ArticlePloS one2013
Evaluation of genome sequencing quality in selected plant species using expressed sequence tags.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
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- The karyotype, genome survey, and assembly of Mud artemisia (Artemisia selengensis).Molecular biology reports · 2021Article
- Genome survey sequencing and identification of genomic SSR markers for Rhododendron micranthum.Bioscience reports · 2020Article
- Genome survey of Zanthoxylum bungeanum and development of genomic-SSR markers in congeneric species.Bioscience reports · 2020Article
- Characterization of DNA methylation variations during fruit development and ripening ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Genome survey sequencing and genetic background characterization of yellow horn based on next-generation sequencing.Molecular biology reports · 2019Article
- Genome survey and SSR analysis ofBioscience reports · 2019Article
- High-throughput sequencing data and the impact of plant gene annotation quality.Journal of experimental botany · 2019Article
- Experimental Verification and Evolutionary Origin of 5'-UTR Polyadenylation Sites inFrontiers in plant science · 2018Article
- Ploidy-dependent changes in the epigenome of symbiotic cells correlate with specific patterns of gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Orphan Crops Browser: a bridge between model and orphan crops.Molecular breeding : new strategies in plant improvement · 2016Article
- Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.).International journal of genomics · 2015Article
- Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.The Plant journal : for cell and molecular biology · 2014Article
- Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith the completion of genome sequencing projects for more than 30 plant species, large volumes of genome sequences have been produced and stored in online databases. Advancements in sequencing technologies have reduced the cost and time of whole genome sequencing enabling more and more plants to be subjected to genome sequencing. Despite this, genome sequence qualities of multiple plants have not been evaluated. METHODOLOGY/PRINCIPAL FINDING: Integrity and accuracy were calculated to evaluate the genome sequence quality of 32 plants. The integrity of a genome sequence is presented by the ratio of chromosome size and genome size (or between scaffold size and genome size), which ranged from 55.31% to nearly 100%. The accuracy of genome sequence was presented by the ratio between matched EST and selected ESTs where 52.93% ∼ 98.28% and 89.02% ∼ 98.85% of the randomly selected clean ESTs could be mapped to chromosome and scaffold sequences, respectively. According to the integrity, accuracy and other analysis of each plant species, thirteen plant species were divided into four levels. Arabidopsis thaliana, Oryza sativa and Zea mays had the highest quality, followed by Brachypodium distachyon, Populus trichocarpa, Vitis vinifera and Glycine max, Sorghum bicolor, Solanum lycopersicum and Fragaria vesca, and Lotus japonicus, Medicago truncatula and Malus × domestica in that order. Assembling the scaffold sequences into chromosome sequences should be the primary task for the remaining nineteen species. Low GC content and repeat DNA influences genome sequence assembly.
conclusionThe quality of plant genome sequences was found to be lower than envisaged and thus the rapid development of genome sequencing projects as well as research on bioinformatics tools and the algorithms of genome sequence assembly should provide increased processing and correction of genome sequences that have already been published.
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