A new combination in Matelea (Asclepiadaceae) and lectotypification of M. parvifolia

Vegetative similarities as well as a syntype specimen with discordant elements have evidently misled botanists to equateLachnostoma hastatulum withGonolobus parvifolius. Both species are considered representatives of a broadly interpreted genusMatelea, subgenusChthamalia. A new combination,M. hastatula, is proposed, andG. parvifolius is lectotypified.     

Phylogenetic relationship of medicinally importantCnidium officinale and Japanese Apiaceae based onrbcL sequences

Cnidium officinale Makino is important medicinally and economically, but its origin is uncertain. The phylogenetic relationship ofC. officinale is provided from the analyses based on the ribulose-1,5-bisphosphate carboxylase/oxgenase gene (rbcL) sequences of 41 species which represent the 34 genera of Aplaceae, the four genera of Araliaceae, and one genus each of Pittosporaceae, Cornaceae, and Caprifoliaceae. The strict consensus tree obtained supports a close relationship ofC. officinale to the Chinese members ofLigusticum, especially toL. chuanxiong. Additionally, the tree shows (1) polyphyly of the genusLigusticum and (2) monophyly of the subfamily Apioideae. Within Apioideae, we recognized some groups in our phylogenetic tree. The grouping is discordant in several respects with the traditional tribal divisions based mainly on fruit morphology.     

Genetic evidence of a relationship between two maize transposable element systems: Cy and Mutator

Summary The Cy transposable element system is composed of two genetically defined elements: an rcy receptor element inserted at the Bronze-1 locus; and an independently segregating regulatory element, Cy. The Cy system is not functionally homologous to any of the non-Mutator transposable element systems. Evidence is presented that supports a relationship between the Cy system and the family of Mu1-homologous transposable elements that are responsible for the Mutator phenomenon. Although related, Cy elements and the Mu1-homologous elements are not identical; Cy is inherited in a near-Mendelian fashion, in contrast to the non-Mendelian inheritance of the Mu1-homologous elements.     

Themariner transposable element in natural populations ofDrosophila teissieri

Themariner transposable elements of several natural populations ofDrosophila teissieri, a rainforest species endemic to tropical Africa, were studied. Natural populations trapped along a transect from Zimbabwe to the Ivory Coast were analyzed by Southern blotting, in situ hybridization, cloning, and sequencing of PCR products. The Brazzaville population had some full-length elements, while the remaining populations had mainly deleted elements. The main class of deleted elements lacked a 500-bp segment. A mechanism is proposed that could generate such elements rapidly. In situ hybridizations showed that there are nomariner elements in pericentromeric heterochromatin. Finally, the phylogeny of theMos1-likemariner full-length elements is consistent with vertical transmission from the ancestor of themelanogaster subgroup. Correspondence to: P. Capy     

Somatic Mutator activity expression is dependent on the strength of Cy trans-active signals in maize

Summary Two receptor element alleles (vp-rcy and bz-rcy) that respond to the trans-active element (Cy) controlling Mutator activity were used to analyze the strength of trans-active signals from Cy elements derived from a Mutator active line. Evidence is presented that the Mutator population tested consists mainly of a class of weak Cy elements designated as Cy:Mu. When Cy:Mu element are present in only a few copies, the strength of the combined transposition signal is weak. It is only when these active elements have a high copy number that the overall transposition signal is sufficiently strong enough to elicit a high frequency of transposition events. This study seeks to investigate the nature of the trans-active signal from Cy:Mu elements. The implication of these results for molecular studies is discussed.Journal Paper No. J-13083 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA, Project No. 2381     

Why Are Young and Old Repetitive Elements Distributed Differently in the Human Genome?

Alu elements are not distributed homogeneously throughout the human genome: old elements are preferentially found in the GC-rich parts of the genome, while young Alus are more often found in the GC-poor parts of the genome. The process giving rise to this differential distribution remains poorly understood. Here we investigate whether this pattern could be due to a preferential degradation of Alu elements integrated in GC-poor regions by small indel mutations. We aligned 5.1 Mb of human and chimpanzee sequences and examined whether the rate of insertion and deletion inside Alu elements differed according to the base composition surrounding them. We found that Alu elements are not preferentially degraded in GC-poor regions by indel events. We also looked at whether very young L1 elements show the same change in distribution compared to older ones. This analysis indicated that L1 elements also show a shift in their distribution, although we could not assess it as precisely as for Alu elements. We propose that the differential distribution of Alu elements is likely to be due to a change in their pattern of insertion or their probability of fixation through evolutionary time.Reviewing Editor: Dr. Stephen Freeland     

Evolution of Ac and Dsl elements in select grasses (Poaceae)

We present data on evolution of the Ac/Ds family of transposable elements in select grasses (Poaceae). An Ac-like element was cloned from a DNA library of the grass Pennisetum glaucum (pearl millet) and 2387 bp of it have been sequenced. When the pearl millet Ac-like sequence is aligned with the corresponding region of the maize Ac sequence, it is found that all sequences corresponding to intron II in maize Ac are absent in pearl millet Ac. Kimura's evolutionary distance between maize and pearl millet Ac sequences is estimated to be 0.429±0.020 nucleotide substitutions per site. This value is not significantly different from the average number of synonymous substitutions for coding regions of the Adh1 gene between maize and pearl millet, which is 0.395±0.051 nucleotide substitutions per site. If we can assume Ac and Adh1 divergence times are equivalent between maize and pearl millet, then the above calculations suggest Ac-like sequences have probably not been strongly constrained by natural selection. The level of DNA sequence divergence between maize and pearl millet Ac sequences, the estimated date when maize and pearl millet diverged (25–40 million years ago), coupled with their reproductive isolation/lack of current genetic exchange, all support the theory that Ac-like sequences have not been recently introduced into pearl millet from maize. Instead, Ac-like sequences were probably present in the progenitor of maize and pearl millet, and have thus existed in the grasses for at least 25 million years. Ac-like sequences may be widely distributed among the grasses. We also present the first 2 Dsl controlling element sequences from teosinte species: Zea luxurians and Zea perennis. A total of 10 Dsl elements had previously been sequenced from maize and a distant maize relative, Tripsacum. When a maximum likelihood network of genetic relationships is constructed for all 12 sequenced Dsl elements, the 2 teosinte Dsl elements are as distant from most maize Dsl elements and from each other, as the maize Dsl elements are from one another. Our new teosinte sequence data support the previous conclusion that Dsl elements have been accumulating mutations independently since maize and Tripsacum diverged. We present a scenario for the origin of Dsl elements.     

Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup

LINE-like retrotransposons, the so-called I elements, control the system of I-R (inducer-reactive) hybrid dysgenesis in Drosophila melanogaster. I elements are present in many Drosophila species. It has been suggested that active, complete I elements, located at different sites on the chromosomes, invaded natural populations of D. melanogaster recently (1920–1970). But old strains lacking active I elements have only defective I elements located in the chromocenter. We have cloned I elements from D. melanogaster and the melanogaster subgroup. In D. melanogaster, the nucleotide sequences of chromocentral I elements differed from those on chromosome arms by as much as 7%. All the I elements of D. mauritiana and D. sechellia are more closely related to the chromosomal I elements of D. melanogaster than to the chromocentral I elements in any species. No sequence difference was observed in the surveyed region between two chromosomal I elements isolated from D. melanogaster and one from D. simulans. These findings strongly support the idea that the defective chromocentral I elements of D. melanogaster originated before the species diverged and the chromosomal I elements were eliminated. The chromosomal I elements reinvaded natural populations of D. melanogaster recently, and were possibly introduced from D. simulans by horizontal transmission.     

Cchobo, a hobo-related sequence in Ceratitis capitata

A hobo-related sequence, Cchobo, with high similarity to the Drosophila melanogaster HFL1 and hobo₁₀₈ elements was isolated from the medfly. Thirteen PCR-derived clones, which share 97.9–100% DNA identity, were sequenced, seven of which do not show frame-shift or stop codon mutations in their conceptual translations. The consensus sequence has 99.7% DNA identity with the D. melanogaster hobo element HFL1. In a phylogenetic analysis with other hobo-related elements, Cchobo clusters with the HFL1 and hobo₁₀₈ elements from D. melanogaster and hobo-related elements from D. simulans, D. mauritiana and Mamestra brassicae. These elements may have undergone horizontal transfer in the recent past. The genomic distribution of Cchobo was studied by FISH to mitotic and polytene chromosomes, which revealed that Cchobo is distributed within both the heterochromatin and euchromatin. Intra- and interstrain polymorphisms were detected both at euchromatic and heterochromatic sites. These findings suggest that active copies of the element may be present in the medfly genome.     

Newly activated germinal Uq elements in maize are clustered on one linkage group independently of the standard Uq element

Summary Allelism tests between the standard Uq element (Uq1) and five newly activated germinal Uq elements (Uq2, Uq3, UQ4, Uq5, and Uq6) demonstrate that these new Uq elements are independent of Uq1. Gametes that either contain one Uq or various combinations of two different and phenotypically distinguishable Uq elements, have been constructed either with or without the a-ruq reporter allele. Genetic analyses of the progenies of the gametes (using the standard a-ruq tested line as the other parent) have indicated that (i) each Uq element, when present alone, has the capacity to express full activity except when a secondary transposition or loss of activity has occurred; (ii) all five new Uq elements are independent of Uq1 with respect to transposition activity; and (iii) these newly originated Uqs are clustered on one linkage group. Uq2 is allelic to Uq4, and Uq3 is allelic to Uq5, whereas Uq6 is linked to both allelic pairs. A putative linkage map of these Uq elements is presented. In reciprocal crosses there is a striking difference in phenotypic segregation of Uq; when transmitted via the male parent Uq loses full expression capacity.     

Retrotransposon populations of <Emphasis Type="Italic">Vicia</Emphasis> species with varying genome size

The (non-LTR) LINE and Ty3-gypsy-type LTR retrotransposon populations of three Vicia species that differ in genome size (Vicia faba, Vicia melanops and Vicia sativa) have been characterised. In each species the LINE retrotransposons comprise a complex, very heterogeneous set of sequences, while the Ty3-gypsy elements are much more homogeneous. Copy numbers of all three retrotransposon groups (Ty1-copia, Ty3-gypsy and LINE) in these species have been estimated by random genomic sequencing and Southern hybridisation analysis. The Ty3-gypsy elements are extremely numerous in all species, accounting for 18–35% of their genomes. The Ty1-copia group elements are somewhat less abundant and LINE elements are present in still lower amounts. Collectively, 20–45% of the genomes of these three Vicia species are comprised of retrotransposons. These data show that the three retrotransposon groups have proliferated to different extents in members of the Vicia genus and high proliferation has been associated with homogenisation of the retrotransposon population.Electronic Supplementary Material Supplementary material is available for this article at .     

Genetic regulation of somatic mutability of two Mu-induced a1 mutants of maize

Summary Previous studies of stocks of two Mutator-induced mutable a1 alleles (a1-Mum2 and al-Mum3) gave results consistent with the presence of one or more autonomous elements regulating the expression of mutability. This article reports on the results of studies designed to map these autonomous elements by using a series of waxy marked translocations. Linkage of waxy with autonomous elements was found for a1-Mum2 by using the translocations wx T2-9d, wx T4-9e and wx T4-9b. Several different linkage values were found in crosses involving wx T2-9d, suggesting that autonomous elements have transposed to different locations on chromosome 2. Linkage of autonomous elements with waxy was found for a1-Mum3 using translocation wx T2-9d. Again, several different linkage values were found. Some of these values were the same as those observed for a1-Mum2, but some were unique. In some crosses, the number of autonomous elements increased by one or two unlinked elements in addition to the linked element in one generation (i. e. the generation of the cross to the translocation series). Such an increase in number is probably the result of transposition of the original autonomous element to an independent locus while retaining the autonomous element at the original locus. Reduction in the number of autonomous elements is probably the result of the independent assortment in crosses of plants with two or more autonomous elements.Journal Paper No. J-14569 of The Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa Project No 2870     

Wood anatomy ofTrimeniaceae

Four collections of three species ofTrimenia and one collection ofPiptocalyx were studied; early-formed and later-formed wood was analyzed for oneTrimenia. Liquid-preserved material permitted analysis of mucilage and starch storage in wood ofT. neocaledonica andP. moorei. BecausePiptocalyx is scandent whereasTrimenia is arborescent, wood differences relative to evolution of a climbing habit could be examined.Piptocalyx contrasts withTrimenia in having wider vessels, more numerous per mm², resulting in a conductive area five times greater per unit area than that of theTrimenia woods averaged.Piptocalyx has appreciably fewer bars per perforation plate and thus much greater conductive area per perforation plate than have the species ofTrimenia. Rays inPiptocalyx are much taller and wider than those ofTrimenia. Wood ofTrimeniaceae is highly primitive in its scalariform perforation plates, scalariform lateral wall pitting on vessels, relatively long vessels elements, and heterocellular rays. Imperforate tracheary elements are septate nucleate fibertracheids (or even libriform fibers) rather than tracheids, but loss of borders on pits (and thus lowered conductive function of the imperforate tracheary elements) can be explained by the development of these elements into starchstoring cells. Some fiber-tracheids inT. neocaledonica are enlarged mucilagecontaining cells. Details of vessel structure inTrimeniaceae are similar to those ofMonimiaceae (s. s.), but similarity to some other lauralean (annonalean) families may be found: in mucilage presence,Trimeniaceae resembleLauraceae rather thanMonimiaceae. Wood ofTrimeniaceae may be regarded as highly mesomorphic, corresponding to the moist habitats in which all of the species occur.     

Studies onCabomba aquatica (Cabombaceae)

Cabomba aquatica has been found for the first time in India. Both, submerged and floating leaves are epistomatic. The stomata are anomocytic and perigenous in their development. The metaxylem vessel elements have simple perforation plates and spiral side wall thickening. Vessel elements are found in roots, rhizomes and aerial stems. The venation pattern is of two types like the dimorphic leaves. On the basis of these and other featuresCabomba deserves family rank.     

Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.)

Members of a novel Master family of class II transposons were identified in the carrot genome. Two elements, 2.5 kb long DcMaster1 and 4.4 kb long DcMaster-a, are characterized by 22 bp imperfect terminal inverted repeats and by 3 bp target site duplications. GenBank search revealed that related elements are also present in Medicago truncatula, including a 5.1 kb element MtMaster-a. Both DcMaster-a and MtMaster-a contain open reading frames encoding for putative transposases with the complete DDE domain typical for plant class II transposable elements belonging to PIF/Harbinger superfamily, where the Master elements form a distinct group. Less than 10 copies of the DcMaster element containing the DDE domain are present in genomes of carrot and other Apiaceae, but more copies with internal deletions or insertions may occur. DcMaster elements were associated with putative coding regions in 8 of 14 identified insertion sites. PCR amplification of carrot genomic DNA using a primer complementary to TIRs of DcMaster gave products <400 bp in size. We speculate that these may all represent a MITE-like family of transposable elements that we named Krak, present in the carrot genome in at least 3,600 copies. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession numbers DQ250792 to DQ250807 and DQ353734 to DQ353752.     

Concomitant regulation of Mu1 transposition and Mutator activity in maize

Summary The mutagenic activity of the maize transposable element system Mutator can be lost by outcrossing to standard, non-Mutator lines or by repetitive intercrossing of genetically diverse Mutator lines. Lines losing Mutator mutagenic activity in either manner retain high copy numbers (10–15 per diploid genome) of the Mutator-associated Mu transposable elements. Frequent transposition of Mu1-related elements is observed only in active Mutator lines, however. The loss of Mutator activity on intercrossing is correlated with an increase in the copy number of Mu1-like elements to 40–50 per diploid genome, implying a self-encoded or self-activated negative regulator of Mu1 transposition. The outcross loss of Mutator activity is only weakly correlated with a low Mu element copy number and may be due to the loss of a positive regulatory factor encoded by a subset of Mu1-like elements. Transposition of Mu elements in active Mutator lines generates multiple new genomic positions for about half the elements each plant generation. The appearance of Mu1-like elements in these new positions is not accompanied by equally high germinal reversion frequencies, suggesting that Mu1 may commonly transpose via a DNA replicative process.     

<Emphasis Type="Italic">Drosophila</Emphasis><Emphasis Type="Italic">P</Emphasis> transposons of the urochordata <Emphasis Type="Italic">Ciona intestinalis</Emphasis>

P transposons belong to the eukaryotic DNA transposons, which are transposed by a cut and paste mechanism using a P-element-coded transposase. They have been detected in Drosophila, and reside as single copies and stable homologous sequences in many vertebrate species. We present the P elements Pcin1, Pcin2 and Pcin3 from Ciona intestinalis, a species of the most primitive chordates, and compare them with those from Ciona savignyi. They showed typical DNA transposon structures, namely terminal inverted repeats and target site duplications. The coding region of Pcin1 consisted of 13 small exons that could be translated into a P-transposon-homologous protein. C. intestinalis and C. savignyi displayed nearly the same phenotype. However, their P elements were highly divergent and the assumed P transposase from C. intestinalis was more closely related to the transposase from Drosophila melanogaster than to the transposase of C. savignyi. The present study showed that P elements with typical features of transposable DNA elements may be found already at the base of the chordate lineage. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

<Emphasis Type="Italic">Mutator</Emphasis>-like elements identified in melon,Arabidopsis and rice contain ULP1 protease domains

The transposon Mutator was first identified in maize, and is one of the most active mobile elements in plants. The Arabidopsis thaliana genome contains at least 200 Mutator-like elements (MULEs), which contain the Mutator-like transposase gene, and often additional genes. We have detected a novel type of MULEs in melon (CUMULE), which, besides the transposase, contains two ubiquitin-like specific protease-like sequences (ULP1). This element is not present in the observed location in some melon cultivars. Multiple copies of this element exist in the Cucumis melo genome, and it has been detected in other Cucurbitaceae species. Analysis of the A. thaliana genome revealed more than 90 CUMULE-like elements, containing one or two Ulp1-like sequences, although no evidence of mobility exists for these elements. We detected various putative transposable elements containing ULP1-like sequences in rice. The discovery of these MULEs in melon and Arabidopsis, and the existence of similar elements in rice and maize, suggest that a proteolytic function may be important for this subset of the MULE transposable elements. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. Nucleotide sequence data reported are available in the GenBank database under the accession number AY524004.