogenetic marbled crayfish, Procambarus virginalis, has been developed as a model relationships between plasticity and epigenetic diversity in detail. This crayfish originated about 30 years ago by autotriploidy from single slough fallax. As result human releases active spreading, established numerous populations very diverse habitats 22 countries tropics cold temperate regions. Studies laboratory field revealed considerable coloration, spination, morphometric parameters, growth, food preference, population structure, trophic position, niche width. Illumina PacBio whole-genome sequencing representatives 19 Europe Madagascar demonstrated extremely low within among populations, indicating that observed ability live strikingly different environments not due adaptation selection on variation. contrast, differences were found DNA methylation patterns hundreds genes, suggesting environmentally induced is mediated mechanisms corresponding changes gene expression. Specific fingerprints persisted local over successive existence ecotypes, but there presently no information whether these signatures transgenerationally inherited or anew each generation recorded adaptive nonadaptive.

Language: Английский

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RETICULATE PHYLOGENY: A NEW TETRAPLOID PARTHENOGENETIC WHIPTAIL LIZARD DERIVED FROM HYBRIDIZATION AMONG FOUR BISEXUAL ANCESTRAL SPECIES OF ASPIDOSCELIS (REPTILIA: SQUAMATA: TEIIDAE)

Bulletin of the Museum of Comparative Zoology, Journal Year: 2023, Volume and Issue: 163(7)

Published: Jan. 25, 2023

We describe the only known tetraploid parthenogenetic species of amniote that has haploid genomes from four distinct ancestral bisexual (gonochoristic) species. These were brought together through three hybridization events occurred over a time span hundreds or thousands years, last which recently in captivity without any experimental manipulation. Inheritance alleles at seven microsatellite deoxyribonucleic acid loci and DNA sequence data for adenosine deaminase intron 9 new confirms its parentage and, with quantification, demonstrates tetraploidy high heterozygosity are maintained parthenogenetically generation after generation. Comparisons univariate multivariate variation scalation between tetraploids their parental taxa reveal strong maternal similarity morphological characters, little to no significant differences, suggesting such females may exist old museum samples misidentified as ancestor. This research on specimens adds support earlier papers provide important insights taxonomic treatment many clones teiid lizards occur Western Hemisphere.

Language: Английский

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