ArticleGenome biology2013
Separating homeologs by phasing in the tetraploid wheat transcriptome.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed, 143 citations in OpenAlex.
- The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos.The New phytologist · 2026Article
- Integrative transcriptomics nominates a 1R-MYB candidate associated with epidermal wax-related traits and osmotic-stress responses in Kentucky bluegrass.Frontiers in plant science · 2026Article
- The FKF1-ELF3-PRC2 module regulates flowering time in response to light in temperate grasses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid WheatbioRxiv : the preprint server for biology · 2025Article
- Review
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
- Plant Tolerance to Drought Stress with Emphasis on Wheat.Plants (Basel, Switzerland) · 2023Review
- Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.Nature communications · 2022Article
- Rubiscosome gene expression is balanced across the hexaploid wheat genome.Photosynthesis research · 2022Article
- Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes.Zoological research · 2022Article
- Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the InvasiveFrontiers in genetics · 2022Article
- Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution.Journal of evolutionary biology · 2021Article
- De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (International journal of molecular sciences · 2021Article
- Relationship between the Phenylpropanoid Pathway and Dwarfism ofInternational journal of molecular sciences · 2021Article
- Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves.Molecular biology and evolution · 2021Article
- Mutational signatures associated with exposure to carcinogenic microplastic compounds bisphenol A and styrene oxide.NAR cancer · 2021Article
- Mapping and Characterization of a Wheat Stem Rust Resistance Gene in Durum Wheat "Kronos".Frontiers in plant science · 2021Article
- Multi-Omics Analysis of Small RNA, Transcriptome, and Degradome inInternational journal of molecular sciences · 2020Article
- Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat.PLoS genetics · 2020Article
- Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundThe high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs.
resultsA total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing.
conclusionsOur study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.
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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.