Heatwave resilience of juvenile white sturgeon is associated with epigenetic and transcriptional alterations DOI Creative Commons
Madison L. Earhart, Tessa S. Blanchard, Nicholas Strowbridge

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Sept. 18, 2023

Abstract Heatwaves are increasing in frequency and severity, posing a significant threat to organisms globally. In aquatic environments heatwaves often associated with low environmental oxygen, which is deadly combination for fish. However, surprisingly little known about the capacity of fishes withstand these interacting stressors. This issue particularly critical species extreme conservation concern such as sturgeon. We assessed tolerance juvenile white sturgeon from an endangered population heatwave exposure investigated how this affects additional acute measured whole-animal thermal hypoxic performance underlying epigenetic transcriptional mechanisms. Sturgeon exposed simulated had increased exhibited complete compensation effects hypoxia. These changes were increase mRNA levels involved stress ( hsp90a, hsp90b, hsp70 hif1a ) following Global DNA methylation was sensitive rapidly responded hypoxia over course hour. data demonstrate that exhibit substantial resilience heatwaves, improved cross-tolerance stressors involving rapid responses both

Language: Английский

Polyploidy as a Fundamental Phenomenon in Evolution, Development, Adaptation and Diseases DOI Open Access
Olga V. Anatskaya, Alexander E. Vinogradov

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(7), P. 3542 - 3542

Published: March 24, 2022

DNA replication during cell proliferation is ‘vertical’ copying, which reproduces an initial amount of genetic information. Polyploidy, results from whole-genome duplication, a fundamental complement to vertical copying. Both organismal and polyploidy can emerge via premature cycle exit or cell-cell fusion, the latter giving rise polyploid hybrid organisms epigenetic hybrids somatic cells. Polyploidy-related increase in biological plasticity, adaptation, stress resistance manifests evolution, development, regeneration, aging, oncogenesis, cardiovascular diseases. Despite prevalence nature importance for medicine, agri- aquaculture, processes mechanisms underlying these features largely remain unknown. The evolutionarily conserved include activation transcription, response stress, damage hypoxia, induction programs morphogenesis, unicellularity, longevity, suggesting that common confer adaptive viability, cells organisms. By increasing polyploidization provide survival under stressful conditions where diploid cannot survive. However, it occurs at expense specific function, thus promoting developmental programming adult diseases risk cancer. Notably, genes arising evolutionary are heavily involved cancer other Ploidy-related changes gene expression presumably originate chromatin modifications derepression bivalent genes. provided evidence elucidates role carcinogenesis, may contribute development new strategies regeneration preventing

Language: Английский

Citations

52
Integrated biochemical, transcriptomic and metabolomic analyses provide insight into heat stress response in Yangtze sturgeon (Acipenser dabryanus) DOI Creative Commons

Yeyu Chen,

Xiaoyun Wu,

Jiansheng Lai

et al.

Ecotoxicology and Environmental Safety, Journal Year: 2022, Volume and Issue: 249, P. 114366 - 114366

Published: Dec. 9, 2022

Temperature fluctuations caused by climate change and global warming pose a great threat to various species. Most fish are particularly vulnerable elevated temperatures. Understanding the mechanism of high-temperature tolerance in can be beneficial for proposing effective strategies help cope with warming. In this study, we systematically studied effects high temperature on Acipenser dabryanus, an ancient living fossil flagship species Yangtze River, at histological, biochemical, transcriptomic metabolomic levels. Intestinal liver tissues from control groups (18 °C) acute heat stress (30 A. dabryanus were sampled histological observation assessed profiling. Histopathological analysis showed that intestine damaged after stress. The plasma cortisol content levels oxidative markers (catalase/glutathione reductase) two aminotransferases (aspartate aminotransferase/alanine aminotransferase) increased significantly response Transcriptomic methods 6707 upregulated 4189 downregulated genes 64 78 metabolites group. Heat shock protein (HSP) striking changes expression under stress, 21 belonging HSP30, HSP40, HSP60, HSP70 HSP90 families short-term majority associated ubiquitin immune-related pathways also markedly addition, combined gene profiles suggested enhancement amino acid metabolism glycometabolism suppression fatty during which could potential energy conservation strategy dabryanus. To best our knowledge, present study represents first attempt reveal mechanisms responses provide insights into improved cultivation

Language: Английский

Citations

40
Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor DOI Creative Commons
Anthony K. Redmond, Dearbhaile Casey, Manu Kumar Gundappa

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 19, 2023

Abstract Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play role in survival through mass extinctions. Paddlefish sturgeon are sister lineages that both show genomic evidence for ancient WGD. Until now this has been interpreted as two independent WGD events due to preponderance of duplicate with histories. Here we although there indeed plurality apparently gene duplications, these derive from shared occurring well over 200 million years ago, likely close the Permian-Triassic extinction period. This was followed by prolonged process reversion stable diploid inheritance (rediploidization), have promoted during Triassic-Jurassic extinction. We sharing masked fact paddlefish lineage divergence occurred before rediploidization had proceeded even half-way. Thus, most resolution diploidy lineage-specific. Because only truly duplicated once established, genomes thus mosaic non-shared duplications resulting event.

Language: Английский

Citations

38
The genomic signatures of evolutionary stasis DOI Creative Commons
Chase Doran Brownstein, Daniel J. MacGuigan, Daemin Kim

et al.

Evolution, Journal Year: 2024, Volume and Issue: 78(5), P. 821 - 834

Published: March 4, 2024

Abstract Evolutionary stasis characterizes lineages that seldom speciate and show little phenotypic change over long stretches of geological time. Although appear to exhibit evolutionary are often called living fossils, no single mechanism is thought be responsible for their slow rates morphological evolution low species diversity. Some analyses molecular in a handful fossil have indicated these clades genomic change. Here, we investigate mechanisms using dataset 1,105 exons 481 vertebrate species. We demonstrate two ancient ray-finned fishes classically gars sturgeons, the lowest substitution protein-coding genes among all jawed vertebrates. Comparably observed at fourfold degenerate sites implying decoupled from selection speculate linked highly effective DNA repair apparatus. gar last sharing common ancestry 100 million years ago produce morphologically intermediate fertile hybrids wild. This makes oldest naturally hybridizing divergence eukaryotes supports theoretical prediction nucleotide across genome accumulation genetic incompatibilities, enabling hybridization deeply divergent slowing rate speciation timescales. Our results help establish as barrier innovation provide explain diversity lineages.

Language: Английский

Citations

14
The dynamics of loss of heterozygosity events in genomes DOI Creative Commons
Abhishek Dutta, Joseph Schacherer

EMBO Reports, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Abstract Genomic instability is a hallmark of tumorigenesis, yet it also plays an essential role in evolution. Large-scale population genomics studies have highlighted the importance loss heterozygosity (LOH) events, which long been overlooked context genetic diversity and instability. Among various types genomic mutations, LOH events are most common affect larger portion genome. They typically arise from recombination-mediated repair double-strand breaks (DSBs) or lesions that processed into DSBs. critical drivers diversity, enabling rapid phenotypic variation contributing to tumorigenesis. Understanding accumulation LOH, along with its underlying mechanisms, distribution, consequences, therefore crucial. In this review, we explore spectrum their impact on fitness phenotype, drawing insights Saccharomyces cerevisiae cancer. We emphasize instability, disease, genome

Language: Английский

Citations

1
The American Paddlefish Genome Provides Novel Insights into Chromosomal Evolution and Bone Mineralization in Early Vertebrates DOI Creative Commons
Peilin Cheng, Yu Huang,

Yunyun Lv

et al.

Molecular Biology and Evolution, Journal Year: 2020, Volume and Issue: 38(4), P. 1595 - 1607

Published: Dec. 15, 2020

Abstract Sturgeons and paddlefishes (Acipenseriformes) occupy the basal position of ray-finned fishes, although they have cartilaginous skeletons as in Chondrichthyes. This evolutionary status their morphological specializations make them a research focus, but complex genomes (polyploidy presence microchromosomes) bring obstacles challenges to molecular studies. Here, we generated first high-quality genome assembly American paddlefish (Polyodon spathula) at chromosome level. Comparative genomic analyses revealed recent species-specific whole-genome duplication event, extensive chromosomal changes, including head-to-head fusions pairs intact, large ancestral chromosomes within paddlefish. We also provide an overview SCPP (secretory calcium-binding phosphoprotein) repertoire that is responsible for tissue mineralization, demonstrating earliest flourishing members occurred least before split between Acipenseriformes teleosts. In summary, this provides genetic resource understanding evolution polyploid nonteleost fishes bone mineralization early vertebrates.

Language: Английский

Citations

61
A brief review of vertebrate sex evolution with a pledge for integrative research: towards ‘sexomics’ DOI Creative Commons
Matthias Stöck, Lukáš Kratochvíl, Heiner Kuhl

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 376(1832), P. 20200426 - 20200426

Published: July 12, 2021

Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors simple to complex genetic mechanisms that evolved repeatedly independently various groups. Here, we review evolution across major clades of vertebrates information on SD, sexual development reproductive modes. We offer an up-to-date divergence times, species diversity, genomic resources, genome size, occurrence nature polyploids, SD systems, chromosomes, genes, dosage compensation sex-biased gene expression. Advances sequencing technologies now enable us study the at broader evolutionary scales, hope pursue a sexomics integrative research initiative vertebrates. The vertebrate sexome comprises interdisciplinary integrated differentiation, reproduction all levels, from genomes, transcriptomes proteomes, organs involved sex-specific processes, including gonads, secondary those transcriptional sex-bias. also includes ontogenetic behavioural aspects malfunction impairment fertility. Starting data generated high-throughput approaches, encourage others contribute expertise building understanding sexomes many key species. This article is part theme issue ‘Challenging paradigm chromosome evolution: empirical theoretical insights focus (Part I)’.

Language: Английский

Citations

53
A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus DOI Creative Commons
Boudjema Imarazene, Kang Du,

Séverine Beille

et al.

Current Biology, Journal Year: 2021, Volume and Issue: 31(21), P. 4800 - 4809.e9

Published: Sept. 7, 2021

Language: Английский

Citations

49
Rapid evolution fuels transcriptional plasticity to ocean acidification DOI
Jingliang Kang, Ivan Nagelkerken, Jodie L. Rummer

et al.

Global Change Biology, Journal Year: 2022, Volume and Issue: 28(9), P. 3007 - 3022

Published: March 3, 2022

Ocean acidification (OA) is postulated to affect the physiology, behavior, and life-history of marine species, but potential for acclimation or adaptation elevated pCO

Language: Английский

Citations

32
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine DOI Creative Commons
Sinan U. Umu, Vanessa Molin Paynter,

Håvard Trondsen

et al.

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(8), P. 100348 - 100348

Published: June 25, 2023

The annotation of microRNAs depends on the availability transcriptomics data and expert knowledge. This has led to a gap between novel genomes high-quality microRNA complements. Using >16,000 from manually curated gene database MirGeneDB, we generated trained covariance models for all conserved families. These are available in our tool MirMachine, which annotates within genomes. We successfully applied MirMachine range animal species, including those with large genome duplications extinct where small RNA sequencing is hard achieve. further describe score expected that can be used assess completeness assemblies. closes long-persisting field by facilitating automated pipelines deeper studies into evolution regulation, even organisms.

Language: Английский

Citations

18