Genome architecture and selective signals compensatorily shape plastic response to a new environment DOI Creative Commons
Ao Li,

Ming-Jie Zhao,

Ziyan Zhang

et al.

The Innovation, Journal Year: 2023, Volume and Issue: 4(4), P. 100464 - 100464

Published: June 21, 2023

Transcriptional plasticity interacts with natural selection in complex ways and is crucial for the survival of species under rapid climate change. How 3D genome architecture affects transcriptional its interaction genetic adaptation are unclear. We transplanted estuarine oysters to a new environment found that genes located active chromatin regions exhibited greater plasticity, changes these were negatively correlated selective signals. This indicates trade-off between signals shaping plastic responses environment. Specifically, mutation, lincRNA, accessibility distal enhancer potentially affect ManⅡa gene, which regulates muscle function oysters. Our findings reveal compensates role environmental response environments provide insights into synergetic epigenetic interactions critical fitness-related trait model marine species.

Language: Английский

Mechanisms of protein evolution DOI Open Access
Vijay Jayaraman, Saacnicteh Toledo‐Patiño, Lianet Noda‐García

et al.

Protein Science, Journal Year: 2022, Volume and Issue: 31(7)

Published: June 22, 2022

Abstract How do proteins evolve? changes in sequence mediate protein structure, and turn function? This question has multiple angles, ranging from biochemistry biophysics to evolutionary biology. review provides a brief integrated view of some key mechanistic aspects evolution. First, we explain how evolution is primarily driven by randomly acquired genetic mutations selection for function, these can even give rise completely new folds. Then, also comment on phenotypic variability, including promiscuity, transcriptional translational errors, may accelerate this process, possibly via “plasticity‐first” mechanisms. Finally, highlight open questions the field evolution, with respect emergence more sophisticated systems such as complexes, pathways, pre‐LUCA enzymes.

Language: Английский

Citations

60
Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity DOI Creative Commons
Ao Li, He Dai, Ximing Guo

et al.

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: Nov. 12, 2021

Abstract Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology important for assessing adaptive potential species under climate change. Analysis a chromosome-level assembly resequencing individuals across wide latitude distribution estuarine oyster ( Crassostrea ariakensis ) revealed unexpectedly low genomic diversity population structures shaped by historical glaciation, geological events oceanographic forces. Strong selection signals were detected genes responding temperature salinity stress, especially expanded solute carrier families, highlighting importance gene expansion environmental adaptation. Genes exhibiting high showed strong upstream regulatory regions that modulate transcription, indicating favoring plasticity. Our findings suggest variation structure marine bivalves are heavily influenced history physical forces, may enhance critical rapidly changing environments.

Language: Английский

Citations

56
Cis- andTrans-variations of Stearoyl-CoA Desaturase Provide New Insights into the Mechanisms of Diverged Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species DOI Creative Commons
Chaogang Wang, Ao Li,

Rihao Cong

et al.

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(2)

Published: Jan. 19, 2023

The evolution of phenotypic plasticity plays an essential role in adaptive responses to climate change; however, its regulatory mechanisms marine organisms which exhibit high still remain poorly understood. temperature-responsive trait oleic acid content and major gene stearoyl-CoA desaturase (Scd) expression have diverged two allopatric congeneric oyster species, cold-adapted Crassostrea gigas warm-adapted angulata. In this study, genetic molecular methods were used characterize fatty desaturation membrane fluidity regulated by Scd. Sixteen causative single-nucleotide polymorphisms (SNPs) identified the promoter/cis-region Scd between wild C. Further functional experiments showed that SNP (g.-333C [C. allele] >T angulata allele]) may influence transcription creating/disrupting binding motif positive trans-factor Y-box factor gigas/C. angulata, mediates higher/lower constitutive Additionally, sterol-regulatory element-binding proteins (Srebp) specifically bind promoter both downregulated during cold stress compared upregulated This partly explains relatively lower environmental sensitivity (plasticity) gigas. study serves as experimental case reveal cis- trans-variations shape pattern plasticity, provides new insights into formation traits prediction potential future change.

Language: Английский

Citations

20
Transcriptome analysis reveals acclimation responses of pearl oysters to marine heatwaves DOI
Yang Xu, Ziman Wang, Yuehuan Zhang

et al.

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 810, P. 151189 - 151189

Published: Oct. 30, 2021

Language: Английский

Citations

36
Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis DOI
Biao Wu, Xi Chen, Mengjun Yu

et al.

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(4), P. 1529 - 1544

Published: Nov. 20, 2021

The Jinjiang oyster Crassostrea ariakensis, naturally distributing in estuarine regions with low salinity, is an important economic and ecological species China. However, studies on its genomics population genetics remain lacking. Here, we assembled the chromosome-level genome of a female C. ariakensis re-sequenced 261 individuals from five locations China representing three typical habitats. was 662.9 Mb contig N50 length 5.9 using PacBio HiFi-CCS long reads, 99.83% sequences were anchored onto 10 pseudochromosomes Hi-C data. A total 26,354 protein-coding genes predicted. We identified significantly expanded gene families which are closely associated osmotic pressure regulation, including CDO, SLC13 SDR. Population structure analysis revealed that clustered into groups (northern, southern Shanghai) (K = 3) their phylogenetic relationship consistently correlated to geographical distribution. Furtherly, differentiation between northern clearly demonstrated by estimated coefficient (FST 0.1154), PSMC distribution showed two effective size separated at 0.1 Ma. Meanwhile flow Shanghai detected. Selective sweep group detected heat response salinity adaptation. This study could provide valuable genomic resources information for further research molecular evolution, genetic breeding, biological function evolutionary adaptation ariakensis.

Language: Английский

Citations

32
Impacts of marine heatwaves on pearl oysters are alleviated following repeated exposure DOI
Yang Xu, Yuehuan Zhang, Jian Liang

et al.

Marine Pollution Bulletin, Journal Year: 2021, Volume and Issue: 173, P. 112932 - 112932

Published: Sept. 14, 2021

Language: Английский

Citations

26
High temperature induced metabolic reprogramming and lipid remodeling in a high-altitude fish species, Triplophysa bleekeri DOI Creative Commons
Dengyue Yuan, Haoyu Wang, Xiaoqin Liu

et al.

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: Oct. 18, 2022

The effect of thermal changes on the physiology and behavior fish is a major research focus in face ongoing global warming. There little information about effects temperature increase wild. However, consequences controlled laboratory conditions can provide insights into what be expected Triplophysa bleekeri , high-plateau fish, exhibits high sensitivity to temperatures, suggesting it good model investigate impact fish. In this study, we analyzed gradual transcriptional metabolic levels T. subjected change 0.5°C/day until temperatures 10°C, 13°C, 16°C, 19°C were reached. Transcriptomics results liver, gut, spleen, trunk kidney showed that pathways are widely involved response increased . Lipidomics further indicated lipid composition was altered by three lipids (PC 14:0e/22:1, PC 18:0e/22:5, TAG 14:3-21:2-21:2) identified as potential biomarkers heat stress Moreover, decline unsaturated fatty acid observed under temperatures. These suggest modify metabolomic pathways. Overall, our help improve understanding physiological responses valuable predicting warming

Language: Английский

Citations

17
Comparative proteomic and phosphoproteomic analysis reveals differential heat response mechanism in two congeneric oyster species DOI Creative Commons
Chaogang Wang, Mingyang Du,

Zhuxiang Jiang

et al.

Ecotoxicology and Environmental Safety, Journal Year: 2023, Volume and Issue: 263, P. 115197 - 115197

Published: July 13, 2023

High-temperature stress caused by global climate change poses a significant threat to marine ectotherms. This study investigated the role of protein phosphorylation modifications in molecular regulation network under heat oysters, which are representative intertidal organisms that experience considerable temperature changes. Firstly, compared extent thermal damage between two congeneric oyster species, relative heat-tolerant Crassostrea angulata (C. angulata) and heat-sensitive gigas gigas), sublethal (37 °C) for 12 h, using various physiological biochemical methods. Subsequently, comparative proteomic phosphoproteomic analyses revealed high-temperature considerably regulated signal transduction, energy metabolism, synthesis, cell survival apoptosis, cytoskeleton remodeling through related receptors kinases. Furthermore, kinase A, mitogen-activated 1, tyrosine-protein Src, serine/threonine AKT, exhibiting differential modification patterns, were identified as hub regulators may enhance glycolysis TCA cycle increase supply, distribute inhibit Caspase-dependent apoptosis activated endogenous mitochondrial cytochrome release maintain cytoskeletal stability, ultimately shaping higher resistance C. angulata. represents first investigation dynamics invertebrates stress, reveals mechanisms underlying responses oysters at level, provides new insights into understanding phosphorylation-mediated during environmental changes predicting adaptive potential context warming.

Language: Английский

Citations

11
Robustness of microbiome function DOI Creative Commons
Kiseok Keith Lee, Yeonwoo Park, Seppe Kuehn

et al.

Current Opinion in Systems Biology, Journal Year: 2023, Volume and Issue: 36, P. 100479 - 100479

Published: Sept. 15, 2023

Language: Английский

Citations

10
Comparative chromatin dynamics reveal differential thermal tolerance mechanisms between two congeneric oyster species DOI
Chaogang Wang,

Zhuxiang Jiang,

Mingyang Du

et al.

Aquaculture, Journal Year: 2023, Volume and Issue: 579, P. 740177 - 740177

Published: Oct. 2, 2023

Language: Английский

Citations

10