Tc8, a Tourist-like transposon in Caenorhabditis elegans.

Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.     

Insertion Preference of Maize and Rice Miniature Inverted Repeat Transposable Elements as Revealed by the Analysis of Nested Elements

A 128-bp insertion into the maize waxy-B2 allele led to the discovery of Tourist, a family of miniature inverted repeat transposable elements (MITEs). As a special category of nonautonomous elements, MITEs are distinguished by their high copy number, small size, and close association with plant genes. In maize, some Tourist elements (named Tourist-Zm) are present as adjacent or nested insertions. To determine whether the formation of multimers is a common feature of MITEs, we performed a more thorough survey, including an estimation of the proportion of multimers, with 30.2 Mb of publicly available rice genome sequence. Among the 6600 MITEs identified, >10% were present as multimers. The proportion of multimers differs for different MITE families. For some MITE families, a high frequency of self-insertions was found. The fact that all 340 multimers are unique indicates that the multimers are not capable of further amplification.     

Survey of transposable elements from rice genomic sequences

Oryza sativa L. (domesticated rice) is a monocotyledonous plant, and its 430 Mb genome has been targeted for complete sequencing. We performed a high-resolution computer-based survey for transposable elements on 910 Kb of rice genomic DNA sequences. Both class I and II transposable elements were present, contributing 19.9% of the sequences surveyed. Class II elements greatly outnumbered class I elements (166 versus 22), although class I elements made up a greater percentage (12.2% versus 6.6%) of nucleotides surveyed. Several Mutator-like elements (MULEs) were identified, including rice elements that harbor truncated host cellular genes. MITEs (miniature inverted-repeat transposable elements) account for 71.6% of the mined transposable elements and are clearly the predominant type of transposable element in the sequences examined. Moreover, a putative Stowaway transposase has been identified based on shared sequence similarity with the mined MITEs and previously identified plant mariner-like elements (MLEs). Members of a group of novel rice elements resembling the structurally unusual members of the Basho family in Arabidopsis suggest a wide distribution of these transposons among plants. Our survey provides a preview of transposable element diversity and abundance in rice, and allows for comparison with genomes of other plant species.     

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives.     

A subtilisin-like serine protease specifically expressed in reproductive organs in rice

To identify genes specifically expressed in flowering pistils and that are related to reproductive phenomena, simplified differential display was performed with cDNA obtained from pistils and ovaries at several stages. One clone preferentially expressed in pistils at flowering and 1 day before flowering was identified as a rice subtilisin-like serine protease (RSP1). Sequence comparisons revealed that RSP1 has several characteristics in common with preproproteins. RT-PCR, northern blot, and in situ hybridization analysis revealed that RSP1 mRNA accumulates in pistils and in the filaments of stamens, whereas mRNA was undetectable in tissue from leaves, roots, panicles, and embryos. The mRNA levels in pistils increased slightly at flowering and decreased afterwards. Possible roles of the subtilisin-like serine protease in plant reproduction are discussed. Received: 27 February 2000 / Revision accepted: 24 October 2000     

Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with stowaway miniature inverted repeat transposable elements (MITEs)

Stowaway is a superfamily of miniature inverted repeat transposable elements (MITEs) that is widespread and abundant in plant genomes. Like other MITEs, however, its origin and mode of amplification are poorly understood. Several lines of evidence point to plant mariner-like elements (MLEs) as the autonomous partners of the nonautonomous Stowaway MITEs. To better understand this relationship, we have taken advantage of the nearly complete genome sequences of two rice subspecies to generate the first inventory of virtually all MLEs and Stowaway families coexisting in a single plant species. Thirty-four different MLEs were found to group into three major clades and 25 families. More than 22,000 Stowaway MITEs were identified and classified into 36 families. On the basis of detailed sequence comparisons, MLEs were confirmed to be the best candidate autonomous elements for Stowaway MITEs. Surprisingly, however, sequence similarity between MLE and Stowaway families was restricted to the terminal inverted repeats (TIRs) and, in a few cases, to adjacent subterminal sequences. These data suggest a model whereby most of the Stowaway MITEs in rice were cross-mobilized by MLE transposases encoded by distantly related elements.     

Discovery of Bisexual Flowers in Pterocarya Stenoptera C. DC.

This paper reports the bisexual structure of the flowers of Pterocarya stenoptera. The bisexual flowers are borne at the end of a leafy shoot of the current year in many-flowered terminal pendulous catkins. They have the same structure as the general female ones. Each flower grows in the axil of a bract, with a pair of bracteoles and four small perianths. Each flower has two or three carpels in the centre of the flower, and upon them there are two or three styles with stigmas on the inner face. They differ from the general female ones in that each of them contains 4-6 stamens, forming a single whorl. The stamens alternates with, or is opposite to, the perianth elements. Sometimes they contain 8 (-10) stamens, forming two whorls, with 6 in the outer whorl and 2 (-4) in the inner whorl, and in this case the pistil in the bisexual flower of terminal catkins often becomes a rudiment. It is interesting that we have also found bisexual flowers in another tree, which are borne in lateral male catkins. They have the same structure as general male ones, and the pistils are often represented by a rudiment. Manning (1940) points out that some female flowers of Pterocarya stenoptera and P. fraxinifolia occasionally have stamens ( ? ) opposite the sepals. In P. stenoptera we have found that both the stamens and the stigmas of bisexual flowers are functional. They are capable of producing functional fruits. This is the same case as in Myrica Gale described by Davey and Gibson (1917). Rendle (1952) points out that in the male flowers of Platycarya the pistils often appeared as a rudiment. He considers, however, the male flowers derived from the bisexual flowers with an indefinite number of stamens. The rudimentary pistils of lateral male catkins in P. stenoptera we found are just the same as the ones found in Platycarya by Rendle. The discovery of the bisexual flowers in P. stenoptera may prove that the unisexual flowers of the present-day Juglandaceae are derived from ancestors with bisexual flowers.This tends to support the hypothesis that Cycadicae is the possible ancestor of the angiosperms.     

Inter- and intra-specific distribution of Stowaway transposable elements in AA-genome species of wild rice

The presence or absence of miniature inverted-repeat transposable elements (MITEs) that belong to Stowaway family was analyzed at three loci, two of which are newly identified, in five wild rice species having the AA genome. The pattern of the presence or absence of MITEs was found to be highly associated with speciation in this plant group. In Oryza rufipogon, the pattern was also associated with differentiation into annual or perennial ecotypes. These results suggest either that gene flow has been highly restricted between different species, as well as between different ecotypes of O. rufipogon after they were differentiated, or that loci with or without MITEs have been selected in nature together with the linked genes that are responsible for adaptation to environments. In addition, a very low polymorphism with regard to the presence or absence of MITEs within each species or each ecotype suggests that the frequency of transposition of MITEs is very low, assuming that the loci that contain MITEs are free from selection pressure. Received: 30 October 1999 / Accepted: 2 December 1999     

PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements

Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements that are widespread and abundant in plant genomes. Most of the hundreds of thousands of MITEs identified to date have been divided into two major groups on the basis of shared structural and sequence characteristics: Tourist-like and Stowaway-like. Since MITEs have no coding capacity, they must rely on transposases encoded by other elements. Two active transposons, the maize P Instability Factor (PIF) and the rice Pong element, have recently been implicated as sources of transposase for Tourist-like MITEs. Here we report that PIF- and Pong-like elements are widespread, diverse, and abundant in eukaryotes with hundreds of element-associated transposases found in a variety of plant, animal, and fungal genomes. The availability of virtually the entire rice genome sequence facilitated the identification of all the PIF/Pong-like elements in this organism and permitted a comprehensive analysis of their relationship with Tourist-like MITEs. Taken together, our results indicate that PIF and Pong are founding members of a large eukaryotic transposon superfamily and that members of this superfamily are responsible for the origin and amplification of Tourist-like MITEs.     

A family of human microRNA genes from miniature inverted-repeat transposable elements

While hundreds of novel microRNA (miRNA) genes have been discovered in the last few years alone, the origin and evolution of these non-coding regulatory sequences remain largely obscure. In this report, we demonstrate that members of a recently discovered family of human miRNA genes, hsa-mir-548, are derived from Made1 transposable elements. Made1 elements are short miniature inverted-repeat transposable elements (MITEs), which consist of two 37 base pair (bp) terminal inverted repeats that flank 6 bp of internal sequence. Thus, Made1 elements are nearly perfect palindromes, and when expressed as RNA they form highly stable hairpin loops. Apparently, these Made1-related structures are recognized by the RNA interference enzymatic machinery and processed to form 22 bp mature miRNA sequences. Consistent with their origin from MITEs, hsa-mir-548 genes are primate-specific and have many potential paralogs in the human genome. There are more than 3,500 putative hsa-mir-548 target genes; analysis of their expression profiles and functional affinities suggests cancer-related regulatory roles for hsa-mir-548. Taken together, the characteristics of Made1 elements, and MITEs in general, point to a specific mechanism for the generation of numerous small regulatory RNAs and target sites throughout the genome. The evolutionary lineage-specific nature of MITEs could also provide for the generation of novel regulatory phenotypes related to species diversification. Finally, we propose that MITEs may represent an evolutionary link between siRNAs and miRNAs.     

蓝花丹二型花雌、雄蕊发育进程及内源激素对花柱生长的影响

为了解二型花雌、雄蕊发育进程及内源激素对长、短花柱生长发育的影响,以蓝花丹(Plumbago auriculata Lam.)为材料,观察分析了长花柱(L型)、短花柱(S型)花朵内雌、雄蕊的发育特征,并分别检测了L、S型花柱中的内源激素水平。结果显示:蓝花丹雌、雄蕊发育进程基本符合逻辑斯蒂变化曲线,并可划分为5个时期,即T1初始发育期、T2转折期(一)、T3快速发育期、T4转折期(二)、T5平稳发育期;在整个发育进程中,L型花朵中雌蕊的生长速率始终高于雄蕊;S型花朵中雌蕊的生长速率在T3期由快转慢,导致T3~T5期雌蕊的生长速率始终低于雄蕊,从而形成了雌蕊低于雄蕊的短花柱特征。这说明花柱的分化是在二型花雌、雄蕊快速发育的T3期开始出现,并逐渐形成花柱异长植物最显著的花部形态特征。IAA、IPA和GA含量均在T1~T3期增加、T4~T5期降低,且在L型花柱中的含量始终高于S型,而ABA含量的变化趋势与这3种生长促进类激素相反,说明在蓝花丹花柱发育过程中,IAA、IPA和GA可能参与调控花柱的伸长生长,而ABA主要在发育后期促使花柱成熟。     

植物基因组中微型反向重复转座元件研究进展

微型反向重复转座元件(miniature inverted repeat transposable element,MITE)是一类特殊的转座元件,在结构上与有缺失的DNA转座子相似,但具有反转录转座子高拷贝数的特点.MITE时常与基因相伴,对基因调控可能起重要作用,因此,MITE正逐渐成为基因和基因组进化及生物多样性研究的一种重要工具.本文综述了植物基因组MITE的结构、分类、活性及其应用研究进展.     

Tourist: a large family of small inverted repeat elements frequently associated with maize genes.

The wx-B2 mutation results from a 128-bp transposable element-like insertion in exon 11 of the maize Waxy gene. Surprisingly, 11 maize genes and one barley gene in the GenBank and EMBL data bases were found to contain similar elements in flanking or intron sequences. Members of this previously undescribed family of elements, designated Tourist, are short (133 bp on average), have conserved terminal inverted repeats, are flanked by a 3-bp direct repeat, and display target site specificity. Based on estimates of repetitiveness of three Tourist elements in maize genomic DNA, the copy number of the Tourist element family may exceed that of all previously reported eukaryotic inverted repeat elements. Taken together, our data suggest that Tourist may be the maize equivalent of the human Alu family of elements with respect to copy number, genomic dispersion, and the high frequency of association with genes.     

Spring: a novel family of miniature inverted-repeat transposable elements is associated with genes in apple

The apple, Malusxdomestica Borkh., belongs to the family Rosaceae and subfamily Maloideae and has a genome size of approximately 750 Mb. In this study, a novel family of transposable elements, designated Spring, has been identified in the apple genome. The four Spring elements, Spring-1 to Spring-4, share all the classic features of miniature inverted-repeat transposable elements (MITEs), including small size (approximately 148 bp), no coding potential, A/T richness, insertion bias toward noncoding regions, terminal inverted repeats (TIRs), target site duplications, and potential for forming secondary structures. Evidence of previous mobility of Spring-4 is demonstrated by sequence alignment of genes encoding 1-aminocyclopropane-1-carboxylic acid synthase from both apple and a related member of the Maloideae subfamily, pear. The Spring elements are flanked by either 8- or 9-bp direct repeats, and they differ significantly in size compared to other previously reported MITEs in plants. The TIRs of these Spring elements are not found in any other previously reported plant genes or transposons, except for apple. The possible role of Spring elements in the apple genome is discussed.     

Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences

Repetitive genomic sequences might have various structural features and properties distinct from those of the known transposable elements (TE). Here, the content and properties of the repetitive sequences present in a 200-kb region around the rice waxy locus were analyzed using the available rice genomic database. In our previous Southern blotting analysis, 70% of the segments in this region showed smeared patterns, but according to the present database analysis, the proportion of repetitive sequences in this region was only 15%. The repetitive segments in this 200-kb region comprised 75 repetitive sequences that we classified into 46 subfamilies: 21 subfamilies were known TEs or repetitive sequences and 25 subfamilies consisted of newly identified TEs or novel types of repetitive sequences. The region contains no long terminal repeat (LTR) retrotransposable elements, but miniature inverted repeat transposable elements (MITEs) constituted a major class among the elements identified. These MITEs showed remarkable structural divergence: 12 elements were found to be new members of known MITE superfamilies, while five elements had novel terminal structures, and did not belong to any known TE families. Interestingly, about 10% of the repetitive sequences, including virus-like sequences did not have any of the usual characteristics of TEs, suggesting that a certain proportion of repetitive sequences that might not share the transpositional mechanisms of known elements are dispersed in the compact rice genome.