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PubMed1999

IFG, a gypsy-like retrotransposon in Pinus (Pinaceae), has an extensive history in pines.

A 1 kb EcoRI restriction fragment cloned from a band visible in an agarose gel of Pinus lambertiana (sugar pine) genomic DNA is present in both subgenera of Pinus with at least 10(4) copies/genome. A full-length copy of this repeated element recovered from a P. radiata (Monterey pine) genomic DNA library was found to possess all of the sequence features associated with gypsy-like retrotransposons. This report describes the biology and history of the IFG (Institute of Forest Genetics) family of retrotransposons. The characterized IFG7 is 5937 bp long. Immediately interior to its 5' and 3' long terminal repeats are sequences consistent with primer binding sites for reverse transcription of the RNA genome. Presumptive gene products associated with retrotransposition appear to be coded in a single reading frame and are in the same order as the gypsy-like retrotransposons and retroviruses. The 1.0 kb EcoRI fragment of IFG elements codes for the 3' half of IFG's reverse transcriptase and the entire RNase H domain. Southern blot analysis suggests IFG was present in Pinaceae before its division into its modern genera. Sequence analysis of IFG 1.0 kb RI fragments and southern analysis also suggest that IFG continued to evolve in Pinus with restriction fragment length polymorphism (RFLP) subfamilies appearing early in the history of each subgenus often correlating with subdivisions of Pinus. Features shared with other plant retrotransposons are also discussed.

Amino Acid Sequence↗

PubMed2001

Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics.

Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37-61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a "generic" pine map and serving as a foundation for studies on genome organization and evolution.

Base Sequence↗

PubMed2003

Genome size and base composition of five Pinus species from the Balkan region.

The 2C DNA content and base composition of five Pinus (2 n=24) species and two Pinus subspecies from the Balkan region have been estimated by flow cytometry. P. heldreichii (five populations) and P. peuce (one population) were assessed for the first time, as also were subspecies of P. nigra (three populations-two of subspecies nigra and one of subspecies dalmatica) along with P. sylvestris, and P. mugo from the same region. The 2C DNA values of these Pinus ranged from 42.5 pg to 54.9 pg (41.7-53.8 x 10(9)bp), and the base composition was quite stable (about 39.5% GC). Significant differences were observed between two subspecies of P. nigra and even between two populations of subsp. nigra. The two other species (P. sylvestris and P. mugo) had 2C values of 42.5 pg and 42.8 pg, respectively, while that of P. peuce was 54.9 pg. These genome sizes are in accordance with published values except for P. sylvestris, which was 20% below estimates made by other authors.

Base Composition↗

PubMed2006

[Fire and Pinus mugo Turra communities in the western Alps (Susa Valley, Italy) during the Lateglacial-Holocene transition: an evidence of refugia area].

In western Italian Alps, small distinct populations of Pinus mugo Turra raise some questions concerning its ecological status and dynamics in the occidental Alps. This note present new palaeobotanical data based on cone imprints of Pinus mugo, identified in travertine systems located in the Val di Susa and dated back to the Late Dryas (11506+/-66 BP) and the Early Holocene (10145+/-225 et 9475+/-670 BP). Heliophilous species and charcoal fragments were also identified, testifying to the oldness of wildfires in this region. The data support the hypothesis that this zone was a refuge area of this pine during the last glaciation. Here we discuss about the postglacial dynamics of the Pinus mugo in the occidental Alps.

Altitude↗

PubMed2006

Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses.

Pines comprise one of the largest coniferous genera, are distributed throughout the Northern Hemisphere, and have an abundant fossil record. Distributions of fossils have been used to derive a three-step hypothesis of early pine evolution, which postulates a Mesozoic origin for the genus, east-west expansions across Laurasia, and retraction into Eocene refugia. Here, we present phylogenetic tests of this hypothesis using chloroplast sequence data from four loci for 83 pine species. We used the fossil-based hypothesis to derive null expectations concerning monophyly of taxonomic groups, dates of cladogenesis, and patterns of diversification. Phylogenetic analyses using several algorithms subsequently provided rigorous tests of these expectations. Our inferred phylogenies illustrated broad congruence with taxonomic groups, but highlighted consistent problems within subgenus Strobus. Estimated minimum dates of divergence derived from relaxed clock methods were largely consistent with the fossil record and yielded a date for the ingroup node of Pinus of 128+/-4 mya, depending upon the calibration used for subgenus Pinus. Ancestral area reconstructions showed Pinus to have most likely originated in Eurasia. Major clades differed in biogeographic patterns, but were consistent with the fossil-based hypothesis. We found weak support, however, for a change in diversification rate in the Eocene as interpretations of fossil distributions would have predicted.

Fossils↗

PubMed2003

Fumonisin production by Gibberella fujikuroi strains from Pinus species.

Fumonisins are important mycotoxins basically produced by strains from the Gibberella fujikuroi species complex (with anamorphs in Fusarium genus) which contaminate food and feed products representing a risk to human and animal health. In this work, we report for the first time the fumonisin production of Fusarium moniliforme Sheldon strains associated to edible pine nuts of Pinus pinea. P. pinea is an important and widely distributed Pinus species in the Mediterranean area where their pine nuts are consumed raw or slightly processed in diverse food products. In this work, characterization and further identification of those strains were performed by polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) of the intergenic spacer region of the rDNA (IGS) with the aid of the eight mating populations (A-H) described for G. fujikuroi species complex. The method was powerful to detect polymorphism, allowing discrimination between individuals and could be used to study the genetic relationships among them and within the G. fujikuroi species complex. Fusarium strains associated to Pinus radiata were also included in the present study. These strains did not produce fumonisins and showed no close relation with the strains isolated from P. pinea. The approach used in this work was rapid and proved to be efficient to assist identification and to characterize and analyse relatedness of new isolates within the G. fujikuroi species complex.

Chromatography, High Pressure Liquid↗

PubMed1998

Gene structure, expression in Escherichia coli and biochemical properties of the NAD+ -dependent glyceraldehyde-3-phosphate dehydrogenase from Pinus sylvestris chloroplasts.

Photosynthetic eukaryotes typically possess two distinct glyceraldehyde-3-phosphate dehydrogenases, an NAD+ -specific enzyme in the cytosol (GapC: EC 1.2.1.12) and an NADP+ -dependent enzyme in the chloroplast (GapAB: EC 1.2.1.13). The gymnosperm Pinus sylvestris is an exception in that it is known to express a gene encoding a transit peptide-bearing GapC-like subunit that is imported into chloroplasts (GapCp), but the enzymatic properties of this novel GAPDH have not been described from any source. We have expressed the mature GapCp unit from Pinus in Escherichia coli and have characterized the active enzyme. GapCp has a specific activity of 89 units per milligram and is strictly NAD+ -dependent, showing no detectable activity with NADP+. Values of the apparent Km for NAD+ and glyceraldehyde-3-phosphate were determined as 62 and 344 microM, respectively. The Pinus GapCpl gene possesses 12 introns, two in the region encoding the transit peptide and ten in the region encoding the mature subunit, all of which are found at positions strictly conserved across genes for higher plant GapC. A cDNA encoding a homologue of GapCp was isolated from the heterosporous fern Marsilea quadrifolia, indicating that NAD+ -dependent chloroplast GAPDH also occurs in other higher plants.

Amino Acid Sequence↗

PubMed2004

Root distribution of Pinus pinaster, P. radiata, Eucalyptus globulus and E. kochii and associated soil chemistry in agricultural land adjacent to tree lines.

We quantified the extent and distribution of roots of four commonly planted tree species (Eucalyptus globulus Labill., Pinus radiata D. Don, P. pinaster Aiton and E. kochii Maiden & Blakely subsp. plenissima C.A. Gardner) in agricultural land adjacent to tree lines, and examined the effect of soil type and root pruning on root morphology. Root distribution in soil adjacent to tree lines was mapped by a trench profile method at 13 sites on the south coast of Western Australia. Soil samples were collected to determine water content and fertility. The lateral extent of tree roots ranged from 10 m for E. kochii to 44 m for P. pinaster. This equated to between 1.5 and 2.5 times tree height (H) for E. globulus and Pinus spp. to 4H for E. kochii. Root density declined logarithmically with distance from the trees and was greatest for P. pinaster and least for E. globulus (P < 0.001). The rate of decrease in root density with distance from the trees was greatest for the Pinus spp. and least for E. kochii (P < 0.05). Root density was generally greatest in the top 0.5 m of the soil profile and decreased with increasing depth. This decrease was relatively gradual in the deep sands, but abrupt in clay subsoil. Root dry mass in the sandy top soil beyond 0.5H ranged between 1.0 and 55.5 Mg km(treeline) (-1) for 6-year-old E. kochii and 50-year-old P. pinaster, respectively. Soil water content generally increased with distance from the trees (P < 0.001). There was no evidence of reduced soil fertility in the top 1.4 m of the soil profile adjacent to the trees. Two to four years after trees had been root pruned, both the lateral extent and vertical distribution of roots were similar for pruned and unpruned trees. The density of roots < 2 mm in diameter was greater for root-pruned trees than for unpruned trees (P < 0.05). We conclude that the study species can compete with agricultural crops based on the lateral extent of their roots and the occurrence of greatest root density within 0.5 m of the soil surface.

Biomass↗

PubMed2006

Proteomic comparison of needles from blister rust-resistant and susceptible Pinus strobus seedlings reveals upregulation of putative disease resistance proteins.

In order to characterize a hypersensitive-like reaction in selected Pinus strobus seedlings to Cronartium ribicola, a proteomic comparison of needles from resistant and susceptible seedlings was undertaken using two-dimensional gel electrophoresis (2-DE). The results revealed 19 polypeptides specific to resistant seedlings and seven of these specific to infected resistant seedlings. There were 13 polypeptides up-regulated (> or = 3-fold increase) in resistant family P327 in comparison to needle tissue from susceptible and mock-inoculated seedlings. Electrospray ionization liquid chromatography and tandem mass spectrometry was used to sequence 11 proteins from the 2-DE gels. Sequences obtained from electrospray ionization liquid chromatography and tandem mass spectrometry were used for MS-BLAST and Pro-ID database searches allowing identification with a 95 to 99% confidence level. Six proteins were determined to be homologs of proteins with known roles in disease resistance, five were determined to be homologs of members of the leucine-rich repeat (LRR) superfamily, and one was a homolog of heat shock protein 90, a protein that serves as a cofactor for certain LRR proteins. This is the first report of members of the LRR family with functional homologs in Pinus strobus and of a molecular basis for white pine blister rust resistance in Pinus strobus.

Amino Acid Sequence↗

PubMed2003

[Relationship between climatic factors and radial growth of Pinus massoniana in Dinghushan Mountain].

Dendroclimatology method was used to study the relationship between ring index of Pinus massoniana and three climate factors in Dinghushan, South China. The ring indices were negatively correlated with the average temperature in June, August and September, and positively correlated with the average temperature of March, whereas no statistically significant correlation was found with monthly precipitation, showing that high summer temperature could limit the radial growth of the species. Meanwhile, tree ring indices showed a strong positive correlation with the relative humidity of April, June, August, September, October and November, and also with the average humidity of the whole year, indicating that atmospheric moisture could not fully satisfy the growth of Pinus massoniana despite of abundant rainfall. The possible impact of climate change on the growth of Pinus massoniana was discussed accordingly.

Climate↗

PubMed2004

[Major features of decline of Pinus sylvestris var. mongolica plantation on sandy land].

In view of the decline of man-made sand-fixation forest of Pinus sylvestris var. mongolica in Zhanggutai sand land of Liaoning Province, this paper studied the major characteristics of the decline. The appearance of the declining man-made sand-fixation forest of Pinus sylvestris var. mongolica was grey green, its needle leaf was very thin, the blooming and fruiting rate was low, the average quantity of cones per tree was only 10.4-16.5, with only 6.96 g to 7.39 g per thousand seeds, and there were many empty and astringent seeds. The seasonal dynamics of nutrients in 2-year-old pine needle leaf was similar, i.e., the N and P contents decreased, while K content increased, showing that the nutrient cycle was imbalance. The chlorophyll content in 2-year-old needle leaf of declined forest was high, while that in 1-year-old healthy forest was also high but with a wide increasing range. The infected harm of shoot blight was the clearest mark to the decline of man-made sand-fixation forest of Pinus sylvestris var. mongolica. After the forest declined, the height and the DBH of the pine trees decreased evidently, and the structure of DBH distribution moved "left". The quantity of weak pine trees increased by 15.9%-27.2%, the roots decreased by 22.9%-28.9%, and the absorbing roots (diameter < 0.5 cm) decreased most seriously.

Agriculture↗

PubMed2004

[Decline regularity and causes of Pinus sylvestris var. mongolica plantation on sandy land].

The study showed that the decline of Pinus sylvestris var. mongolica plantation out of its natural distribution area was a phenomenon of premature senility. The infected harm of shoot blight was the direct cause of Pinus sylvestris var. mongolica dying, but wasn't the basic reason. The decline of Pinus sylvestris var. mongolica was caused by the interaction of biological and other factors, which was "the third disease" beyond infectious and non-infectious diseases, namely, "decline disease of forest". Climate difference, improper management, unbalanced usage of soil water, and high content of N settled from air were the inducing factors, among which, climate difference and unbalanced usage of soil water were the main ones, while insect harm and shoot blight were the promoting factors.

Agriculture↗

PubMed2000

General characteristics of Pinus spp. seed fatty acid compositions, and importance of delta5-olefinic acids in the taxonomy and phylogeny of the genus.

The delta5-unsaturated polymethylene-interrupted fatty acid (delta5-UPIFA) contents and profiles of gymnosperm seeds are useful chemometric data for the taxonomy and phylogeny of that division, and these acids may also have some biomedical or nutritional applications. We recapitulate here all data available on pine (Pinus; the largest genus in the family Pinaceae) seed fatty acid (SFA) compositions, including 28 unpublished compositions. This overview encompasses 76 species, subspecies, and varieties, which is approximately one-half of all extant pines officially recognized at these taxon levels. Qualitatively, the SFA from all pine species analyzed so far are identical. The genus Pinus is coherently united--but this qualitative feature can be extended to the whole family Pinaceae--by the presence of delta5-UPIFA with C18 [taxoleic (5,9-18:2) and pinolenic (5,9,12-18:3) acids] and C20 chains [5,11-20:2, and sciadonic (5,11,14-20:3) acids]. Not a single pine species was found so far with any of these acids missing. Linoleic acid is almost always, except in a few cases, the prominent SFA, in the range 40-60% of total fatty acids. The second habitual SFA is oleic acid, from 12 to 30%. Exceptions, however, occur, particularly in the Cembroides subsection, where oleic acid reaches ca. 45%, a value higher than that of linoleic acid. Alpha-linolenic acid, on the other hand, is a minor constituent of pine SFA, almost always less than 1%, but that would reach 2.7% in one species (P. merkusii). The sum of saturated acids [16:0 (major) and 18:0 (minor) acids principally] is most often less than 10% of total SFA, and anteiso-17:0 acid is present in all species in amounts up to 0.3%. Regarding C18 delta5-UPIFA, taxoleic acid reaches a maximum of 4.5% of total SFA, whereas pinolenic acid varies from 0.1 to 25.3%. The very minor coniferonic (5,9,12,15-18:4) acid is less than 0.2% in all species. The C20 elongation product of pinolenic acid, bishomo-pinolenic (7,11,14-20:3) acid, is a frequent though minor SFA constituent (maximum, 0.7%). When considering C20 delta5-UPIFA, a difference is noted between the subgenera Strobus and Pinus. In the former subgenus, 5,11-20:2 and sciadonic acids are < or =0.3 and < or =1.9%, respectively, whereas in the latter subgenus, they are most often > or =0.3 and > or =2.0%, respectively. The highest values for 5,11-20:2 and sciadonic acids are 0.5% (many species) and 7.0% (P. pinaster). The 5,11,14,17-20:4 (juniperonic) acid is present occasionally in trace amounts. The highest level of total delta5-UPIFA is 30-31% (P. sylvestris), and the lowest level is 0.6% (P. monophylla). Uniting as well as discriminating features that may complement the knowledge about the taxonomy and phylogeny of pines are emphasized.

Cycadopsida↗

PubMed1972

The biosynthesis of (+)- -pinene in Pinus species.

1. The degradation of (+)-alpha-pinene biosynthesized from 3RS-[2-(14)C]mevalonate by Pinus radiata or Pinus nigra revealed an asymmetrical labelling pattern whereby the moiety derived from isopentenyl pyrophosphate contained at least 90% of the incorporated tracer. This pattern differed both in asymmetry and position of labelling from previous results obtained with P. nigra, but is consistent with the generally accepted hypothetical mechanism for the biosynthesis of the pinane skeleton. 2. (+)-alpha-Pinene biosynthesized in Pinus attenuata and in the previously named two species from 3RS-[2-(14)C,(4R)-4-(3)H(1)]mevalonate and its (4S)-isomer retained all the 4R hydrogen atoms (within the experimental error) but lost all the 4S hydrogen atoms of the precursor. This stereospecificity of hydrogen loss is the same as that previously found for the formation of geraniol and nerol in other plant species, and the result may be reasonably inferred to be general for monoterpenes.

Carbon Isotopes↗

PubMed1996

The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms.

A DNA sequence, TPE1, representing the internal domain of a Ty1-copia retroelement, was isolated from genomic DNA of Pinus elliottii Engelm. var. elliottii (slash pine). Genomic Southern analysis showed that this sequence, carrying partial reverse transcriptase and integrase gene sequences, is highly amplified within the genome of slash pine and part of a dispersed element >4.8 kbp. Fluorescent in situ hybridization to metaphase chromosomes shows that the element is relatively uniformly dispersed over all 12 chromosome pairs and is highly abundant in the genome. It is largely excluded from centromeric regions and intercalary chromosomal sites representing the 18S-5.8S-25S rRNA genes. Southern hybridization with specific DNA probes for the reverse transcriptase gene shows that TPE1 represents a large subgroup of heterogeneous Ty1-copia retrotransposons in Pinus species. Because no TPE1 transcription could be detected, it is most likely an inactive element--at least in needle tissue. Further evidence for inactivity was found in recombinant reverse transcriptase and integrase sequences. The distribution of TPE1 within different gymnosperms that contain Ty1-copia group retrotransposons, as shown by a PCR assay, was investigated by Southern hybridization. The TPE1 family is highly amplified and conserved in all Pinus species analyzed, showing a similar genomic organization in the three- and five-needle pine species investigated. It is also present in spruce, bald cypress (swamp cypress), and in gingko but in fewer copies and a different genomic organization.

Amino Acid Sequence↗

PubMed2000

Chloroplast evolution in the Pinus montezumae complex: a coalescent approach to hybridization.

This study addresses the evolutionary history of the chloroplast genomes of two closely related pine species, Pinus hartwegii Lindl. and P. montezumae Lamb (subsect. Ponderosae) using coalescent theory and some of the statistical tools that have been developed from it during the past two decades. Pinus hartwegii and P. montezumae are closely related species in the P. montezumae complex (subsect. Ponderosae) of Mexico and Central America. Pinus hartwegii is a high elevation species, whereas P. montezumae occurs at lower elevations. The two species occur on many of the same mountains throughout Mexico. A total of 350 individuals of P. hartwegii and P. montezumae were collected from Nevado de Colima (Jalisco), Cerro Potosí (Nuevo León), Iztaccihuatl/Popocatepetl (México), and Nevado de Toluca (México). The chloroplast genome of P. hartwegii and P. montezumae was mapped using eight restriction enzymes. Fifty-one different haplotypes were characterized; 38 of 160 restriction sites were polymorphic. Clades of most parsimoniously related chloroplast haplotypes are geographically localized and do not overlap in distribution, and the geographically localized clades of haplotypes include both P. hartwegii and P. montezumae. Some haplotypes in the clades occur in only one of the two species, whereas other haplotypes occur in both species. These data strongly suggest ancient and/or ongoing hybridization between P. hartwegii and P. montezumae and a shared chloroplast genome history within geographic regions of Mexico.

Altitude↗

PubMed1999

High population differentiation and genetic variation in the endangered Mexican pine Pinus Rzedowskii (Pinaceae).

Pinus rzedowskii is an endangered pine species from Michoacán (central México), which has been previously reported from only three localities. Classified within the subgenus Strobus, it exhibits intermediate morphological characters between subgenera Strobus and Pinus. We analyzed genetic aspects that could shed light on the evolution and conservation of this species. The genetic structure of nine populations was examined using 14 isozyme loci. Pinus rzedowskii has a relatively high level of genetic variation with 46.8% of the loci assayed being polymorphic, a total of 35 alleles, and a mean heterozygosity per population of 0.219. We calculated Wright's F(ST) statistic to estimate gene flow indirectly and to evaluate whether or not there was genetic structuring among populations. We found a marked differentiation among populations (F(ST) = 0.175) and significant inbreeding (F(IS) = 0.247). No pattern of isolation by distance was found. We also constructed a dendrogram based on a genetic distance matrix to obtain an overview of the possible historical relationships among populations. Finally, we found a convex relationship between the genetic distance among populations and the number of ancestral lineages, suggesting that demographically this species has not been at risk recently. Although endangered, with small and fragmented populations, P. rzedowskii shows higher levels of genetic variation than other conifer species with larger populations or similar conservation status.

Journal Article↗

PubMed2001

Partial cambial mortality in high-elevation Pinus aristata (Pinaceae).

Partial cambial mortality is a growth form that is characteristic of Pinus aristata trees. To better elucidate their cambial death pattern, tree size and aspect of cambial death data were gathered from three Pinus aristata forests in central Colorado, USA. Stripping frequency tended to be higher for larger diameter classes. Partial cambial mortality exhibits significant directionality within each stand. Furthermore, cambial death was measured to be most frequent on the wind-exposed side of stripped trees in two of the three study sites and appeared to be at the third. Data presented here support the hypothesis that wind plays a role in the occurrence of partial cambial mortality in Pinus aristata. The mechanisms by which wind causes cambial mortality remain unclear.

Journal Article↗