ArticleMolecular genetics and genomics : MGG2005
Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.
Article in Molecular genetics and genomics : MGG, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 91 citations in OpenAlex.
- A Natural LTR Retrotransposon Insertion in the Promoter of GhNAC140-Dt Boosts Cotton Lint Yield.Plant biotechnology journal · 2026Article
- Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species.BMC genomics · 2023Article
- Exploiting the miniature inverted-repeat transposable elements insertion polymorphisms as an efficient DNA marker system for genome analysis and evolutionary studies in wheat and related species.Frontiers in plant science · 2022Article
- The 10,000-Year Success Story of Wheat!Foods (Basel, Switzerland) · 2021Review
- A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes.Scientific data · 2021Article
- On the Trail ofInternational journal of molecular sciences · 2020Article
- Genome-Wide Analysis of the Lateral Organ Boundaries Domain Gene Family in Brassica Napus.Genes · 2020Article
- The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation.Molecular cell · 2020Article
- Article
- DPTEdb, an integrative database of transposable elements in dioecious plants.Database : the journal of biological databases and curation · 2016Article
- Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations.BMC plant biology · 2015Article
- Article
- Organization and evolution of transposable elements along the bread wheat chromosome 3B.Genome biology · 2014Article
- Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization.Plant cell reports · 2013Article
- Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification.Plant physiology · 2013Article
- Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat.Genome biology and evolution · 2013Article
- Unique and conserved microRNAs in wheat chromosome 5D revealed by next-generation sequencing.PloS one · 2013Article
- Accessing complex crop genomes with next-generation sequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Review
- Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley.Plant molecular biology · 2012Article
- Subgenomic analysis of microRNAs in polyploid wheat.Functional & integrative genomics · 2012Article
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9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed.
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