ArticleGenome research2019
Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants.
Article in Genome research, 2019. 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, 44 citations in OpenAlex.
- A simple and high-throughput single pollen genotyping pipeline to study meiosis in apple (Malus x domestica).Plant methods · 2026Article
- Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Haplotype-resolved T2T genome assembly of the Populus nigra NL-1976.Scientific data · 2025Article
- Naturally impaired side-chain shortening of aromatic 3-ketoacyl-CoAs reveals the biosynthetic pathway of plant acetophenones.Nature plants · 2025Article
- Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears.Nature genetics · 2025Article
- Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points.Nature protocols · 2025Review
- Long-read genome sequencing reveals the sequence characteristics of pear self-incompatibility locus.Molecular horticulture · 2025Article
- Evolution of Plant Genome Size and Composition.Genomics, proteomics & bioinformatics · 2024Review
- Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.Plant communications · 2024Article
- Haplotype-resolved assembly of a pig genome using single-sperm sequencing.Communications biology · 2024Article
- Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange.Horticulture research · 2024Article
- Whole-genome sequencing in medicinal plants: current progress and prospect.Science China. Life sciences · 2024Review
- PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study.Database : the journal of biological databases and curation · 2023Article
- Recent Advances in Assembly of Complex Plant Genomes.Genomics, proteomics & bioinformatics · 2023Review
- Telomere-to-telomere and haplotype-resolved genome of the kiwifruit Actinidia eriantha.Molecular horticulture · 2023Article
- Gamete Binning to Achieve Haplotype-Resolved Genome Assembly.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning.Frontiers in plant science · 2023Article
- De novo phasing resolves haplotype sequences in complex plant genomes.Plant biotechnology journal · 2022Review
- Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar.Nature genetics · 2022Article
- gcaPDA: a haplotype-resolved diploid assembler.BMC bioinformatics · 2022Article
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome assemblies from diploid organisms create mosaic sequences alternating between parental alleles, which can create erroneous gene models and other problems. In animals, a popular strategy to generate haploid genome-resolved assemblies has been the sampling of (haploid) gametes, and the advent of single-cell sequencing has further advanced such methods. However, several challenges for the isolation and amplification of DNA from plant gametes have limited such approaches in plants. Here, we combined a new approach for pollen protoplast isolation with a single-cell DNA amplification technique and then used a "barcoding" bioinformatics strategy to incorporate haploid-specific sequence data from 12 pollen cells, ultimately enabling the efficient and accurate phasing of the pear genome into its A and B haploid genomes. Beyond revealing that 8.12% of the genes in the pear reference genome feature mosaic assemblies and enabling a previously impossible analysis of allelic affects in pear gene expression, our new haploid genome assemblies provide high-resolution information about recombination during meiosis in pollen. Considering that outcrossing pear is an angiosperm species featuring very high heterozygosity, our method for rapidly phasing genome assemblies is potentially applicable to several yet-unsequenced outcrossing angiosperm species in nature.
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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.