Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps

Finding genes that are under positive selection is a difficult task, especially in non-model organisms. Here, we have analyzed expressed sequence tag (EST) data from 4 species (Pinus pinaster, Pinus taeda, Picea glauca, and Pseudotsuga menziesii) to investigate selection patterns during their evolution and to identify genes likely to be under positive selection. To confirm selection, population samples of these genes have been sequenced in Pinus sylvestris, a species that was not included in the EST data set. The estimates of branch-specific Ka/Ks (nonsynonymous/synonymous substitution rates) across all genes in the EST data set were similar or smaller than estimates from other higher plant species. There was no evidence for the traditional indication of positive selection, Ka/Ks above 1. However, several lines of evidence based on polymorphism patterns suggest that genes with high Ka/Ks (0.20-0.52) in the EST data set are in fact more affected by positive selection in P. sylvestris than genes with low Ka/Ks (0.01-0.04). The high Ka/Ks genes have a lower level of polymorphism and more negative Tajima's D than the low Ka/Ks genes. Further, in the high Ka/Ks group, the Hudson-Kreitman-Aguade test is significant. This suggests that the EST data set is a good starting point for finding genes under positive selection in conifers and that even moderate Ka/Ks values could be indicative of selection. A group of 5 genes with high Ka/Ks collectively show evidence for positive selection within P. sylvestris.     

Genetic comparison between Pinus sylvestris and P. mugo using isozymes and chloroplast DNA

Pinus sylvestris and P. mugo populations from Poland and Czechoslovakia were compared using genetic variability at isozyme markers, chloroplast DNA variation, and mating system measurements. Two isozyme loci were found to differ between the species. P. mugo was as variable at isozyme loci as P. sylvestris. Diagnostic cpDNA fragments were found using the restriction enzyme Bcl-I. Populations that were morphologically classified as hybrids were found to be pure species, based both on isozyme and cpDNA results.     

Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China

Although homoploid hybrid speciation in plants is probably more common than previously realized, there are few well-documented cases of homoploid hybrid origin in conifers. We examined genetic divergence between two currently widespread pines in Northeast China, Pinus sylvestris var. mongolica and Pinus densiflora, and also whether two narrowly distributed pines in the same region, Pinus funebris and Pinus takahasii, might have originated from the two widespread species by homoploid hybrid speciation. Our results, based on population genetic analysis of chloroplast (cp), mitochondrial (mt) DNA, and nuclear gene sequence variation, showed that the two widespread species were divergent for both cp- and mtDNA variation, and also for haplotype variation at two of eight nuclear gene loci surveyed. Our analysis further indicated that P. sylvestris var. mongolica and P. densiflora remained allopatric during the most severe Quaternary glacial period that occurred in Northeast China, but subsequently exhibited rapid range expansions. P. funebris and P. takahasii, were found to contain a mixture of chlorotypes and nuclear haplotypes that distinguish P. sylvestris var. mongolica and P. densiflora, in support of the hypothesis that they possibly originated via homoploid hybrid speciation following secondary contact and hybridization between P. sylvestris var. mongolica and P. densiflora.     

Abundant mitochondrial genome diversity,population differentiation and convergent evolution in pines.

We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and theta) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.     

松科植物基因组总DNA提取方法的比较

目的:研究对比了用不同方法提取红松、樟子松和红皮云杉等3种松科植物叶片基因组DNA的效果,以寻找适合提取松科植物叶片基因组DNA的方法。方法:分别比较了用传统的CTAB法、SDS法以及3种改良的CTAB法提取的上述3种松科植物叶片基因组DNA的电泳、纯度和酶切效果。结果:采用不同方法提取的3种松科植物叶片基因组DNA的质量差异较大。结论:常规CTAB法和SDS法无法提取出高质量松科植物基因组DNA,而改良后的CTAB法的提取效果较好。     

Chloroplast DNA Diversity among Trees, Populations and Species in the California Closed-Cone Pines (Pinus Radiata, Pinus Muricata and Pinus Attenuata)

The amount, distribution and mutational nature of chloroplast DNA polymorphisms were studied via analysis of restriction fragment length polymorphisms in three closely related species of conifers, the California closed-cone pines-knobcone pine: Pinus attenuata Lemm.; bishop pine: Pinus muricata D. Don; and Monterey pine: Pinus radiata D. Don. Genomic DNA from 384 trees representing 19 populations were digested with 9-20 restriction enzymes and probed with cloned cpDNA fragments from Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] that comprise 82% of the chloroplast genome. Up to 313 restriction sites were surveyed, and 25 of these were observed to be polymorphic among or within species. Differences among species accounted for the majority of genetic (haplotypic) diversity observed [G(st) = 84(+/-13)%]; nucleotide diversity among species was estimated to be 0.3(+/-0.1)%. Knobcone pine and Monterey pine displayed almost no genetic variation within or among populations. Bishop pine also showed little variability within populations, but did display strong population differences [G(st) = 87(+/-8)%] that were a result of three distinct geographic groups. Mean nucleotide diversity within populations was 0.003(+/-0.002)%; intrapopulation polymorphisms were found in only five populations. This pattern of genetic variation contrasts strongly with findings from study of nuclear genes (allozymes) in the group, where most genetic diversity resides within populations rather than among populations or species. Regions of the genome subject to frequent length mutations were identified; estimates of subdivision based on length variant frequencies in one region differed strikingly from those based on site mutations or allozymes. Two trees were identified with a major chloroplast DNA inversion that closely resembled one documented between Pinus and Pseudotsuga.     

Modern pollen and stomate deposition in lake surface sediments from across the treeline on the Kola Peninsula, Russia

We sampled and analyzed surface sediments from 31 lakes along a latitudinal transect crossing the coniferous treeline on the Kola Peninsula, Russia. The major vegetation zones along the transect were tundra, birch-forest tundra, pine-forest tundra, and forest. The results indicate that the major vegetation types in our study area have distinct pollen spectra. Sum-of-squares cluster analysis and principal components analysis (PCA) groupings of pollen sites correspond to the major vegetation zones. PCA ordination of taxa indicates that the first axis separates taxa typical of the forest zone (Pinus, Picea) from taxa typical of tundra and forest-tundra zones (Polypodiaceae, Ericaceae, and Betula). The current position of the coniferous treeline, defined in our region by Pinus sylvestris, occurs roughly where Pinus pollen values reach 35% or greater. Arboreal pollen (AP)/non-arboreal pollen (NAP) ratios were calculated for each site and plotted against geographic distance along the transect. AP/NAP ratios of 7 or greater are found within pine-forest tundra and forest vegetation zones. Pinus stomates (dispersed stomatal guard cells) are absent from sites north of the coniferous treeline and all but two samples from the forested sites contain stomates. Stomate concentrations among the samples are highly variable and range from 10 to 458 per ml and positively correlate with the changing Pinus pollen values.     

More introgression with less gene flow: chloroplast vs. mitochondrial DNA in the Picea asperata complex in China, and comparison with other Conifers

Recent work has suggested that rates of introgression should be inversely related to levels of gene flow because introgressed populations cannot be 'rescued' by intraspecific gene flow if it is too low. Mitochondrial and chloroplast DNA (mtDNA and cpDNA) experience very different levels of gene flow in conifers due to their contrasted maternal and paternal modes of transmission, hence the prediction that mtDNA should introgress more readily than cpDNA in this group. Here, we use sequence data from both mtDNA and cpDNA to test this hypothesis in a group of closely related spruces species, the Picea asperata complex from China. Nine mitochondrial and nine chloroplast haplotypes were recovered from 459 individuals in 46 natural populations belonging to five species of the Picea asperata complex. Low variation was found in the two mtDNA introns along with a high level of differentiation among populations ( G _ST = 0.90). In contrast, we detected higher variation and lower differentiation among populations at cpDNA markers ( G _ST = 0.56), a trend shared by most conifer species studied so far. We found that cpDNA variation, although far from being fully diagnostic, is more species-specific than mtDNA variation: four groups of populations were identified using cpDNA markers, all of them related to species or groups of species, whereas for mtDNA, geographical variation prevails over species differentiation. The literature suggests that mtDNA haplotypes are often shared among related conifer species, whereas cpDNA haplotypes are more species-specific. Hence, increased intraspecific gene flow appears to decrease differentiation within species but not among species.     

4种针叶幼树的光合生理特性与大气湿度关系的研究

应用２２５ＭＫ３ＩＲＧＡ在室内控制的环境条件下测定研究了侧柏,樟子松,油松和杆等４种针叶幼树的净光合速率,暗呼吸强度,光补偿点与大气湿度的关系,研究结果证明,各种幼树的净光合速率均随大气湿度的降低而减弱,二者之间的关系可用ｙ＝ａ＋ｂｌｎｘ方程表达。其变化速率（ｂ）在树种间有明显差异,它可以反映出不同树种对大气干旱忍耐力即抗旱性的差异“ｂ＂值小的树种表明其抗旱性强。依此排列出的上述４种幼树的抗旱性强     

Taxonomic and population differentiation of mitochondrial diversity inPinus banksiana andPinus conforta

We have studied two mitochondrial DNA polymorphisms in 741 individuals from 16 allopatric populations ofPinus banksiana Lamb. andPinus contorta Dougl. Restriction fragments of both polymorphisms distinguished the two species qualitatively, except in aP. Banksiana population whose ancestors were involved in hybridization withP. contorta.COXI-associated restriction fragments were monomorphic within species, whileCOXII-associated restriction fragments were highly variable inP. contorta (H_es=0.68). Population differentiation was substantial inP. contorta (F_st=0.31 among subspecies; mean F_st=0.66 within subspecies) and consistent with predictions for maternally inherited markers. Plant mitochondrial markers appear to be useful for the investigation of seed migration routes, hybridization and introgression, breeding zone designation, and the development of germ plasm conservation sampling strategies.     

Intraspecific variation in Heterobasidion annosum for mortality rate on Pinus sylvestris and Picea abies seedlings grown in pure culture

One-month-old Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) seedlings were inoculated in vitro with Heterobasidion annosum strains, four each of the P-, S- and F-intersterility groups. Variation among strains and between the IS groups in virulence, expressed in mortality rate, was detected during twelve months after inoculation. Most of the strains were more virulent on spruce than on pine, and mortality of spruce seedlings was significantly higher. The P strains displayed similar virulence on both hosts, while S strains caused higher mortality of spruce seedlings and significantly lower mortality of pine seedlings. Strains of the F group were less virulent, but killed significantly (P < 0.05) more spruce than pine seedlings. In the interspecific analyses with two hosts, the isolates and IS groups accounted for most of the explained variation in the host mortality.     

Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species of Pinus, representing all recognized subsections of the genus, and 2 species of Picea and Cathaya as outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement including Pinus nelsonii and P. aristata. Within subgenus Pinus, there is moderate support for the monophyly of a narrowly circumscribed subsect. Pinus (=subsect. Sylvestres) and strong support for a clade of North and Central American hard pines. The Himalayan P. roxburghii may be sister species to these "New World hard pines," which have two well-supported subgroups, subsect. Ponderosae and a clade of the remaining five subsections. The position of subsect. Contortae conflicts with its placement in a chloroplast DNA restriction site study. Within subgenus Strobus there is consistent support for the monophyly of a broadly circumscribed subsect. Strobi (including P. krempfii and a polyphyletic subsect. Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects. Gerardianae, Cembroides, and Balfourianae are poorly resolved. Support for the monophyly of subgenus Pinus and subgenus Strobus is not consistently obtained.     

Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. Taeda, P. Sylvestris or Picea abies

Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r(2) = 0.78 - 0.86), and somewhat lower for embryogenic cultures (r(2) = 0.68 - 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r(2) = 0.52 - 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces.     

Rapid expansion of microsatellite sequences in pines

Microsatellite persistence time and evolutionary change was studied among five species of pines, which included a pair of closely related species (Pinus sylvestris and Pinus resinosa) in the subgenus Pinus, their relative Pinus radiata, and another closely related species pair (Pinus strobus and Pinus lambertiana) in the subgenus Strobus. The effective population sizes of these species are known to have ranged from the very small bottlenecks of P. resinosa to vast populations of P. sylvestris. This background allowed us to place the microsatellite evolution in a well-defined phylogenetic setting. Of 30 loci originating from P. strobus and P. radiata, we were able to consistently amplify 4 in most of the these pine species. These priming sites had been conserved for over 100 Myr. The four microsatellites were sequenced in the five species. Flanking sequences were compared to establish that the loci were orthologous. All microsatellites had persisted in these species, despite very different population sizes. We found a recent microsatellite duplication: a closely related pair of loci in P. strobus, where the other four species had just one locus. On two independent occasions, the repeat area of this same microsatellite (locus RPS 105a/b) had grown from a very low repeat number to 15 or 17 in the last 10-25 Myr. Other parts of the same compound microsatellite had remained virtually unchanged. Locus PR 4.6 is known to be polymorphic in both P. radiata and P. sylvestris, but the polymorphism in the two species is due to different motifs. The very large pine genomes are highly repetitive, and microsatellite loci also occur as gene families.     

Growth and nutrient uptake of coniferous seedlings: Comparison among 10 species at various seedbed densities

Summary The evaluation of biomass production and uptake of N, P, K, Ca, and Mg for various plant components (roots, stems, and foliage) and totals by 10 species of 2-0 coniferous seedlings grown at a controlled range of densities in a highly productive forest nursery documents considerable differences among species and seedling parameters. The species are ranked by biomass and nutrient-element relationships on a unit area of seedbed basis, quantifying the magnitude of the differences among the species at the various density levels. The 10 species include Abies balsamea, Larix leptolepis, Picea abies, Picea glauca, Picea mariana, Picea pungens, Pinus resinosa, Pinus strobus, Pinus sylvestris, and Pseudotsuga menziesii.Contribution of the Forest Resources Council, School of Environmental and Resource Management, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210.Contribution of the Forest Resources Council, School of Environmental and Resource Management, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210.     

Detection and physical mapping of the 18S-5.8S-26S rDNA and the pKFJ660 probe with microsatellite sequences derived from the rice blast fungus (Magnaporthe grisea) in conifer species

Sequences homologous to the pKFJ660 probe, a fragment of DNA derived from the rice blast fungus (Magnaporthe grisea) carrying TC/AG repeat microsatellite sequences and 30 bp direct repeats were identified in the genome of Picea (spruce) and Pinus (pine) species by fluorescence in situ hybridization (FISH) and slot blot analyses. Slot blot analysis using the pKFJ660 probe revealed hybridization signals with genomic DNAs from various pine and spruce species. Further analyses indicated that the copy number of the (AG)30 motif was higher than 5 x 10(4) per plant genome for all plant samples tested, but the copy number of the sequences homologous to the whole pKFJ660 probe varies considerably among the 25 plant species tested. In situ hybridization of metaphase chromosomes from Pinus resinosa, P. banksiana and P. strobus showed the presence of sequences homologous to this probe on several chromosomes in a dispersed pattern. Major signals were observed on a few chromosomes indicating that some of these sequences are clustered in specific genomic locations. The locations of these repeats were compared to those of 18S-5.8S-26S rDNA in pine species. Chromosomal distribution of 18S-5.8S-26S rDNA varied among the three pine species (P. resinosa, P. banksiana and P. strobus) studied. Ribosomal DNA (rDNA) sites were identified on 14 to 20 chromosomes in these pine species.     

Host selection in Tomicus piniperda L.: composition of monoterpene hydrocarbons in relation to attack frequency in the shoot feeding phase

The aim of this study was to investigate the host selection capacity of the pine shoot beetle, Tomicus piniperda, in the shoot-feeding phase and analyze the chiral and non-chiral host volatiles by means of GC-MS and 2D-GC in five Pinus species originating from France (Pinus sylvestris, P. halepensis, P. nigra laricio, P. pinaster maritima, P. pinaster mesogeensis). Dominating monoterpenes were (-)-alpha-pinene, (+)-alpha-pinene, (-)-beta-pinene and (+)-3-carene. The amounts of the enantiomers varied considerably within and among the species. In a principal component analysis-plot, based on the absolute amounts of 18 monoterpene hydrocarbons, separation of the pine species into two groups was obtained. P. halepensis and P. sylvestris were grouped according to the amount of (+)-alpha-pinene and (+)-3-carene, while P. nigra laricio, P. pinaster maritima and P. pinaster mesogeensis were grouped according to (-)-alpha-pinene and (-)-beta-pinene. P. nigra laricio was the species most attacked and P, halepensis the one least attacked by T. piniperda.     

Freezing Tolerance,Pigments and SOD of Five Conifers in Shenyang

Cultivated Picea koraiensis Nakai, Pinus sylvestris var. mongolica Litvin, P. koraiensis Sieb et Zuce, P. tabulaeformis Carr. and P. bungeana Zucc. were studied. Changes in chlorophylls carotenoids contents, SOD activities and iso-zymograms were monitored for the needles of the 5 evergreen conifers and related to their freezing tolerance during winter of 1.987–1988 in Shenyang. It shows that the chlorophylls were degradated to various extent in the winter while the carotenoids were still synthesized during the soil-frozen period. SOD activities increased from July to November for all 5 conifers and the more tolerate the species, the higher the SOD activities during winter. The results suggest that SOD possibly has important contribution to freezing tolerance besides protecting the needles from winter photooxidation. SOD iso-zymograms and their variation showed differance among species as well, but it is hard to draw a generalized conclussion.     

Response of juveniles of seven forest tree species and their populations to different combinations of simulated climate change-related stressors: spring-frost,heat, drought,increased UV radiation and ozone concentration under elevated CO2 level

Journal of Plant Research - The study aimed to assess response of juvenile progeny of seven forest tree species, Pinus sylvestris, Picea abies, Betula pendula, Alnus glutinosa, Populus tremula,...