Skip to main content

Haplotype-resolved genomes

Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves


Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade, we show that despite genome size reduction during evolution, these bivalves maintain remarkable genetic variability. By constructing a haplotype-resolved genome for Crassostrea sikamea, we identify widespread haplotype divergent sequences (HDSs), representing genomic regions unique to each haplotype.

We show that HDSs are driven by transposable elements, playing a key role in creating and maintaining genetic diversity during oyster evolution. Comparisons of haplotype-resolved genomes across four bivalve orders uncover diverse HDS origins, highlighting a role in genetic innovation and expression regulation across broad timescales. Further analyses show that, in oysters, haplotype polymorphisms drive gene expression variation, which is likely to promote phenotypic plasticity and adaptation. These findings advance our understanding of the relationships among genome structure, diversity, and adaptability in a highly successful invertebrate group.

Limitations of the study


Our study has some limitations. The haplotype-resolved genomes analyzed, despite their high quality, contain residual gaps and phasing errors that may limit nucleotide-level resolution for analyses requiring precise structural breakpoint identification or centromere/telomere divergence characterization. A complete telomere-to-telomere assembly would resolve such complex regions. Additionally, while our cross-order comparisons revealed broad evolutionary patterns, expanding taxonomic sampling to produce high-quality haplotype-resolved genomes from additional bivalve lineages, as well as multiple individuals within the compared species, would improve the resolution and general relevance of our conclusions on structural variation dynamics.

Genetics, Genomics, DNA Sequencing, Gene Therapy, CRISPR, Genetic Engineering, Human Genome, Molecular Biology, Mutation, Genetic Variation, Epigenetics, Genetic Disorders, Heredity, Biotechnology, Precision Medicine, Genetic Research, Genome Editing, RNA Biology, Genetic Mapping, Personalized Medicine

#Genetics, #Genomics, #DNASequencing, #GeneTherapy, #CRISPR, #GeneticEngineering, #HumanGenome, #MolecularBiology, #Mutation, #GeneticVariation, #Epigenetics, #GeneticDisorders, #Heredity, #Biotechnology, #PrecisionMedicine, #GeneticResearch, #GenomeEditing, #RNABiology, #GeneticMapping, #PersonalizedMedicine


Comments

Post a Comment

Popular posts from this blog

Fruitful innovation

Fruitful innovation: Transforming watermelon genetics with advanced base editors The development of new adenine base editors (ABE) and adenine-to-thymine/ guanine base editors (AKBE) is transforming watermelon genetic engineering. These innovative tools enable precise A:T-to-G and A:T-to-T base substitutions, allowing for targeted genetic modifications. The research highlights the efficiency of these editors in generating specific mutations, such as a flowerless phenotype in ClFT (Y84H) mutant plants. This advancement not only enhances the understanding of gene function but also significantly improves molecular breeding, paving the way for more efficient watermelon crop improvement. Traditional breeding methods for watermelon often face challenges in achieving desired genetic traits efficiently and accurately. While CRISPR/Cas9 has provided a powerful tool for genome editing, its precision and scope are sometimes limited. These limitations highlight the need for more advanced gene-e...
Post a Comment
Read more

Genetic factors with clinical trial stoppage

Genetic factors associated with reasons for clinical trial stoppage Many drug discovery projects are started but few progress fully through clinical trials to approval. Previous work has shown that human genetics support for the therapeutic hypothesis increases the chance of trial progression. Here, we applied natural language processing to classify the free-text reasons for 28,561 clinical trials that stopped before their endpoints were met. We then evaluated these classes in light of the underlying evidence for the therapeutic hypothesis and target properties. We found that trials are more likely to stop because of a lack of efficacy in the absence of strong genetic evidence from human populations or genetically modified animal models. Furthermore, certain trials are more likely to stop for safety reasons if the drug target gene is highly constrained in human populations and if the gene is broadly expressed across tissues. These results support the growing use of human genetics to ...
Post a Comment
Read more

Genetics study on COVID-19

Large genetic study on severe COVID-19 Bonn researchers confirm three other genes for increased risk in addition to the known TLR7 gene Whether or not a person becomes seriously ill with COVID-19 depends, among other things, on genetic factors. With this in mind, researchers from the University Hospital Bonn (UKB) and the University of Bonn, in cooperation with other research teams from Germany, the Netherlands, Spain and Italy, investigated a particularly large group of affected individuals. They confirmed the central and already known role of the TLR7 gene in severe courses of the disease in men, but were also able to find evidence for a contribution of the gene in women. In addition, they were able to show that genetic changes in three other genes of the innate immune system contribute to severe COVID-19. The results have now been published in the journal " Human Genetics and Genomics Advances ". Even though the number of severe cases following infection with the SARS-CoV-...
Post a Comment
Read more