The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.

Differentiation between wheat chromosomes 4B and 4D

A linkage map based on homoeologous recombination, induced by the absence of the Ph1 locus, between chromosome 4D of Triticum aestivum L. (genomes AABBDD) and chromosome 4B of T. turgidum L. (genomes AABB) was compared with a linkage map of chromosome 4Am of T. monococcum L. and a consensus map of chromosomes 4B and 4D of T. aestivum based on homologous recombination. The 4D/4B homoeologous map was only one-third the length of the homologous maps and all intervals were reduced relative to the 4B-4D consensus map. After the homoeologous map was corrected for this overall reduction in recombination, the distribution of recombination in the short arm was similar in both types of maps. In the long arm, homoeologous recombination declined disproportionally in the distal to proximal direction. This gradient was shown to be largely caused by severe segregation distortion reflecting selection against 4D genetic material. The segregation distortion had a maximum that coincided with the centromere and likely had a polygenic cause. Chromosomes 4D and 4B were colinear and recombination between them occurred in almost all intervals where homologous recombination occurred. These findings suggest that these chromosomes are not differentiated structurally and that the differentiation is not segmental. In the presence of Ph1, metaphase I chromosome pairing between chromosomes composed of homologous and differentiated regions correlated with the lengths of the homologous regions. No compensatory allocation of crossovers into the homologous regions was detected. In this respect, the present results are in dramatic contrast with the crossover allocation into the pseudoautosomal region in the mammalian male meiosis.

Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes

Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated sequence content in a genome, we suggest that the amount and activity of repeated sequences are important factors determining the number of genes in a genome.

Microstructural and compositional characteristics of GaN films grown on a ZnO-buffered Si (111) wafer

Polycrystalline GaN thin films have been deposited epitaxially on a ZnO-buffered (111)-oriented Si substrate by molecular beam epitaxy. The microstructural and compositional characteristics of the films were studied by analytical transmission electron microscopy (TEM). A SiO(2) amorphous layer about 3.5 nm in thickness between the Si/ZnO interface has been identified by means of spatially resolved electron energy loss spectroscopy. Cross-sectional and plan-view TEM investigations reveal (GaN/ZnO/SiO(2)/Si) layers exhibiting definite a crystallographic relationship: [111](Si)//[111](ZnO)//[0001](GaN) along the epitaxy direction. GaN films are polycrystalline with nanoscale grains ( approximately 100 nm in size) grown along [0001] direction with about 20 degrees between the (1l00) planes of adjacent grains. A three-dimensional growth mode for the buffer layer and the film is proposed to explain the formation of the as-grown polycrystalline GaN films and the functionality of the buffer layer.

Recombination of chromosomes 3A(m) and 5A(m) of Triticum monococcum with homeologous chromosomes 3A and 5A of wheat: the distribution of recombination across chromosomes

Recombination of chromosomes 3A(m) and 5A(m) of Triticum monococcum with closely homeologous chromosomes 3A and 5A of T. aestivum was compared with recombination across corresponding homologous chromosome pairs. Differentiation between the homeologues impacted recombination in the proximal regions of the long arms the most and in the distal regions of the long arms the least. It is concluded that this variation principally reflects allocation of multiple crossovers across an arm and positive crossover interference across chromosome arms. Recombination rates between homeologous chromosomes 5A(m) and 5A differed in the opposite sexes.

Position effects of ribosomal RNA multigene loci on meiotic recombination in wheat

Homeologous wheat chromosome arms that differ by the presence or absence of a Nor locus or greatly differ in the numbers of copies of rRNA genes per Nor locus show conspicuous differences in the distribution of recombination. To assess directly the position effects of Nor loci on recombination across chromosome arms, a Triticum monococcum Nor9 haplotype was substituted for Triticum aestivum Nor9 haplotypes on two T. aestivum 1A chromosomes in the isogenic background of cv Chinese Spring. The numbers of rRNA genes in the 1A Nor9 haplotypes are greatly reduced relative to the T. monococcum haplotype. The substitution resulted in reduced recombination rate in the vicinity of the Nor9 locus. An intra-arm compensatory increase was observed in the proximal region of the arm so that the genetic length of the chromosome arm was unchanged. These findings suggest that Nor loci suppress recombination in their vicinity and change recombination patterns in Nor-bearing chromosome arms.

Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing aegilops species

RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.

Recognition of homeology by the wheat Ph1 locus

Chromosome 1A(m) of Triticum monococcum is closely homeologous to T. aestivum chromosome 1A but recombines with it little in the presence of the wheat suppressor of homeologous chromosome pairing, Ph1. In the absence of Ph1, the two chromosomes recombine as if they were completely homologous. Chromosomes having either terminal or interstitial segments of chromosome 1A(m) in 1A were constructed and their recombination with 1A was investigated in the presence of Ph1. No recombination was detected in the homeologous (1A(m)/1A) segments, irrespective of whether terminally or interstitially positioned in a chromosome, whereas the levels of recombination in the juxtaposed homologous (1A/1A) segments was normal or close to normal relative to completely homologous 1A chromosomes. These observations show that Phl does not regulate chromosome pairing by premeiotic chromosome alignment and a mitotic spindle-centromere interaction, as has been suggested, but processes homology along the entire length of chromosomes.

Engineering of interstitial foreign chromosome segments containing the K(+)/Na (+) selectivity gene Kna1 by sequential homoeologous recombination in durum wheat

Targeted homoeologous recombination mediated by the absence of the Ph1 locus is currently the most efficient technique by which foreign genes can be introgressed into polyploid wheat species. Because intra-arm homoeologous double cross-overs are rare, introgressed foreign genes are usually on terminal foreign chromosome segments. Since the minimum length of such a segment is determined by the position of a gene in the chromosome, large chromosome segments with undesirable genetic effects are often introgressed. Introgression of foreign genes on short interstitial segments based on two cycles of homoeologous recombination is described here. The utility of the technique is demonstrated by the introgression of the Kna1 locus, which controls K(+)/Na(+) selectivity in T. aesivum L., on short interstitial segments of chromosome 4D into chromosome 4B of Triticum turgidum L. The level of recombination in a homoeologous segment is not significantly affected by a juxtaposed proximal homologous segment in the absence of the Ph1 locus.

Genetic map of diploid wheat, Triticum monococcum L., and its comparison with maps of Hordeum vulgare L

A genetic map of diploid wheat, Triticum monococcum L., involving 335 markers, including RFLP DNA markers, isozymes, seed storage proteins, rRNA, and morphological loci, is reported. T. monococcum and barley linkage groups are remarkably conserved. They differ by a reciprocal translocation involving the long arms of chromosomes 4 and 5, and paracentric inversions in the long arm of chromosomes 1 and 4; the latter is in a segment of chromosome arm 4L translocated to 5L in T. monococcum. The order of the markers in the inverted segments in the T. monococcum genome is the same as in the B and D genomes of T. aestivum L. The T. monococcum map differs from the barley maps in the distribution of recombination within chromosomes. The major 5S rRNA loci were mapped on the short arms of T. monococcum chromosomes 1 and 5 and the long arms of barley chromosomes 2 and 3. Since these chromosome arms are colinear, the major 5S rRNA loci must be subjected to positional changes in the evolving Triticeae genome that do not perturb chromosome colinearity. The positional changes of the major 5S rRNA loci in Triticeae genomes are analogous to those of the 18S-5.8S-26S rRNA loci.

Mapping of the K(+)/Na (+) discrimination locus Kna1 in wheat

In saline environments, bread wheat, Triticum aestivum L. (genomes AABBDD), accumulates less Na(+) and more K(+) in expanding and young leaves than durum wheat, T. turgidum L. (genomes AABB). Higher K(+)/Na(+) ratios in leaves of bread wheat correlate with its higher salt tolerance. Chromosome 4D from bread wheat was shown in previous work to play an important role in the control of this trait and was recombined with chromosome 4B in the absence of the Ph1 locus. A population of plants disomic for 4D/4B recombined chromosomes in the genetic background of T. turgidum was developed to investigate the genetic control of K(+)/Na(+) discrimination by chromosome 4D. Evidence was obtained that the trait is controlled by a single locus, designated Kna1, in the long arm of chromosome 4D. In the present work, K(+)/Na(+) discrimination was determined for additional families with 4D/4B chromosomes. The concentrations of Na(+) and K(+)/Na(+) ratios in the youngest leaf blades clustered in two nonoverlapping classes, and all recombinant families could be unequivocally assigned to Kna1 and kna1 classes. The Kna1 locus scored this way was mapped on a short region in the 4DL arm and was completely linked to Xwg199, Xabc305, Xbcd.402, Xpsr567, and Xpsr375; it was also mapped as a quantitative trait. The results of the QTL analysis, based on the K(+)/Na(+) ratios in the young leaves of greenhousegrown plants and flag leaves of field-grown plants, agreed with the position of Knal determined as a qualitative trait. Several aspects of gene introgression by manipulation of the Ph1 locus are discussed.

Linkage relationships among stress-induced genes in wheat

Linkage relationships among genes responding to water-deficit, salt stress, and heat shock were investigated in diploid wheat, Triticum monococcum L. The position of these gene loci relative to closely linked markers and the centromeres is reported. It is proposed to continue to use the present T. monococcum mapping population and the genetic maps based thereon as a framework for future determination of relationships among other genes related to environmental stress in the tribe Triticeae.

Testing of methyleneiminodiacetic-catechol and other aromatic chelating agents for decorporation of 238Pu and 241Am in rats

The removal of 238Pu and 241Am by five chelating agents prepared in China was compared in pilot experiments with removal by Ca-DTPA and LICAM(C). The most promising substance is quinamic acid (a methyliminodiacetic polyquinoline derivative, code name 811 or 703-73), especially in combination with Ca-DTPA. However, the best over-all reduction of both 238Pu and 241Am in all the organs studied was achieved by Ca-DTPA-administered at a ten-fold human equivalent dosage.