A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Science, Journal Year: 2025, Volume and Issue: 387(6737), P. 1001 - 1007

Published: Feb. 27, 2025

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—each represent diverse radiation with myriad morphological, ecological, behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed living on basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members all eight classes two high-quality genome assemblies monoplacophorans. Our analyses confirm proposed morphology show widespread genomic variation. flexibility likely explains both historic challenges their genomes evolutionary success.

Language: Английский

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Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment

Genes, Journal Year: 2023, Volume and Issue: 14(4), P. 876 - 876

Published: April 7, 2023

The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical–chemical ocean farming conditions. Furthermore, production threatened by broad range microorganisms, pollution, environmental stressors eventually impact its survival growth. Herein, understanding genomic basis local adaption pivotal developing sustainable shellfish aquaculture. We present high-quality reference genome M. chilensis, first chromosome-level for Mytilidae member in South America. assembled size was 1.93 Gb, with contig N50 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, into 14 chromosomes congruence karyological evidence. comprises 34,530 genes 4795 non-coding RNAs. A total 57% contains repetitive sequences predominancy LTR-retrotransposons unknown elements. Comparative analysis coruscus conducted, revealing genic rearrangements distributed whole genome. Notably, transposable Steamer-like elements associated horizontal transmissible cancer explored genomes, suggesting putative relationships at chromosome level Bivalvia. Genome expression also showing differences between two ecologically different populations. evidence suggests adaptation physiological plasticity can be analyzed develop production. provides molecular knowledge complex.

Language: Английский

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Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 198, P. 108129 - 108129

Published: June 13, 2024

Language: Английский

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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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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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Exploring the evolution of sex determination related genes through a cross-species genomics analysis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Abstract The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood many animal groups. Bivalves, a diverse class molluscs with variety reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution sexual systems. However, absence comprehensive framework has limited progress this field, particularly regarding study sex-determination related genes (SRGs). In study, we performed genome-wide sequence evolutionary analysis Dmrt, Sox, Fox gene families more than 40 bivalve species. For first time, provide extensive phylogenetic-aware dataset these SRGs, find support to hypothesis that Dmrt-1L Sox-H may act as primary sex-determining genes, by showing their high levels diversity within genomic context. To validate our findings, same two well-characterized systems, mammals Drosophila . former, found male Sry exhibits pattern amino acid similar bivalves, consistent its role master regulator. contrast, no such was observed among fruit fly cascade, which is controlled chromosomic mechanism. Overall, findings highlight similarities some mammal possibly driven comparable architecture cascades. This work underscores once again importance employing comparative approach when understudied non-model

Language: Английский

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The mytilin gene cluster: shedding light on the enigmatic origin of mussel dispensable genes

Fish & Shellfish Immunology, Journal Year: 2025, Volume and Issue: unknown, P. 110286 - 110286

Published: March 1, 2025

Mussels exhibit a sophisticated innate immune response characterized by many highly variable molecules responsible for recognizing and killing potential pathogenic microorganisms. The complexity of this molecular arsenal is marked the occurrence gene presence-absence (PAV), phenomenon that targets numerous expanded lineage-specific families. This enhances inter-individual sequence variability, further enriching diversity repertoire involved in response. Until now, origin mussel dispensable genes, which, unlike core are not shared all individuals, has remained elusive. In study, analyzing resequenced genomes more than 160 individuals four distinct species Mytilus complex, we characterize mytilin genes encoding hemocyte-specific antimicrobial peptides (AMPs). We define canonical architecture comprising protein-coding two pseudogenes most haplotypes. However, organization locus displays intra-specific due to presence alleles, frequent pseudogenization G1 structural variants associated with additional which often retain features support functional preservation. Molecular phylogeny supports an ancient predating radiation modern species. suggests widespread extant haplotypes derive from larger complex ancestral cluster vestigial AMPs have been retained only few populations where their may contributed fitness advantages local adaptation.

Language: Английский

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Molluscan systematics: historical perspectives and the way ahead

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 6, 2024

ABSTRACT Mollusca, the second‐most diverse animal phylum, is estimated to have over 100,000 living species with great genetic and phenotypic diversity, a rich fossil record, considerable evolutionary significance. Early work on molluscan systematics was grounded in morphological anatomical studies. With transition from oligo gene Sanger sequencing cutting‐edge genomic technologies, molecular data has been increasingly utilised, providing abundant information for reconstructing phylogenetic tree. However, relationships among within most major lineages of Mollusca long contentious, often due limited markers, insufficient taxon sampling conflict. Fortunately, remarkable progress made recent years, which shed light how groups evolved. In this review systematics, we first synthesise current understanding Tree Life at higher taxonomic levels. We then discuss micromolluscs, adult individuals body size smaller than 5 mm, offer unique insights into Mollusca's vast diversity deep phylogeny. Despite advancements, our knowledge phylogeny still needs refinement. Further advancements will arise integrating comprehensive sets, including genome‐scale data, exceptional fossils, digital (including internal structures). Enhanced access these combined increased collaboration morphologists, palaeontologists, developmental biologists, phylogeneticists, significantly advance field.

Language: Английский

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Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(10)

Published: Oct. 1, 2023

Bivalves are a diverse group of molluscs that have recently attained central role in plenty biological research fields, thanks to their peculiar life history traits. Here, we propose bivalves should be considered as emerging model systems also sex-determination (SD) studies, since they would allow investigate: 1) the transition between environmental and genetic SD, with respect different reproductive backgrounds sexual (from species strict gonochorism various forms hermaphroditism); 2) genomic evolution sex chromosomes (SCs), considering no heteromorphic SCs currently known homomorphic been identified only few scallops; 3) putative mitochondria at some level SD signaling pathway, mechanism may resemble cytoplasmatic male sterility plants; 4) evolutionary SD-related gene (SRG) families other animal groups. In particular, think this last topic lay foundations for expanding our understanding bivalve current knowledge is quite fragmented limited species. As matter fact, tracing phylogenetic diversity SRG (such Dmrt, Sox, Fox genes) not perform more targeted functional experiments analyses, but foster possibility establishing solid comparative framework.

Language: Английский

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