Epigenetic Resources: Gaps in Aquatic Animal Germplasm Research DOI
Fangcheng Li, Junfang Zhang, Xiangbing Cheng

et al.

Reviews in Aquaculture, Journal Year: 2024, Volume and Issue: 17(1)

Published: Dec. 5, 2024

ABSTRACT Aquatic animal germplasm research plays a vital role in biodiversity conservation and sustainable aquaculture. The traditional view is that diversity of resources commonly attributed to genetic variation. However, recent studies transgenerational epigenetics have shown epigenetic information can also be passed down offspring, which consistent with the definition germplasm. Therefore, it necessary define information, such as DNA methylation, histone modifications, ncRNAs, through generations, incorporate them into concept Germplasm should include not only but resources. Epigenetic variation arise from genetic, environmental, or stochastic factors. Genetic co‐determine phenotypic traits. It has been demonstrated inherited across generations aquatic animals. modification, ncRNAs are involved addressing environmental challenges, maintaining diversity, improving breeding strategies, combating inbreeding decline, age determination. future on important for conservation, development, utilization. This review proposes new theoretical framework elucidate place collects articles past 8 years explore inheritance Integrating enhances our understanding population dynamics, adaptation, evolutionary processes, thereby informing strategies enhancing aquaculture practices. By considering both resources, we address challenges facing more comprehensively.

Language: Английский

Post-invasion selection acts on standing genetic variation despite a severe founding bottleneck DOI Creative Commons
Kathleen A. Dogantzis, Rika Raffiudin, Ramadhani Eka Putra

et al.

Current Biology, Journal Year: 2024, Volume and Issue: 34(6), P. 1349 - 1356.e4

Published: Feb. 29, 2024

Language: Английский

Citations

6
Phylogenetic analysis and detection of positive selection in the SIRT gene family across vertebrates DOI Creative Commons

Qiuxi Zhou,

Xiongtao Yang,

Da Li

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 5, 2025

SIRT6, a member of the sirtuin protein family, is recognized as tumor suppressor. This study investigates evolutionary history SIRT gene family and examines selective pressures shaping their functional divergence. Insights into evolution these genes may enhance our understanding roles in disease pathology. Seventy-three amino acid sequences full-length mRNA from 22 vertebrate species one invertebrate were retrieved public databases. Phylogenetic relationships among seven members reconstructed using Bayesian inference. Codon-based models applied to detect site-specific positive selection, likelihood ratio tests (LRTs) used compare model fits. Positively selected sites identified empirical Bayes (BEB) methods. analysis revealed that vertebrates originated duplication events. Asymmetric rates natural selection primary drivers Eleven positively (23I, 310 S, 311I, 313 A, 316 K, 320 C, 321 322Q, 323 H, 327E, 328P) with high confidence (posterior probability ≥ 99%), suggesting critical The characterized by selection. phylogenetic tree elucidates members, SIRT6 emerging key node. this represent mutation hotspots, providing potential targets for future cancer therapy research.

Language: Английский

Citations

0
Phenotypic plasticity and genetic variation of Prosopis juliflora (Sw.) DC. across diverse rangelands in northeastern Ethiopia DOI Creative Commons
Minyahel Tilahun, Ayana Angassa,

Zinabu Bora

et al.

Ecological Processes, Journal Year: 2025, Volume and Issue: 14(1)

Published: Jan. 10, 2025

Abstract Introduction Prosopis juliflora (Sw.) DC. substantially threatens dry rangelands due to its invasive attributes, exacerbated by climate change, land-use practices, and anthropogenic activities. Despite the urgent need understand ecological impacts, comprehensive studies examining relationship between functional traits reproductive fitness across diverse habitats scenarios are lacking. This study investigated of in Afar region Ethiopia, focusing on three types: dry-season grazing lands, wet-season wildlife reserves. Methods Plant samples were collected from 192 plots assess their adaptive potential genetic variation, alongside relevant physiographic climatic data. approach aims elucidate contributions these factors observed variation plasticity rangeland types differing land use intensity. Generalized linear mixed models co-occurrence networks employed analyze complex interaction. Results Our findings revealed significant fruiting onset duration, with lands demonstrating a shorter duration compared Genetic was for total seed mass number, indicating robust adaptability. The relative growth rate higher reserves highlighting advantages nutrient-rich environments. Additionally, analysis identified soil type as critical factor influencing trait performance. Conclusions underscores targeted management strategies mitigate impacts , emphasizing role nutrients fitness. offer valuable insights into dynamics species ecosystems inform conservation efforts.

Language: Английский

Citations

0
The effect of lead exposure over several generations on the wings condition of Drosophila melanogaster DOI
Indah Permatasari, Iin Hindun, Diani Fatmawati

et al.

AIP conference proceedings, Journal Year: 2025, Volume and Issue: 3253, P. 020075 - 020075

Published: Jan. 1, 2025

Language: Английский

Citations

0
The Role of Phenotypic Plasticity and Within‐Environment Trait Variability in the Assembly of the Nectar Microbiome and Plant–Microbe–Animal Interactions DOI Creative Commons
Sergio Quevedo‐Caraballo, Sergio Álvarez‐Pérez

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(3)

Published: March 1, 2025

ABSTRACT The study of the rules that govern relationship between phenotypic plasticity, genetic structure, and ecological success has traditionally focused on animals, plants, a few model microbial species, whereas non‐model microorganisms have received much less attention in this regard. floral nectar angiosperms is an ephemeral, island‐like habitat for different highly adapted yeasts bacteria. growth depends their ability to efficiently use available nutrients tolerate challenging physicochemical conditions, including high osmotic pressures, unbalanced carbon‐to‐nitrogen ratios, presence diverse defensive compounds plant origin. production alternative states response environmental cues (i.e., plasticity) or independently from these (within‐environment trait variability) might be particularly relevant nectar, which rapid needed population persistence improve chance animal‐mediated dispersal. In article, we microbiome as example encourage further research causes consequences plasticity within‐environment variability microbes. We review previous work mechanisms potential significance displayed by Additionally, provide overview some topics require attention, trade‐offs traits are adaptation dynamic environments direct indirect effects fitness flower‐visiting other conclude microbes essential get better understanding community assembly establishment interactions similar strongly selective habitats.

Language: Английский

Citations

0
A review of the human microRNA and the Mycobacterium tuberculosis epigenetic effects on the emergence drug resistance DOI

Yashna Sukdeo,

Nozibusiso Pearl Shozi,

Nonsikelelo Ndimande

et al.

Life Sciences, Journal Year: 2025, Volume and Issue: unknown, P. 123637 - 123637

Published: April 1, 2025

Language: Английский

Citations

0
Epigenetic background of lineage-specific gene expression landscapes of four Staphylococcus aureus hospital isolates DOI Creative Commons
Ilya S. Korotetskiy, Sergey V. Shilov, Tatyana Kuznetsova

et al.

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(5), P. e0322006 - e0322006

Published: May 5, 2025

Bacteria with similar genomes can exhibit different phenotypes due to alternative gene expression patterns. In this study, we analysed four antibiotic-resistant Staphylococcus aureus hospital isolates using transcriptomics, PacBio genome sequencing, and methylomics analyses. Transcriptomic data were obtained from cultures exposed gentamicin, the iodine-alanine complex CC-196, their combination. We observed strain-specific patterns of core accessory genes that remained stable under antimicrobial stress – a phenomenon term Clonal Gene Expression Stability (CGES) is main discovery paper. An involvement epigenetic mechanisms in stabilization CGES was hypothesized statistically verified. Canonical methylation controlled by type I restriction-modification systems accounted for ~ 10% epigenetically modified adenine residues, whereas multiple non-canonically adenines distributed sporadically imperfect DNA targeting methyltransferases. Protein-coding sequences characterized significantly lower frequency nucleotides. Epigenetic modifications near transcription start codons showed significant negative association levels. While role regulation remains debatable, variations non-canonical modification may serve as markers CGES.

Language: Английский

Citations

0
DNA methylation-mediated energy metabolism provides new insight into the quality losses during oyster reproductive process DOI
Xinxing Wang,

Yuheng Wei,

Rihao Cong

et al.

Aquaculture, Journal Year: 2024, Volume and Issue: 583, P. 740595 - 740595

Published: Jan. 21, 2024

Language: Английский

Citations

2
Spatial covariation between genetic and epigenetic diversity in wild plant and animal populations: a meta-analysis DOI Creative Commons

Nadia Langford,

Laura Fargeot, Simon Blanchet

et al.

Journal of Experimental Biology, Journal Year: 2024, Volume and Issue: 227(Suppl_1)

Published: March 7, 2024

ABSTRACT Epigenetic variation may be crucial in understanding the structure of wild populations, thereby aiding their management and conservation. However, relationship between epigenetic genetic remains poorly understood, especially populations. To address this, we conducted a meta-analysis studies that examined structures plant animal We aimed to determine whether is spatially independent highlight conditions under which might informative. show significant positive correlation pairwise differentiation, indicating diversity closely linked differentiation. The was weaker for population pairs were weakly differentiated genetically, suggesting such cases, marks marks. Additionally, found global levels differentiation similar across except when populations genetically. In either higher or lower than Our results suggest information particularly relevant have recently diverged genetically are connected by gene flow. Future should consider inferring role local adaptation Furthermore, there need identify factors sustain links improve our interplay these two forms

Language: Английский

Citations

1
Epigenetic diversity of genes with copy number variations among natural populations of the three‐spined stickleback DOI Creative Commons
Frédéric J. J. Chain, Britta Meyer, Melanie J. Heckwolf

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(7)

Published: July 1, 2024

Abstract Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression misexpression of duplicated can be detrimental subject negative selection. this scenario, newly duplicate may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them persist in populations as copy number variations (CNVs). animals plants, younger duplicates tend have higher levels DNA methylation lower suggesting epigenetic regulation could promote retention duplications via expression repression silencing. Here, we test hypothesis that variation coincides with young segregating CNVs six three‐spined stickleback span a salinity gradient from 4 30 PSU. Using reduced‐representation bisulfite sequencing, found CNV differentiation outliers rarely overlapped. Whereas lineage‐specific were highly methylated, just two showed significant association between promoter level number, not interact our dataset. If most new regulated dosage by mechanisms, results do support strong contribution soon after duplication. Instead, consistent preference already methylated.

Language: Английский

Citations

1