ArticlePlant physiology2008
Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice.
Article in Plant physiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Continuous infiltration and evolutionary trajectory of nuclear organelle DNA inGenome research · 2025Article
- Transcriptomic correlates of nutritional manipulation in a facultatively social bee.The Journal of experimental biology · 2025Article
- Natural Diversity of Heat-Induced Transcription of Retrotransposons in Arabidopsis thaliana.Genome biology and evolution · 2024Article
- Patterns of Chromosomal Variation, Homoeologous Exchange, and Their Relationship with Genomic Features in Early Generations of a Synthetic Rice Segmental Allotetraploid.International journal of molecular sciences · 2023Article
- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
- Genetic Variation of the Serine Acetyltransferase Gene Family for Sulfur Assimilation in Maize.Genes · 2021Article
- A New Way of Rice Breeding: Polyploid Rice Breeding.Plants (Basel, Switzerland) · 2021Review
- Identification and molecular characterization of mutant line deficiency in three waxy proteins of common wheat (Triticum aestivum L.).Scientific reports · 2021Article
- Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa).BMC genomics · 2020Article
- Genetic differentiation of Mutator insertion polymorphisms and association with agronomic traits in waxy and common maize.Genes & genomics · 2020Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- Identification of an active miniature inverted-repeat transposable element mJing in rice.The Plant journal : for cell and molecular biology · 2019Article
- Population-specific dynamics and selection patterns of transposable element insertions in European natural populations.Molecular ecology · 2019Article
- The Landscape ofFrontiers in plant science · 2019Article
- Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution.Scientific reports · 2017Article
- Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice.Scientific reports · 2017Article
- Domestication of rice has reduced the occurrence of transposable elements within gene coding regions.BMC genomics · 2017Article
- Miniature Inverted Repeat Transposable Element Insertions Provide a Source of Intron Length Polymorphism Markers in the Carrot (Frontiers in plant science · 2017Article
- Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.BMC genomics · 2016Article
- Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum.Molecular genetics and genomics : MGG · 2016Article
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5 authors.
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Abstract
Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (>100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.
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