ArticleBiology2012
Why assembling plant genome sequences is so challenging.
Article in Biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
57 citing papers in PubMed.
- Ancient wheat DNA: How and what for?Journal, genetic engineering & biotechnology · 2026Article
- Artificial intelligence in plant salt stress research: from predictive models to multi-omics integration.Journal of experimental botany · 2026Review
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Annotating the genome at single-nucleotide resolution with DNA foundation models.Nature methods · 2025Article
- Genome-wide identification and expression pattern analysis of the CPP transcription factor family in Medicago sativa L.BMC plant biology · 2025Article
- Genome Survey Sequencing ofGenes · 2025Article
- Beyond the genome: the role of functional markers in contemporary plant breeding.Frontiers in plant science · 2025Review
- Low-pass nanopore sequencing for measurement of global methylation levels in plants.BMC genomics · 2024Article
- A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.BMC genomics · 2024Article
- Photosynthesis: Genetic Strategies Adopted to Gain Higher Efficiency.International journal of molecular sciences · 2024Review
- Article
- Polyploids of Brassicaceae: Genomic Insights and Assembly Strategies.Plants (Basel, Switzerland) · 2024Review
- The reference genome sequence ofFrontiers in plant science · 2024Article
- Manual correction of genome annotation improved alternative splicing identification of Artemisia annua.Planta · 2023Article
- ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs.Molecular ecology resources · 2023Article
- Genome Survey Sequencing and Genetic Background Characterization ofPlants (Basel, Switzerland) · 2022Article
- Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki.G3 (Bethesda, Md.) · 2022Article
- Hopomics:Metabolites · 2022Article
- The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features.GigaScience · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed.
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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.