ArticleBMC plant biology2016
Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication.
Article in BMC plant biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Integrated Multi-Omics Analysis Reveals the Survival Strategy of Dongxiang Wild Rice (DXWR,Plants (Basel, Switzerland) · 2025Article
- The genomes of the most diverse AA genome rice species provide a resource for rice improvement and studies of rice evolution and domestication.BMC genomics · 2025Article
- MicroRNA2871b of Dongxiang Wild Rice (International journal of molecular sciences · 2023Article
- Genome-Wide Comparison of Structural Variations and Transposon Alterations in Soybean Cultivars Induced by Spaceflight.International journal of molecular sciences · 2022Article
- A Wild Rice RhizobacteriumInternational journal of molecular sciences · 2022Article
- Full-Length Genome of anFrontiers in microbiology · 2022Article
- Full-length chloroplast genome of Dongxiang wild rice reveals small single-copy region switching.Frontiers in plant science · 2022Article
- Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding.BMC genomics · 2021Article
- Genomic Feature Analysis of Betacoronavirus Provides Insights Into SARS and COVID-19 Pandemics.Frontiers in microbiology · 2021Article
- Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element.BMC genomics · 2020Article
- Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed.Microbiome · 2020Article
- De novo assembly of a wild pear (Pyrus betuleafolia) genome.Plant biotechnology journal · 2020Article
- The evolution study onJournal of genetics · 2019Article
- Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5' and 3' End Small RNAs.Frontiers in genetics · 2019Article
- Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.International journal of genomics · 2019Article
- Comparative analysis of the root transcriptomes of cultivated and wild rice varieties in response to Magnaporthe oryzae infection revealed both common and species-specific pathogen responses.Rice (New York, N.Y.) · 2018Article
- Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.).Biological research · 2018Article
- Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines.Plant molecular biology reporter · 2018Article
- Article
- Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Bioscience reports · 2017Article
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10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIt is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level.
resultsInstead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627.
conclusionsThese results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.
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