Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(17), P. 13641 - 13641

Published: Sept. 4, 2023

The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of northwest Pacific and holds a significant position shellfish aquaculture market China. However, natural resources this species have been declining, population genetic studies M. coruscus are also lacking. In study, we conducted whole-genome resequencing (WGR) from eight different latitudes along Chinese coast identified total 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that diversity Zhoushan region was lower compared with populations other regions. Furthermore, observed evolutionary tree clustered into two primary branches, Zhangzhou (ZZ) separate branch. ZZ partly isolated regions, but distribution branches not geographically homogeneous, nested pattern emerged, consistent differentiation index (FST) results. To investigate selection characteristics, utilized northern (Dalian Qingdao) central (Zhoushan Xiangshan) as reference southern target population. scan analysis several genes associated thermal responses, including Hsp70 CYP450. These may play important roles adaptation to living environments. Overall, our study provides comprehensive understanding genomic China valuable resource for future on breeding species.

Language: Английский

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New genes helped acorn barnacles adapt to a sessile lifestyle

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(5), P. 970 - 981

Published: April 23, 2024

Language: Английский

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Rapid Adaptation to Temperature via a Potential Genomic Island of Divergence in the Invasive Green Crab, Carcinus maenas

Frontiers in Ecology and Evolution, Journal Year: 2020, Volume and Issue: 8

Published: Nov. 26, 2020

Widespread species often adapt easily to novel conditions – both those found in new habitats and generated by climate change. However, rapid adaptation may be hindered the marine realm, where long-distance dispersal consequently high gene flow are predicted limit potential for local adaptation. Here, we use a highly dispersive invasive crab test nature speed of temperature sea. Using single nucleotide polymorphisms (SNPs) from cardiac transcriptome sequencing, characterized six populations European green ( Carcinus maenas ) located across parallel thermal gradients their native ranges. We compared SNP frequencies with temperatures previously data on heat cold tolerance identify candidate markers associated population-level differences physiology. Of 10,790 SNPs, 104 were identified as frequency outliers, signal that was strongly driven association and/or tolerance. Seventy-two these outlier markers, representing 28 different genes, cluster SNPs inversion polymorphism using linkage disequilibrium network analysis. This unique set, which otherwise low levels disequilibrium, this showed significant enrichment coding substitutions relative full set. These 72 appear transmitted unit, represent putative genomic island divergence varied organismal relationship strikingly similar populations, all very strong correlation (R 2 = 0.96 over populations). Notably, three have diverged recently (<100 years) show little no neutral divergence, suggesting region responding relatively short time scale. indicates based action perhaps partially explaining extraordinary ability species.

Language: Английский

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From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 6417 - 6433

Published: May 8, 2021

The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations highly heterogeneous environments. Adult barnacles may be exposed dissimilar levels thermal stress depending on where they settle in intertidal (i.e., closer upper or lower tidal boundary). For instance, near limit experience episodic summer temperatures above recorded heat coma levels. This differential at microhabitat level also dependent aspect sun exposure. In present study, we used pool-seq approaches conduct genome wide screen for loci responding zonation across North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated whose frequencies vary their position rocky intertidal) all surveyed habitats. Notably, most young private Atlantic. These show high differentiation ecologically extreme microhabitats concomitant with elevated variation Tajima's D, suggesting action non-neutral processes. Overall, these findings support hypothesis that spatially selection general repeatable feature this species, natural can maintain functional

Language: Английский

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An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 16(2), P. 279 - 292

Published: June 6, 2022

Understanding the genetic targets of natural selection is one most challenging goals population genetics. Some earliest candidate genes were identified from associations between allozyme allele frequencies and environmental variation. One such example clinal polymorphism in arginine kinase (

Language: Английский

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Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia)

Heliyon, Journal Year: 2021, Volume and Issue: 7(6), P. e07291 - e07291

Published: June 1, 2021

Members of the infraclass Cirripedia, commonly called barnacles, are unique among subphylum Crustacea in that they exhibit a biphasic life cycle with planktonic larval stage and sessile adult stage. Understanding their mechanisms attachment hampered by lack genomic resources. Here, we present 746 Mb genome assembly Lepas anserifera – first sequenced stalked barnacle genome. We estimate Cirripedia arose ~495 million years ago (MYA) further diversified since Mesozoic. A demographic analysis revealed remarkable population changes relation to sea-level fluctuations last 2 MYA. Comparative analyses expansion number developmental related genes families genomes, such as Br–C, PCP20 Lola, which potentially important for evolution metamorphosis, cuticle development central nervous system. Phylogenetic tissue expression profiling showed possible roles gene duplication, functional diversification co-option shaping barnacles. Overall, our study provides not only valuable draft comparative crustacean evolution, but also facilitates studies biofouling control.

Language: Английский

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Ecological Load and Balancing Selection in Circumboreal Barnacles

Molecular Biology and Evolution, Journal Year: 2020, Volume and Issue: 38(2), P. 676 - 685

Published: Sept. 5, 2020

Abstract Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question how adaptation to high variability is maintained in face strong juvenile dispersal and mortality. Here, we show that 4% genes genome balancing selection across entire range species. Many these harbor mutations 2 My evolution between Pacific Atlantic oceans. These are involved ion regulation, pain reception, heat tolerance, functions which essential highly variable ecosystems. The data also reveal complex population structure within basins, driven by trans-Arctic interchange last glaciation. Divergence populations high, foreshadowing onset allopatric speciation, suggesting enough maintain functional variation for millions years demography.

Language: Английский

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Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions

Marine Biotechnology, Journal Year: 2021, Volume and Issue: 23(3), P. 402 - 416

Published: May 1, 2021

Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made constructions ships. Despite considerable ecological economic impacts, there is surprising void of basic genomic knowledge, barnacle reference genome lacking. We here set out to characterize the bay Balanus improvisus (= Amphibalanus improvisus) based short-read whole-genome sequencing experimental size estimation. show both experimentally (DNA staining flow cytometry) computationally (k-mer analysis) that B. has haploid ~ 740 Mbp. A pilot assembly rendered total 600 Mbp was highly fragmented with an N50 only 2.2 kbp. Further assembly-based assembly-free analyses revealed very limited contiguity due having extremely high nucleotide diversity (π) coding regions (average π ≈ 5% average fourfold degenerate sites 20%), overall repeat content (at least 40%). also report variation α-octopamine receptor OctA = 3.6%), which might increase risk populations evolve resistance toward antifouling agents. The features described can help planning for future high-quality genome, urgently needed properly explore understand proteins interest biology biotechnology developing better strategies.

Language: Английский

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Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides

Animal Microbiome, Journal Year: 2020, Volume and Issue: 2(1)

Published: Nov. 13, 2020

Abstract Background Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit intertidal. In this study, we of barnacle Semibalanus balanoides . We first describe two body tissues: feeding appendages, or cirri, gut. Next, examine whether there are between each tissue barnacles collected from thermally extreme microhabitats shores’ upper lower tidal zones. Results Overall, S. consisted 18 phyla 408 genera. Our results showed although cirri gut shared a portion their amplicon sequence variants (ASVs), was distinct. Over 80% ASVs found in were also gut, 44% cirri. Notably, not subset microbiome. Additionally, identified responsive microhabitat differences. Conclusion study indicate maintains distinct its tissues, is more stable than extremes

Language: Английский

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The molecular background of the aspartate aminotransferase polymorphism in Littorina snails maintained by strong selection on small spatial scales

Gene, Journal Year: 2023, Volume and Issue: 876, P. 147517 - 147517

Published: May 29, 2023

Allozymes present several classical examples of divergent selection, including the variation in cytosolic aspartate aminotransferase (AAT) intertidal snails Littorina saxatilis. AAT is a part asparate-malate shuttle, interidal molluscs involved anaerobic respiration during desiccation. Previous allozyme studies reported sharp gradient frequencies AAT100and AAT120 alleles between low and high shores Northern Europe differences their enzymatic activity, supporting role adaptation to However, populations Iberian Peninsula showed opposite allele cline. Using mRNA sequencing genome pool-seq analyses we characterize DNA sequences different alleles, report amino acid replacements behind show that same Southern have protein sequences. Gene phylogeny reveals AAT100 northern represent old polymorphism, shared among closely related species Littorina, while southern more recently derived from AAT100. Further, Aat gene expressed at constitutive level genotypes conditions, structural regulation enzyme activity. Finally, location structure L. saxatilis presence two additional non-functional copies. Altogether, provide missing link scans bring together results produced over decades genetic research.

Language: Английский

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