ArticleBMC genomics2016
Genome-wide characterization of non-reference transposons in crops suggests non-random insertion.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
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- Genome-wide adenine N6-methylation map reveals epigenomic regulation of lipid accumulation in Nannochloropsis.Plant communications · 2024Article
- AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution.Cells · 2021Review
- Reprogramming of Retrotransposon Activity during Speciation of the Genus Citrus.Genome biology and evolution · 2019Article
- Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat.Scientific reports · 2019Article
- Article
- Genome-Wide Survey and Comparative Analysis of Long Terminal Repeat (LTR) Retrotransposon Families in Four Gossypium Species.Scientific reports · 2018Article
- Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon.Genome biology and evolution · 2018Article
- Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize.BMC genomics · 2017Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposons (transposable elements or TEs) are DNA sequences that can change their position within the genome. A large number of TEs have been identified in reference genome of each crop(named accumulated TEs), which are the important part of genome. However, whether there existed TEs with different insert positions in resequenced crop accession genomes from those of reference genome (named non-reference transposable elements, non-ref TEs), and what the characteristics (such as the number, type and distribution) are. To identify and characterize crop non-ref TEs, we analyzed non-ref TEs in more than 125 accessions from rice (Oryza sativa), maize (Zea mays) and sorghum (Sorghum bicolor) using resequenced data with paired-end mapping methods.
resultsWe identified 13,066, 23,866 and 35,679 non-ref TEs in rice, maize and sorghum, respectively. Genome-wide characterization analysis shows that most of non-ref TEs were unique and non-ref TE classes shows different among rice, maize and sorghum. We found that non-ref TEs have a strong positive correlation with gene number and have a bias toward insertion near genes, but with a preference for avoiding coding regions in maize and sorghum. The genes affected by non-ref TE insertion were functionally enriched for stress response mechanisms in all three crops.
conclusionsThese observations suggest that transposon insertion is not a random event and it makes genomic diversity, which may affect the intraspecific adaption and evolution of crops.
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