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Transposons are major components of all eukaryotic genomes. Although traditionally regarded as causes of detrimental mutations, recent evidence suggests that transposons may play a role in host gene diversification and evolution. For example, host gene transduction by retroelements has been suggested to be both common and to have the potential to create new chimeric genes by the shuffling of existing sequences. We have previously shown that the maize (Zea mays subsp. mays) retrotranspnson Bs1 has transduced sequences from three different host genes. Here, we provide evidence that these transduction events led to the generation of a chimeric new gene that is both transcribed and translated. Expression of Bs1 is tightly controlled and occurs during a narrow developmental window in early ear development. Although all Bs1-associated transduction events took place before Zea speciation, a full uninterrupted open reading frame encoding the BSI protein may have arisen in domesticated maize or in the diverse populations of its progenitor Z. mays subs., parviglumis. We discuss potential functions based on domain conservation and evidence for functional constraints between the transduced sequences and their host gene counterparts. [ABSTRACT FROM AUTHOR]

The genomes of plants, like virtually all other eukaryotic organisms, harbor a diverse array of mobile elements, or transposons. In terms of numbers, the predominant type of transposons in many plants is the miniature inverted-repeat transposable element (MITE). There are three archetypal MITEs, known as Tourist, Stowaway, and Emigrant, each of which can be defined by a specific terminal inverted-repeat (TIR) sequence signature. Although their presence was known for over a decade, only recently have open reading frames (ORFs) been identified that correspond to putative transposases for each of the archetypes. We have identified two Stowaway elements that encode a putative transposase and are similar to members of the previously characterized IS630–Tc1-mariner superfamily. In this report, we provide a high-resolution phylogenetic analysis of the evolutionary relationship between Stowaway, Emigrant, and members of the IS630–Tc1-mariner superfamily. We show that although Emigrant is closely related to the pogo-like family of elements, Stowaway may represent a novel family. Integration of our results with previously published data leads to the conclusion that the three main types of MITEs have different evolutionary histories despite similarity in structure.Key words: Stowaway, Emigrant, MITE, mariner, transposon.La pluspart des plantes et autres organismes eucaryotes contiennent en leur genome un éventail varié d'éléments mobiles ou transposons. Chez les plantes, le type de transposon le plus abondant est les MITEs (« miniature inverted-repeat transposable elements »). Les trois MITEs archétypes sont nommées Tourist, Stowaway et Emigrant et sont définis par leurs séquences terminales répétée inverses (TIRs) ayant des signatures spécifiques. Bien que ces éléments soient connus depuis plus d'une décennie, les cadres ouverts de lectures (ORFs) encodant les transposases présumées de chaque archétype n'ont été découverts que récemment. Nous avons identifié deux éléments Stowaway dont les transposases sont semblables à celle des membres de la super-famille de transposons IS630–Tc1-mariner, characterisée antérieurement. Dans cet article, nous présentons une analyse phylogénétique des relations entre Stowaway, Emigrant et les membres de la super-famille IS630–Tc1-mariner. Nous démontrons que, tandis qu' Emigrant est apparenté a la famille des éléments de type pogo, Stowaway représente probablement une nouvelle famille. L'intégration de nos résultats et de données publiés précédemment mène à la conclusion que les trois principaux types de MITE ont des histoires évolutives distinctes, malgré leurs structures similaires.Mots clés : Stowaway, Emigrant, MITE, mariner, transposon. [ABSTRACT FROM AUTHOR]

Asserts that terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Structural organization of TRIM elements; Past mobility of TRIM; Involvement of transduction of host genes in TRIM element.

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene. [ABSTRACT FROM AUTHOR]