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Revolver and superior: novel transposon-like gene families of the plant kingdom.

ABSTRACT: High-throughput sequencing of eukaryotic genomes has revived interest in the structure and function of repetitive genomic sequences, previously referred to as junk DNA. Repetitive sequences, including transposable elements, are now believed to play a significant role in genomic differentiation and evolution. Some are also expressed as regulatory noncoding RNAs. Vast DNA databases exist for higher eukaryotes; however, with the exception of homologues of known repetitive-sequence-families and transposable elements, most repetitive elements still need to be annotated. Revolver and Superior, both discovered in the Triticeae, are novel classes of transposon-like genes and major components of large cereal genomes. Revolver was isolated from rye via genome subtraction of sequences common to rye and wheat. Superior was isolated from rye by cleavage with EcoO109I, the recognition sites of which consist of a 5'- PuGGNCCPy-3' multi-sequence. Revolver is 2929-3041 bp long with an inverted repeat sequence on each end. The Superior family elements are 1292-1432 bp in length, with divergent 5' regions, indicating the presence of considerable structural diversity. Revolver and Superior are transcriptionally active elements; Revolver harbors a single gene consisting of three exons and two introns, encoding a protein of 139 amino acid residues. Revolver variants range in size from 2665 bp to 4269 bp, with some variants lacking the 5' region, indicating structural diversity around the first exon. Revolver and Superior are dispersed across all seven chromosomes of rye. Revolver has existed since the diploid progenitor of wheat, and has been amplified or lost in several species during the evolution of the Triticeae. This article reviews the recently discovered Revolver and Superior families of plant transposons, which do not share identity with any known autonomous transposable elements or repetitive elements from any living species.

SUBMITTER: Tomita M

PROVIDER: S-EPMC2851119 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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Revolver and superior: novel transposon-like gene families of the plant kingdom.

Tomita Motonori M

Current genomics 20100301 1

High-throughput sequencing of eukaryotic genomes has revived interest in the structure and function of repetitive genomic sequences, previously referred to as junk DNA. Repetitive sequences, including transposable elements, are now believed to play a significant role in genomic differentiation and evolution. Some are also expressed as regulatory noncoding RNAs. Vast DNA databases exist for higher eukaryotes; however, with the exception of homologues of known repetitive-sequence-families and tran ...[more]

PMID: 20808526

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Project description:BACKGROUND: As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement. RESULTS: We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis. CONCLUSION: The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.

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Revolver and superior: novel transposon-like gene families of the plant kingdom.

Publications

Revolver and superior: novel transposon-like gene families of the plant kingdom.

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