ArticlePlant molecular biology2021
DNA barcoding of Oryza: conventional, specific, and super barcodes.
Article in Plant molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Phylogenetic study and accurate identification of Tamarix species in China based on complete chloroplast genomes.BMC plant biology · 2026Article
- Complete chloroplast genome of Triticum aestivum cultivar 'Keumkang' from Korea (Poaceae) and comparative chloroplast genomes of the members of the Triticum genus.Journal of the science of food and agriculture · 2026Article
- Non-Authentic Genotypes-An Unrevealed Problem in Plant Research and Breeding.Plants (Basel, Switzerland) · 2026Article
- Assessment of suitable cultivation area for Paris polyphylla var. chinensis and var. yunnanensis under anthropogenic disturbance based on ensemble modeling and germplasm identification.BMC plant biology · 2026Article
- Comparative plastome analysis and phylogenetic relationships of ChineseFrontiers in plant science · 2026Article
- Plastome variation and phylogenetic relationships ofFrontiers in plant science · 2026Article
- DNA Barcoding for Tracing Biodiversity in Mixed Crop Food Products: A Proof of Concept Within the BioValue Project.Foods (Basel, Switzerland) · 2025Article
- Major Genes for Powdery Mildew Resistance in Research and Breeding of Barley: A Few Brief Narratives and Recommendations.Plants (Basel, Switzerland) · 2025Review
- Oryza genome evolution through a tetraploid lens.Nature genetics · 2025Article
- Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae).Plant diversity · 2025Article
- Development of a robust SNP marker set for genotyping diverse gene bank collections of polyploid roses.BMC plant biology · 2024Article
- Comparative study on chloroplast genome ofEcology and evolution · 2024Article
- Complete plastome genomes of three medicinal heliotropiaceae species: comparative analyses and phylogenetic relationships.BMC plant biology · 2024Article
- Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer.BMC plant biology · 2024Article
- Characterization of the complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2024Article
- Whether niche changes promote the evolution of species: a case study ofFrontiers in plant science · 2024Article
- Decoding the complete chloroplast genome ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2023Article
- Identification of three cultivated varieties of Scutellaria baicalensis using the complete chloroplast genome as a super-barcode.Scientific reports · 2023Article
- Article
- Non-Authenticity of Spring Barley Genotypes Revealed in Gene Bank Accessions.Plants (Basel, Switzerland) · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
10 authors.
Funding
Abstract
key messageWe applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.
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