Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: June 26, 2023

Abstract Background Transposable elements (TEs) can represent one of the major sources genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics multiple animal clades, molluscs a substantially understudied phylum. Here, we take advantage recent increase in mollusc resources adopt an automated TE annotation pipeline combined with phylogenetic tree-based classification, as well extensive manual curation efforts, characterize repertories 27 bivalve genomes particular emphasis on DDE/D class II elements, long interspersed nuclear (LINEs), dynamics. Results We found I highly dominant genomes, LINE despite less represented terms copy number per genome, being most common retroposon group covering up 10% genome. mined 86,488 reverse transcriptases (RVT) containing coming from 12 clades distributed all known superfamilies 14,275 DDE/D-containing transposons 16 distinct superfamilies. uncovered previously underestimated rich diverse ancestral transposon complement that could be traced back ancestor lived ~ 500 Mya. Moreover, identified instances lineage-specific emergence loss different LINEs lineages interesting cases CR1- Zenon, Proto2, RTE-X, Academ underwent bivalve-specific amplification likely associated diversification. Finally, this diversity is maintained extant by equally set long-living potentially active suggested history transcription profiles both male female gonads. Conclusions bivalves host exceptional compared other molluscs. Their mainly follow “stealth drivers” model evolution where diversified families are able survive co-exist period time shaping early phases genome Overall, provide not only first comparative large but phylum such Mollusca, also reference library ORF-containing which represents important resource identification characterization genomes.

Language: Английский

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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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Stage-Specific Transcriptomes of the Mussel Mytilus coruscus Reveals the Developmental Program for the Planktonic to Benthic Transition

Genes, Journal Year: 2023, Volume and Issue: 14(2), P. 287 - 287

Published: Jan. 21, 2023

Many marine invertebrate larvae undergo complex morphological and physiological changes during the planktonic—benthic transition (a.k.a. metamorphosis). In this study, transcriptome analysis of different developmental stages was used to uncover molecular mechanisms underpinning larval settlement metamorphosis mussel, Mytilus coruscus. Analysis highly upregulated differentially expressed genes (DEGs) at pediveliger stage revealed enrichment immune-related genes. The results may indicate that co-opt molecules immune system sense respond external chemical cues neuroendocrine signaling pathways forecast trigger response. upregulation adhesive protein linked byssal thread secretion indicates anchoring capacity required for arises prior metamorphosis. gene expression support a role systems in mussel provide basis future studies disentangle networks biology important lifecycle transformation.

Language: Английский

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Transcriptome profiling reveals the strategy of thermal tolerance enhancement caused by heat-hardening in Mytilus coruscus

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 903, P. 165785 - 165785

Published: July 25, 2023

Language: Английский

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Effect of low-salt on the survival of mussel Mytilus coruscus and its molecular responses to chronic prolonged low-salt stress

Aquaculture, Journal Year: 2024, Volume and Issue: 585, P. 740689 - 740689

Published: Feb. 20, 2024

Language: Английский

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Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program

Aquaculture, Journal Year: 2021, Volume and Issue: 548, P. 737633 - 737633

Published: Oct. 25, 2021

Language: Английский

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The genome of the zebra mussel,Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol

G3 Genes Genomes Genetics, Journal Year: 2021, Volume and Issue: 12(2)

Published: Dec. 13, 2021

Abstract The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia Europe and North America, causing billions of dollars damage dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination long-read sequencing Hi-C-based scaffolding generate high-quality chromosome-scale assembly. Through comparative analysis transcriptomics experiments, gained insights into processes that likely control invasive success mussels, including shell formation, synthesis byssal threads, thermal tolerance. We identified multiple intact steamer-like elements, retrotransposon has been linked transmissible cancer marine clams. also found an unusual 67 kb mitochondrial containing numerous tandem repeats, making it largest observed Eumetazoa. Together findings create rich resource species research efforts.

Language: Английский

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SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(5), P. 1044 - 1060

Published: April 25, 2023

Blue mussels from the genus Mytilus are an abundant component of benthic community, found in high latitude habitats. These foundation species relevant to aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range environmental conditions and edulis complex readily hybridize regions where their distributions overlap. Significant effort has been made investigate consequences stress on mussel physiology, reproductive isolation, local adaptation. Yet our understanding genomic mechanisms underlying such processes remains limited. In this study, we developed multi medium-density 60 K SNP-array including four genus. SNPs included platform were called 138 23 distributed populations, sequenced using whole-genome low coverage approach. The array contains polymorphic which capture genetic diversity present populations thriving across gradient (~59 SNPs) set published validated informative for identification diagnosis transmissible cancer (610 SNPs). will allow consistent genotyping individuals, facilitating investigation ecological evolutionary these taxa. applications extend shellfish aquaculture, contributing optimization industry via selection blue mussels, parentage assignment, inbreeding assessment traceability. Further as genome association studies (GWAS) key production traits those related resilience especially safeguard under climate change.

Language: Английский

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Molecular responses of Mytilus coruscus hemocytes to lipopolysaccharide and peptidoglycan as revealed by 4D-DIA based quantitative proteomics analysis

Fish & Shellfish Immunology, Journal Year: 2025, Volume and Issue: 158, P. 110143 - 110143

Published: Jan. 20, 2025

Language: Английский

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De novo transcriptome assembly of the Perna viridis: A novel invertebrate model for ecotoxicological studies

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: Jan. 25, 2025

Mussels, particularly Perna viridis, are vital sentinel species for toxicology and biomonitoring in environmental health. This plays a crucial role aquaculture significantly impacts the fisheries sector. Despite ecological economic importance of this species, its omics resources still scarce. We generated gill-specific reference transcriptome viridis using 292 million short Illumina reads from eight pooled gill tissue samples isolated twenty-four individuals. The Trinity assembler 438,842 transcripts with an N50 1,958 bp. Several databases were employed annotation process. dataset greatly expands bivalve advances our knowledge transcriptomics, molecular biology, toxicology, cancer research.

Language: Английский

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