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 hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia

GigaScience, Journal Year: 2021, Volume and Issue: 10(4)

Published: April 1, 2021

Abstract Background The hard-shelled mussel (Mytilus coruscus) is widely distributed in the temperate seas of East Asia and an important commercial bivalve China. Chromosome-level genome information this species will contribute not only to development genetic breeding but also studies on larval ecology, climate change biology, marine aquaculture, biofouling, antifouling. Findings We applied a combination Illumina sequencing, Oxford Nanopore Technologies high-throughput chromosome conformation capture technologies construct chromosome-level mussel, with total length 1.57 Gb median contig 1.49 Mb. Approximately 90.9% assemblies were anchored 14 linkage groups. assayed completeness using BUSCO. In metazoan dataset, present have 89.4% complete, 1.9% incomplete, 8.7% missing BUSCOs. Gene modeling enabled annotation 37,478 protein-coding genes 26,917 non-coding RNA loci. Phylogenetic analysis showed that M. coruscus sister taxon clade including Modiolus philippinarum Bathymodiolus platifrons. Conserved synteny was observed between king scallop, suggesting shared ancestrally. Transcriptomic profiling indicated pathways catecholamine biosynthesis adrenergic signaling cardiomyocytes might be involved metamorphosis. Conclusions assembly provide novel insights into evolution serve as fundamental platform for regarding planktonic-sessile transition, diversity, genomic bivalve.

Language: Английский

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Genome of Kumamoto Oyster Crassostrea sikamea Provides Insights Into Bivalve Evolution and Environmental Adaptation

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(4)

Published: April 1, 2025

ABSTRACT The Kumamoto oyster, Crassostrea sikamea , is a marine bivalve naturally distributed along the coasts of southern China and Japan, with hatchery population that has been under domestication in United States since its introduction from Japan 1940s. To understand evolutionary history environmental adaptation, we produced chromosome‐level genome assembly C. conducted whole‐genome resequencing 141 individuals US six wild populations Japan. assembled size 616 Mb covering all 10 chromosomes contig N50 4.21 scaffold 62.25 Mb. Phylogenetic analysis indicated diverged angulata gigas clade about 9.9 million years ago. Synteny revealed significant chromosomal rearrangements during evolution leading to oysters, but remarkable conservation oyster over ~180 years, surprising disparity evolution. three distinct clusters for US, Japanese, Chinese populations, closer Japanese population, confirming origin. No differentiation was detected among five indicating strong gene flow. Between 402 genes exhibited selection signals, including myosin heavy chain were also differentiated domesticated lines eastern suggesting changes these may be important domestic production. Among 768 showing signals between natural China, related stress response are most enriched, responding critical local adaptation. These findings provide insights into as well useful resources comparative genomics genetic improvement cultured stocks.

Language: Английский

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Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: March 8, 2022

The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for restoration or aquaculture activities. Significant mortality events have reported in species throughout its native range as result diseases (microbial infections, leukemia) acute environmental stress. In this context, characterization genome can provide highly needed resources enable basic (e.g., oncogenesis cancer transmission, adaptation biology) applied (clam stock enhancement, genomic selection) sciences.Using combination long short-read sequencing technologies, 1.86 Gb chromosome-level assembly was generated. scaffolded into 19 chromosomes, with an N50 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than few members Venerida sequenced so far, coding regions representing only 2% assembly. Indeed, half composed repeated elements, including transposable elements. Major chromosome rearrangements were detected between another recent derived from genetically segregated stock. Comparative analysis allowed identification marked diversification immune-related proteins, particularly extensive tandem duplications expansions tumor necrosis factors (TNFs) C1q domain-containing some which previously shown play role interactions infectious microbes. study also generated comparative repertoire highlighting diversity and, instances, specificity LTR-retrotransposons Steamer elements bivalves.The immune molecules M. may allow cope varying complex microbial landscapes. identified study, should be prime target investigation cell development transmission among bivalve mollusks.

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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Chromosome‐level reference genome for European flat oyster (Ostrea edulis L.)

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 15(11), P. 1713 - 1729

Published: Aug. 4, 2022

Abstract The European flat oyster ( Ostrea edulis L.) is a bivalve naturally distributed across Europe, which was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite growing interest in genetic applications to support population management aquaculture, reference genome this species lacking date. Here, we report chromosome‐level assembly annotation the Flat genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation RNA sequencing. A contig (N50: 2.38 Mb) scaffolded into expected karyotype 10 pseudochromosomes. final 935.13 Mb, with scaffold‐N50 95.56 predicted repeat landscape dominated by unclassified elements specific O. . verified accuracy completeness multiple approaches, including novel linkage map built ddRAD‐Seq technology, comprising 4016 SNPs from four full‐sib families (eight parents 163 F1 offspring). Annotation integrating multitissue transcriptome data, comparative protein evidence ab‐initio gene prediction identified 35,699 protein‐coding genes. Chromosome‐level synteny demonstrated against high‐quality assemblies, independently French individual. Comparative genomics used characterize family expansions during evolution that potentially facilitated adaptation. This new will enable high‐resolution conservation aquaculture initiatives, improves our understanding evolution.

Language: Английский

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A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster

DNA Research, Journal Year: 2022, Volume and Issue: 29(6)

Published: Sept. 12, 2022

Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, assembly of pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This includes 14 pairs scaffolds (>38 Mb) corresponding (2n = 28). The accuracy assembly, as measured by an analysis k-mers, is estimated be 99.99997%. Moreover, haplotypes 95.2% 95.9%, respectively, complete single-copy BUSCO genes, demonstrating quality assembly. Transposons comprise 53.3% major contributor structural variations. Despite overall collinearity between haplotypes, one chromosomal contains megabase-scale non-syntenic regions, which necessarily have never detected resolved conventional haplotype-merged assemblies. These regions encode expanded gene families NACHT, DZIP3/hRUL138-like HEPN, immunoglobulin domains, multiplying immunity repertoire, hypothesize important for innate immune capability oysters. oyster provides insight into remarkable haplotype diversity animals.

Language: Английский

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Evidence of multiple genome duplication events in Mytilus evolution

BMC Genomics, Journal Year: 2022, Volume and Issue: 23(1)

Published: May 2, 2022

Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and recent advances in genomes sequencing technologies genome assembly techniques. With present work, we want to contribute growing efforts by filling this gap, presenting a new high-quality reference for Mytilus edulis investigating evolutionary history within Mytilidae family, relation other species class Bivalvia.Here present, first time, discovery of multiple whole duplication events family and, more generally, Bivalvia. In addition, calculation evolution rates three Mytilinae subfamily sheds light onto highlights key orthologs interest study divergences.The presented here will enable correct identification molecular markers evolutionary, population genetics, conservation studies. have capability become model shellfish climate change adaptation using genome-enabled systems biology multi-disciplinary studies interactions between abiotic stressors, pathogen attacks, aquaculture practises.

Language: Английский

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The First High-Quality Genome Assembly of Freshwater Pearl Mussel Sinohyriopsis cumingii: New Insights into Pearl Biomineralization

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(6), P. 3146 - 3146

Published: March 9, 2024

China leads the world in freshwater pearl production, an industry which triangle sail mussel (Sinohyriopsis cumingii) plays a pivotal role. In this paper, we report high-quality chromosome-level genome assembly of S. cumingii with size 2.90 Gb—the largest yet reported among bivalves—and 89.92% anchorage onto 19 linkage groups. The assembled has 37,696 protein-coding genes and 50.86% repeat elements. A comparative genomic analysis revealed expansions 752 gene families, mostly associated biomineralization, 237 under strong positive selection. Notably, fibrillin family exhibited expansion selection simultaneously, it also multiple high expressions after mantle implantation by transcriptome analysis. Furthermore, RNA silencing vitro calcium carbonate crystallization assay highlighted role played one deposition aragonite transformation. This study provides valuable resource offers new insights into mechanism biomineralization.

Language: Английский

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Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 15(11), P. 1730 - 1748

Published: Aug. 19, 2022

The European flat oyster (

Language: Английский

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