ArticleG3 (Bethesda, Md.)2022
Assembly of complete diploid-phased chromosomes from draft genome sequences.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's disease in Vitis arizonica and its hybrids.G3 (Bethesda, Md.) · 2026Article
- Parallel adaptation and admixture drive the evolution of virulence in the grapevine downy mildew pathogen.PLoS pathogens · 2026Article
- Dissection of the Ren6 and Ren7 powdery mildew resistance loci in Vitis piasezkii DVIT2027 using phased parental-progeny genomes and intraspecific locus graph reconstruction.G3 (Bethesda, Md.) · 2025Article
- Dissection of the Ren6 and Ren7 powdery mildew resistance loci in Vitis piasezkii DVIT2027 using phased parental-progeny genomes and intraspecific locus graph reconstruction.G3 (Bethesda, Md.) · 2025Article
- Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid.Genome biology · 2025Article
- Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae.bioRxiv : the preprint server for biology · 2025Article
- Advances in grape and pathogen genomics toward durable grapevine disease resistance.Journal of experimental botany · 2025Review
- Advances in grape and pathogen genomics toward durable grapevine disease resistance.Journal of experimental botany · 2025Review
- Evolutionary conservation of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae.Nature communications · 2025Article
- The genome ofHorticulture research · 2025Article
- Genome Scan Analysis for Advancing Knowledge and Conservation Strategies of Primitivo Clones (Plants (Basel, Switzerland) · 2025Article
- The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired.GigaByte (Hong Kong, China) · 2025Article
- Genome-Wide Identification, Characterisation, and Evolution of the Transcription Factor WRKY in Grapevine (International journal of molecular sciences · 2024Article
- Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation.Horticulture research · 2024Article
- Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1.G3 (Bethesda, Md.) · 2023Article
- A super-pangenome of the North American wild grape species.Genome biology · 2023Article
- The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes.Horticulture research · 2023Article
- Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study.G3 (Bethesda, Md.) · 2023Article
- Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate.Communications biology · 2023Article
- The complete reference genome for grapevine (Horticulture research · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain assembly errors because of repeats, heterozygosity, or the chosen assembly strategy. Although algorithms that produce partially phased assemblies exist, haploid draft assemblies that may lack biological information remain favored because they are easier to generate and use. We developed HaploSync, a suite of tools that produces fully phased, chromosome-scale diploid genome assemblies, and performs extensive quality control to limit assembly artifacts. HaploSync scaffolds sequences from a draft diploid assembly into phased pseudomolecules guided by a genetic map and/or the genome of a closely related species. HaploSync generates a report that visualizes the relationships between current and legacy sequences, for both haplotypes, and displays their gene and marker content. This quality control helps the user identify misassemblies and guides Haplosync's correction of scaffolding errors. Finally, HaploSync fills assembly gaps with unplaced sequences and resolves collapsed homozygous regions. In a series of plant, fungal, and animal kingdom case studies, we demonstrate that HaploSync efficiently increases the assembly contiguity of phased chromosomes, improves completeness by filling gaps, corrects scaffolding, and correctly phases highly heterozygous, complex regions.
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