ArticleThe Plant cell2016
Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences.
Article in The Plant cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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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Who cites it
36 citing papers in PubMed.
- White paper: standards for handling and analyzing plant pan-genomes.F1000Research · 2025Review
- Insights into the Genomic Background of Nine Common Chinese Medicinal Plants by Flow Cytometry and Genome Survey.Plants (Basel, Switzerland) · 2024Article
- Genome assembly of the bearded iris,GigaByte (Hong Kong, China) · 2023Article
- Metabolomics and genetics of reproductive bud development inFrontiers in plant science · 2023Article
- The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome.The Plant cell · 2022Article
- CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota).Database : the journal of biological databases and curation · 2022Article
- Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.Plant biotechnology journal · 2022Article
- Strategies of tolerance reflected in two North American maple genomes.The Plant journal : for cell and molecular biology · 2022Article
- Green plant genomes: What we know in an era of rapidly expanding opportunities.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- FirstGigaByte (Hong Kong, China) · 2022Article
- Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies.Molecular ecology · 2021Article
- Telomere-to-telomere genome assembly of asparaginase-producing Trichoderma simmonsii.BMC genomics · 2021Article
- TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.Nucleic acids research · 2021Article
- The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments.BMC genomics · 2021Article
- LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome.BMC plant biology · 2021Article
- High-Throughput Genotyping Technologies in Plant Taxonomy.Methods in molecular biology (Clifton, N.J.) · 2021Article
- High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome.GigaScience · 2020Article
- The genome evolution and domestication of tropical fruit mango.Genome biology · 2020Article
- Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.Nature communications · 2020Article
- Chromosome-Scale Assembly of Winter Oilseed RapeFrontiers in plant science · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome sequencing is becoming cheaper and faster thanks to the introduction of next-generation sequencing techniques. Dozens of new plant genome sequences have been released in recent years, ranging from small to gigantic repeat-rich or polyploid genomes. Most genome projects have a dual purpose: delivering a contiguous, complete genome assembly and creating a full catalog of correctly predicted genes. Frequently, the completeness of a species' gene catalog is measured using a set of marker genes that are expected to be present. This expectation can be defined along an evolutionary gradient, ranging from highly conserved genes to species-specific genes. Large-scale population resequencing studies have revealed that gene space is fairly variable even between closely related individuals, which limits the definition of the expected gene space, and, consequently, the accuracy of estimates used to assess genome and gene space completeness. We argue that, based on the desired applications of a genome sequencing project, different completeness scores for the genome assembly and/or gene space should be determined. Using examples from several dicot and monocot genomes, we outline some pitfalls and recommendations regarding methods to estimate completeness during different steps of genome assembly and annotation.
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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.