ArticleCommunications biology2020
Variant phasing and haplotypic expression from long-read sequencing in maize.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Review
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing.Nature communications · 2025Article
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Genome analyses and breeding of polyploid crops.Nature plants · 2025Review
- Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD.Nucleic acids research · 2024Article
- Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus.BMC biology · 2023Article
- Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data.Genome biology · 2023Article
- Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding.Current opinion in biotechnology · 2023Review
- Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.Nature biotechnology · 2022Article
- Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos).G3 (Bethesda, Md.) · 2022Article
- Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety.G3 (Bethesda, Md.) · 2021Article
- Leveraging histone modifications to improve genome annotations.G3 (Bethesda, Md.) · 2021Article
- Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay.NAR genomics and bioinformatics · 2021Article
- Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora.G3 (Bethesda, Md.) · 2021Article
- Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation.Plant communications · 2021Article
- An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics.Acta neuropathologica communications · 2021Review
- Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.Nature communications · 2020Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic activity. We performed an isoform-level phasing study using two maize inbred lines and their reciprocal crosses, based on single-molecule, full-length cDNA sequencing. To phase and analyze transcripts between hybrids and parents, we developed IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data from embryo, endosperm and root tissues, and identified allele-specific, gene-level and isoform-level differential expression between the inbred parental lines and hybrid offspring. After phasing 6907 genes in the reciprocal hybrids, we annotated the SNPs and identified large-effect genes. In addition, we identified parent-of-origin isoforms, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.
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