ReviewPlant biotechnology journal2022
De novo phasing resolves haplotype sequences in complex plant genomes.
Review in Plant biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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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.
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Who cites it
23 citing papers in PubMed, 27 citations in OpenAlex.
- The genome of the medicinal plant Uncaria rhynchophylla provides new insights into monoterpenoid indole alkaloid metabolism and its molecular regulatory mechanism.Molecular horticulture · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- Chromosome-level haplotype-resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass (Lolium multiflorum Lam.).The plant genome · 2025Article
- Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points.Nature protocols · 2025Review
- Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit.The Plant journal : for cell and molecular biology · 2025Article
- M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications.GigaScience · 2025Article
- Re-calibration of flow cytometry standards for plant genome size estimation.Frontiers in plant science · 2025Article
- Evolution of Plant Genome Size and Composition.Genomics, proteomics & bioinformatics · 2024Review
- Haplotype-resolved genome assembly and resequencing analysis provide insights into genome evolution and allelic imbalance in Pinus densiflora.Nature genetics · 2024Article
- The genomes of Australian wild limes.Plant molecular biology · 2024Article
- Advancing chromosomal-scale, haplotype-resolved genome assembly: beading with Hi-C data.Advanced biotechnology · 2024Article
- Detecting microsatellite instability by length comparison of microsatellites in the 3' untranslated region with RNA-seq.Briefings in bioinformatics · 2024Article
- Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes:Plants (Basel, Switzerland) · 2024Article
- The genome of Citrus australasica reveals disease resistance and other species specific genes.BMC plant biology · 2024Article
- Technology-enabled great leap in deciphering plant genomes.Nature plants · 2024Review
- A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.).Scientific data · 2024Article
- A haplotype-resolved gap-free genome assembly provides novel insight into monoterpenoid diversification inHorticulture research · 2024Article
- DataColor: unveiling biological data relationships through distinctive color mapping.Horticulture research · 2024Article
- MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Recent Advances in Assembly of Complex Plant Genomes.Genomics, proteomics & bioinformatics · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as consensus genomes consisting of haplotype mixtures, thus increasing the need for genome phasing. Here, we review the operating principles and characteristics of several freely available and widely used phasing tools (TrioCanu, FALCON-Phase, and ALLHiC). An examination of downstream analyses using haplotype-resolved genome assemblies in plants indicated significant differences among haplotypes regarding chromosomal rearrangements, sequence insertions, and expression of specific alleles that contribute to the acquisition of the biological characteristics of plant species. Finally, we suggest directions to solve addressing limitations of current genome-phasing methods. This review provides insights into the current progress, limitations, and future directions of de novo genome phasing, which will enable researchers to easily access and utilize genome-phasing in studies involving highly heterozygous complex plant genomes.
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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.