The 5S RNA genes inPinus radiata and the spacer region as a probe for relationships betweenPinus species

The 5S RNA genes inPinus radiata occur in two size classes of about 850 and 525 bp in length. Representatives from both the long and short size classes were cloned and sequenced. The primary difference in the two size classes was shown to be a 330 bp insertion in the spacer region of the long units. Within an individual breeding clone ofP. radiata there was some sequence heterogeneity between representatives of the short class. The 5S RNA genes in thirty pine species were characterised using either a clone of the short size class or a subclone of the 330 bp insertion characterizing the long size class. Eleven species of subg.Strobus were examined and all lacked the long type of unit of radiata pine. The New World species of subg.Pinus all had both short and long units whereas the Old World species had long units. The implications of these results for the evolution of the 5S DNA sequences and the phylogenetic relationships withinPinus are discussed.     

Identification of larch species (Larix decidua, Larix kaempferi and Larix X eurolepis) and estimation of hybrid fraction in seed lots by RAPD fingerprints

Species-specific RAPD markers were used to identify the different larch species (Larix decidua and Larix kaempferi) and their interspecific hybrid (Larix X eurolepis). Although morphological differences between pure species and the hybrids exist, differentiation is not always possible, especially at an early stage (seed or plantlet). Eleven RAPD markers differentiated the two larch species, and 4 species-specific markers were sufficient to estimate the F₁ hybrid fraction in a seed lot. The species-specific markers were tested on individual trees of European and Japanese larches of diverse geographic origins and on several seed lots of different origins (F₁, F₂ hybrids and pure species). The 4 specific markers found for the European larch and the Japanese larch were monomorphic and present in all provenances and in all F₁ hybrid trees tested. Polymorphic SCAR fragments were obtained for 3 of the 11 fragments originally selected for the RAPD screening phase. For 2 of them, the sequence had some homology with the mitochondrial genome of other organisms and is thus mitochondrial. The two mitochondrial fragments and the OPF-13₁₀₀₀ fragment exhibited one polymorphic band, thereby maintaining its species-specific identity: OPF-13₁₀₀₀ is specific to the European larch. The 4 RAPD primers selected in this study offer a reliable, quick and cheap tool for the identification of different larch species (Larix decidua and Larix kaempferi) and their interspecific hybrid (Larix X eurolepis). Received: 28 February 1999 / Accepted: 29 April 1999     

Heterosis in hybrid larch (Larix decidua x leptolepis)

Summary Individual 33-year-old forest trees of the deciduous conifer speciesLarix decidua, Larix leptolepis andLarix decidua x leptolepis were investigated with respect to the phenomenon of stem heterosis in hybrid larch; the first part of this study compares the gas exchange responses of leaves. CO₂ assimilation per leaf area was similar in the three larch species, but on a dry weight basis the nitrogen content of the needles and maximum CO₂ assimilation rate (A_max) were slightly higher in the hybrid. This increase was accompanied by a higher protein content than in the Japanese and a lower specific leaf weight than in the European larch. All three species were similar in terms of the photosynthetic nitrogen use and stomatal conductance atA _max. The similar slopes of the area-related steady-state responses of gas exchange against irradiance, evaporative demand and internal CO₂ concentration led to similar rates of CO₂ uptake under ambient conditions. The natural combinations and variability of the environmental factors also reduced the small dry weight-related difference inA _max between hybrid larch and the parent species, such that all trees achieved similar daily carbon gains. Thus, the ecological significance of small interspecific differences in the metabolism of leaves has very little effect under the natural habitat conditions of a temperate climate. The second part of the study will investigate the effect of growth characteristics on the heterosis of hybrid larch.     

The role of larch budmoth (Zeiraphera diniana Gn.) on forest succession in a larch (Larix decidua Mill.) and Swiss stone pine (Pinus cembra L.) stand in the Susa Valley (Piedmont, Italy)

In the Alps, larch (Larix decidua Mill.) is severely affected by larch budmoth (Zeiraphera diniana Guénée) (LBM) attacks. The impact of these outbreaks on the Swiss stone pine (Pinus cembra L.) and on the dynamic processes acting in subalpine forest stands are still not well known. Dendroecological methods were used in this study to reconstruct past LBM outbreaks in Susa Valley, Piedmont, Italy. The analysis was carried out on 62 cores from larch and 101 cores from stone pine. The length and severity of each outbreak was quantified for both species and for each tree by means of the programme OUTBREAK. The frequency of the outbreaks was determined using singular spectral analysis and superposed epoch analysis was used to test the significance of the associations between outbreaks and tree-ring growth. In order to verify if trees belonging to different age classes are differently affected by LBM, the reconstructed outbreaks are then classified taking into account the cambial age of the tree at the moment of the outbreak. From 1760 to 1999, 19 outbreaks were recorded in the larch chronologies, while only three outbreaks in the stone pine chronologies. The larch growth is strongly influenced by LBM and the identified outbreaks are equally distributed in all the three age classes. On the stone pine the sporadic occurrence of the identified events made difficult any interpretation of the eventual effect of LBM. Our results lead us to argue that LBM has not played an important role both in determining the stone pine growth rate and in influencing the present observed succession from the stage dominated by larch, to a stage dominated by stone pine or by a mixed stone pine-larch forest.     

Two classes of 5S rDNA unit arrays of the silver fir, Abies alba Mill.: structure, localization and evolution

The structure and organization of the 5S ribosomal DNA units of the silver fir, Abies alba Mill., as well as their position in the chromosome complement were investigated. PCR amplification of the gene and nontranscribed spacer region, sequence analysis and Southern hybridization, using a homologous probe, detected DNA sequences of approximately 550 bp and 700 bp. Sequence analysis of the spacers revealed that the difference in length between the sequences occurred in the middle spacer region as a result of the amplification of a 75-bp sequence of the short unit class, which is organized in four 54- to 68-bp tandem repeats in the long spacer unit. The 5S rDNA transcribed region is 120 bp long and shows high sequence similarity with other gymnosperm species. The comparative analysis of 5 and 3 flanking sequences of 5S rRNA genes of silver fir and other gymnosperms indicates that A. alba spacer units have the same rate of evolution and are more closely related to Larix and Pseudotsuga than to Pinus and Picea. Southern hybridization and fluorescence in situ hybridization of metaphase chromosomes of A. alba suggest that the short and long spacer units are organized as separate tandem arrays at two chromosomal loci on chromosomes V and XI.     

Heterogeneity in the ribosomal RNA genes of the yeast Yarrowia lipolytica; cloning and analysis of two size classes of repeats

Southern blotting of DNA from the ascomycetous yeast Yarrowia lipolytica revealed two major size classes of DNA units coding for rRNAs, which differ in length by about 1000 bp. We have cloned an rDNA unit of each size class. R-looping experiments revealed that the rRNA genes of both units are uninterrupted; subsequent heteroduplex analysis showed that the size difference both units is located within the nontranscribed spacer. Sequence analysis revealed that a major part of these spacers consists of a complex pattern of repetitions in periodicities of up to about 150 bp and that the difference between both rDNA units are located mainly in this repetitive region. Apart from different lengths of the repetitive regions, both rDNA units also reveal extended microheterogeneity within their homologous parts. Furthermore, no gene for 5S rRNA was observed in the spacer region. Therefore, the organization of the spacer of Yarrowia rDNA is clearly different from that of Saccharomyces cerevisiae.     

针叶松遗传转化操作的研究进展(英文)

1986年从火炬松方面获得了首例针叶松愈伤组织以后,针叶松遗传转化研究取得了明显的进展。1991年从Larix decidua方面获得了第一个转基因再生植株。最近,通过农瘤杆菌介导的转化方式在Larix kaempferi ( L. Decidua杂交树种上获得了转基因针叶松,通过鸟枪法在Picea glauca、Picea mariana、Picea abies、Larix laricina、Pinus radiata上亦获得了转基因植株。已经有多种办法用于转化针叶松。本文就目前在针叶松上所用的遗传转化方法??诸如：T－DNA转化法、农瘤杆菌介导转法化、鸟枪法、电转化法等给以粗略的评论。     

Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta)

The organization, structure, and nucleotide variability of the ribosomal repeat unit was compared among families, genera, and species of cockroaches (Insecta:Blattodea). Sequence comparisons and molecular phylogenetic analyses were used to describe rDNA repeat unit variation at differing taxonomic levels. A reverse similar 1200 bp fragment of the 28S rDNA sequence was assessed for its potential utility in reconstructing higher-level phylogenetic relationships in cockroaches. Parsimony and maximum likelihood analyses of these data strongly support the expected pattern of relationships among cockroach groups. The examined 5' end of the 28S rDNA is shown to be an informative marker for larger studies of cockroach phylogeny. Comparative analysis of the nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among closely related species of Blattella and Periplaneta reveals that ITS sequences can vary widely in primary sequence, length, and folding pattern. Secondary structure estimates for the ITS region of Blattella species indicate that variation in this spacer region can also influence the folding pattern of the 5.8S subunit. These results support the idea that ITS sequences play an important role in the stability and function of the rRNA cluster.     

Development and characterization of microsatellite loci in western larch (Larix occidentalis Nutt.)

Western larch (Larix occidentalis Nutt.) is an important ecological and commercial species in the Pacific Northwest. We isolated nine microsatellite loci with variable polymorphism ranging from five to 19 alleles per locus. Observed and expected heterozygosities averaged 0.42 and 0.64 and ranged from 0.11 to 0.83 and from 0.48 to 0.80, respectively. These markers, along with those already existing, will be useful for the species' gene resource management activities.     

Patterns of sequence divergence in 5' intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories

We compared the pattern of nucleotide difference in 8034 genes and in their 5' intergenic spacers between conspecific pairs of genomes from 10 species of pathogenic bacteria. Certain genes or spacers showed much greater sequence divergence between the genotypes compared to others; such divergent regions plausibly originated by recombinational events by which a gene and/or spacers was donated from a divergent genome. Different patterns of divergence in genes and spacers identified different recombinational patterns. For example, in Chlamydophila pneumoniae, there were examples of both unusually divergent spacers and unusually divergent genes, but there were no cases in which a gene and its spacer were both unusually divergent. This pattern suggests that, in C. pneumoniae, recombination events have broken up the linkage between genes and 5' spacers. By contrast, in Streptococcus agalactiae, there were a number of cases in which both spacer and gene were unusually divergent, indicating that a number of large-scale recombination events that included both genes and 5' spacers have occurred; there was evidence of at least two large-scale recombination events in the genomic region including the pur genes in S. agalactiae.     

Colour of larch heartwood and relationships to extractives and brown-rot decay resistance

Larch heartwood is appreciated for its good mechanical properties, its colour and its texture, and it is often used outdoors because of its natural durability (decay resistance). In this study the colour of larch heartwood was studied in relation to extractives and decay resistance, with the aim to estimate durability of larch heartwood from its colour. On a total of 293 trees colour in the CIE L*a*b* space (L* lightness, a* red/green axis, b* yellow/blue axis), extractives content (acetone and hot-water extractives, amount of phenolics) and the brown-rot decay resistance were determined. For calculating the relative decay resistance ( x), mass loss after inoculation for 16 weeks with two fungi [ Coniophora puteana (Schum.ex.Fr.) Karst., Poria placenta (Fr.) Cke, European standard EN 113] of larch heartwood samples was compared to Scots pine ( Pinus sylvestris L) sapwood reference samples (EN 350-1). Different species [Japanese larch ( Larix kaempferi Lamb.), Hybrid larch (Larix deciduax L. kaempferi) and European larch ( L. decidua Mill.)], provenances and age classes (38-year, >150-year) were included. Japanese larch heartwood turned out to be significantly more reddish (higher a*-values) compared to the European larch provenances. Reddishness of the hybrids was intermediate. The red hue (+a*) was strongly correlated with the amount of phenols ( r =0.84) and decay resistance ( r =0.63) and therefore suitable for prediction of both parameters. The results suggest that colour measurements of larch heartwood could be of benefit in tree breeding programs and for an optimised utilization of larch timber.     

Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles (Coleoptera: Coccinellidae)

DNA sequences of the first ribosomal internal transcribed spacer (ITS1) were isolated from 10 ladybird beetle species (Coleoptera: Coccinellidae) representing four subfamilies (Coccinellinae, Chilocorinae, Scymninae, and Coccidulinae). The spacers ranged in length from 791 to 2,572 bp, thereby including one of the longest ITS1s and exhibiting one of the most extreme cases of ITS1 size variation in eukaryotes recorded to date. The causes of length variation were therefore analyzed. Almost no putatively homologous sequence similarities were identified for the taxa included. The only exception was for the subfamily Coccinellinae, which yielded sequence similarities in six regions of approximately 550 nucleotide positions, primarily at the 5' and 3' ends of ITS1. The majority of differences in ITS1 length between taxa could be attributed to the presence of repetitive elements with comparatively long repeat units. Repetition arose several times independently and was confined to the middle of the spacer which, in contrast to the 5' and 3' ends, had not been inferred in previous studies to be subject to functional constraints. These elements were characterized by high rates of evolutionary change, most likely as a result of high substitution rates in combination with inefficient homogenization across repeats. The repeated origin and subsequent divergence of "long" repetitive elements should thus be assumed to be an important factor in the evolution of coccinellid ITS1.     

Isolation, characterization, and inheritance of microsatellite loci in alpine larch and western larch.

Microsatellite loci or simple sequence repeat loci (SSRs) were isolated in alpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.). In total, 14 SSR loci were characterized; two [(TCT)4, A7] came from published Larix DNA sequence data, one (CA)17 was obtained from a partial non-enriched alpine larch total genomic DNA library, and the remaining 11 loci were obtained from larch genomic DNAs enriched for (CA)n repeats. The SSR regions in these clones could be divided into three categories: perfect repeat sequences without interruption, imperfect repeat sequences with interruption(s), and compound repeat sequences with adjacent tandem simple dinucleotides. Eight of the 14 loci analyzed were found to be polymorphic and useful markers after silver-staining polyacrylamide gel electrophoresis. In addition, several SSR primers developed for alpine larch were able to successfully amplify polymorphic loci in its related species, western larch, and among other closely related taxa within the Larix genus. The inheritance of microsatellite loci was verified by analysis of haploid megagametophyte and diploid embryo tissues of progeny obtained from controlled crosses between western larch and alpine larch. All microsatellite loci analyzed had alleles that segregated according to expected Mendelian frequencies. Two species-specific markers (UAKLly10a and UAKLla1) allow easy and rapid identification of specific genetic entry of alpine larch and western larch at any stage in the sporophyte phase of the life cycle. Therefore, these markers are efficient in identifying the parental species and to validate controlled crosses between these two closely related species. These results are important in tree improvement programs of alpine larch and western larch aimed at producing genetically improved hybrid stock for reforestation in Western Canada and U.S.A.     

Two highly informative dinucleotide SSR multiplexes for the conifer Larix decidua (European larch)

We have designed two highly polymorphic microsatellite multiplexes for Larix decidua Mill (European larch), a coniferous tree species with a fragmented distribution across Europe. The multiplexes combine microsatellites previously designed for the sister species L. kaempferi and newly identified microsatellites obtained by pyrosequencing of an enriched microsatellite library and subsequent marker candidate selection. As we wanted to target highly polymorphic markers, only microsatellite motifs with a high number of repeats (≥ 12) were selected. An important proportion of the marker candidates presented multiple bands, bad amplification or insufficient polymorphism. Such difficulties were expected owing to the large genome size of the studied species. Our strategy for marker validation followed most recent recommendations for microsatellite development, for example verifying marker quality in terms of polymorphism and accurate allele binning before multiplexing. The most promising loci were combined in two multiplexes, a 7-plex and a 6-plex. These were tested on a sample of 413 individuals from 18 populations distributed across the natural range. The 13 loci had from 9 to 36 alleles. Markers were successfully tested in another laboratory, confirming robustness of the marker protocols. We also tested transferability on six other larch species from Asia and North America. Overall, this study shows that, even in species with large genome size and relatively low overall polymorphism, microsatellites can be successfully developed using next-generation sequencing technologies, provided that some additional precautions are taken compared to species lacking these characteristics.     

Tandem repeat DNA localizing on the proximal DAPI bands of chromosomes in Larix, Pinaceae.

Repetitive DNA was cloned from HindIII-digested genomic DNA of Larix leptolepis. The repetitive DNA was about 170 bp long, had an AT content of 67%, and was organized tandemly in the genome. Using fluorescence in situ hybridization and subsequent DAPI banding, the repetitive DNA was localized in DAPI bands at the proximal region of one arm of chromosomes in L. leptolepis and Larix chinensis. Southern blot hybridization to genomic DNA of seven species and five varieties probed with cloned repetitive DNA showed that the repetitive DNA family was present in a tandem organization in genomes of all Larix taxa examined. In addition to the 170-bp sequence, a 220-bp sequence belonging to the same DNA family was also present in 10 taxa. The 220-bp repeat unit was a partial duplication of the 170-bp repeat unit. The 220-bp repeat unit was more abundant in L. chinensis and Larix potaninii var. macrocarpa than in other taxa. The repetitive DNA composed 2.0-3.4% of the genome in most taxa and 0.3 and 0.5% of the genome in L. chinensis and L. potaninii var. macrocarpa, respectively. The unique distribution of the 220-bp repeat unit in Larix indicates the close relationship of these two species. In the family Pinaceae, the LPD (Larix proximal DAPI band specific repeat sequence family) family sequence is widely distributed, but their amount is very small except in the genus Larix. The abundant LPD family in Larix will occur after its speciation.     

Distribution of extractive substances in wood of the Siberian larch (Larix sibirica Ledeb.)

A distribution of extractive substances by height on the trunk and radius of the wood of the Siberian larch (Larix sibirica Ledeb.) was investigated. The maximum flavonoid content in terms of dihydroquercetin (the main flavonoid of the larch wood) was shown to be in the butt part of the tree. In the radial direction, this parameter increased from the center to periphery of the heartwood and reached the maximum value at the sapwood boundary. The maximum content of arabinogalactan (AG) was observed in the bottom and in the top of the trunk. The distribution of the extractive substances was studied in roots of the Siberian larch for the first time.