ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2022
A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins.Marine biotechnology (New York, N.Y.) · 2026Article
- High-quality genome and transcriptome resources for the East Asian freshwater mussel Nodularia douglasiae.Scientific data · 2026Article
- Environmental Exosomes/Small Extracellular Vesicles: Evidence of Extracellular RNA Release by Aquatic Organisms.Marine biotechnology (New York, N.Y.) · 2026Article
- Immune Memory-like Responses of Akoya Pearl Oyster to Pinctada Birnavirus.Pathogens (Basel, Switzerland) · 2026Article
- Chromosome-level genome assembly and annotation of the emblematic silver-lipped pearl oyster Pinctada maxima Jameson 1901.Scientific data · 2026Article
- Article
- A phased chromosome-level genome of the annelid tubeworm Galeolaria caespitosa.The Journal of heredity · 2025Article
- The chromosome-level genome assembly and annotation of the silver-lipped pearl oyster, Pinctada maxima.Scientific data · 2025Article
- Nearly T2T, phased genome assemblies of corals reveal haplotype diversity and the evolutionary process of gene expansion.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Chromosome-level genome assembly of Pontederia cordata L. provides insights into its rapid adaptation and variation of flower colours.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Article
- Evolution of the Cdk4/6-Cdkn2 system in invertebrates.Genes to cells : devoted to molecular & cellular mechanisms · 2024Article
- Core genes of biomineralization and cis-regulatory long non-coding RNA regulate shell growth in bivalves.Journal of advanced research · 2024Article
- A chromosome-level genome assembly of the disco clam, Ctenoides ales.G3 (Bethesda, Md.) · 2024Article
- The chromosome level genome assembly of the Asian green mussel, Perna viridis.Scientific data · 2024Article
- The First High-Quality Genome Assembly of Freshwater Pearl MusselInternational journal of molecular sciences · 2024Article
- A novel birnavirus identified as the causative agent of summer atrophy of pearl oyster (PeerJ · 2024Article
- Gene presence/absence variation iniScience · 2023Article
- Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters.BMC biology · 2023Article
- The genome of the reef-building glass spongeRoyal Society open science · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.