ArticlePlant physiology2008
Replication of nonautonomous retroelements in soybean appears to be both recent and common.
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 25 papers.
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Who cites it
25 citing papers in PubMed, 46 citations in OpenAlex.
- Review
- ThePlant direct · 2019Article
- Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution.Frontiers in plant science · 2018Article
- Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-GenomeG3 (Bethesda, Md.) · 2017Article
- Article
- The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Article
- Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris).Frontiers in plant science · 2014Article
- The phytochrome gene family in soybean and a dominant negative effect of a soybean PHYA transgene on endogenous Arabidopsis PHYA.Plant cell reports · 2013Article
- The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome.Annals of botany · 2013Article
- Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome.BMC genomics · 2012Article
- Structural variants in the soybean genome localize to clusters of biotic stress-response genes.Plant physiology · 2012Article
- Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine.Plant physiology · 2012Article
- Molecular tools for exploring polyploid genomes in plants.International journal of molecular sciences · 2012Review
- Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence.Molecular genetics and genomics : MGG · 2012Article
- Spliceosomal intron size expansion in domesticated grapevine (Vitis vinifera).BMC research notes · 2011Article
- Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat.Genetics · 2010Article
- Specific resistances against Pseudomonas syringae effectors AvrB and AvrRpm1 have evolved differently in common bean (Phaseolus vulgaris), soybean (Glycine max), and Arabidopsis thaliana.The New phytologist · 2010Article
- Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris.The Plant cell · 2010Article
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Authors and funding
38 authors at 11 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.
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