ArticleGenome biology and evolution2013
Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Weed competitive ability in wheat: a peek through in its functional significance, present status and future prospects.Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Review
- Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification.Plant molecular biology · 2017Article
- Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification.Genetica · 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
- Article
- Chromosome Specific Substitution Lines of Aegilops geniculata Alter Parameters of Bread Making Quality of Wheat.PloS one · 2016Article
- Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation.Proceedings. Biological sciences · 2015Article
- Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi.Genome biology and evolution · 2014Article
- Article
- Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization.Plant cell reports · 2013Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindrica and Ae. geniculata using 454 identified more than 70% of the sequences as known TEs, mainly long terminal repeat (LTR) retrotransposons. Comparing the abundance of reads as well as patterns of sequence diversity and divergence within and among genomes assessed the dynamics of 44 major LTR retrotransposon families of the 165 identified. In particular, molecular population genetics on individual TE copies distinguished recently active from quiescent families and highlighted different evolutionary trajectories of retrotransposons among related species. This work presents a suite of tools suitable for current sequencing data, allowing to address the genome-wide evolutionary dynamics of TEs at the family level and advancing our understanding of the evolution of nonmodel genomes.
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