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Ganopoulos I, Aravanopoulos F, Madesis P, Pasentsis K, Bosmali I, Ouzounis C, Tsaftaris A. Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing. PLoS One 2013; 8:e60945. [PMID: 23577179 PMCID: PMC3618329 DOI: 10.1371/journal.pone.0060945] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 03/06/2013] [Indexed: 11/19/2022] Open
Abstract
Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples.
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Affiliation(s)
- Ioannis Ganopoulos
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Greece
| | - Filippos Aravanopoulos
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Laboratory of Forest Genetics and Tree Breeding, Faculty of Forestry and Natural Environment, Aristotle University of Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Konstantinos Pasentsis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Irene Bosmali
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Christos Ouzounis
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Athanasios Tsaftaris
- Institute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Greece
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Parks M, Cronn R, Liston A. Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae). BMC Evol Biol 2012; 12:100. [PMID: 22731878 PMCID: PMC3475122 DOI: 10.1186/1471-2148-12-100] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/14/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating 'noisy' data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or elevated rates of evolution. RESULTS We investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups. While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses. Close investigation of these nodes revealed dramatically different responses to data removal. Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included. Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear. When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set. CONCLUSIONS These results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies. For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses.
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Affiliation(s)
- Matthew Parks
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR 97331, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA
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Hirooka Y, Rossman AY, Samuels GJ, Lechat C, Chaverri P. A monograph of Allantonectria, Nectria, and Pleonectria (Nectriaceae, Hypocreales, Ascomycota) and their pycnidial, sporodochial, and synnematous anamorphs. Stud Mycol 2012; 71:1-210. [PMID: 22685364 PMCID: PMC3310236 DOI: 10.3114/sim0001] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Although Nectria is the type genus of Nectriaceae (Hypocreales, Sordariomycetes, Pezizomycotina, Ascomycota), the systematics of the teleomorphic and anamorphic state of Nectriasensu Rossman has not been studied in detail. The objectives of this study are to 1) provide a phylogenetic overview to determine if species of Nectria with Gyrostroma, Tubercularia, and Zythiostroma anamorphs form a monophyletic group; 2) define Nectria, segregate genera, and their species using morphologically informative characters of teleomorphic and anamorphic states; and 3) provide descriptions and illustrations of these genera and species. To accomplish these objectives, results of phylogenetic analyses of DNA sequence data from six loci (act, ITS, LSU, rpb1, tef1 and tub), were integrated with morphological characterisations of anamorphs and teleomorphs. Results from the phylogenetic analyses demonstrate that species previously regarded as the genus Nectria having Gyrostroma,Tubercularia, and Zythiostroma anamorphs belong in two major paraphyletic clades. The first major clade regarded as the genus Pleonectria contains 26 species with ascoconidia produced by ascospores in asci, perithecial walls having bright yellow scurf, and immersed or superficial pycnidial anamorphs (Zythiostroma = Gyrostroma). A lineage basal to the Pleonectria clade includes Nectria miltina having very small, aseptate ascospores, and trichoderma-like conidiophores and occurring on monocotyledonous plants. These characteristics are unusual in Pleonectria, thus we recognise the monotypic genus Allantonectria with Allantonectria miltina. The second major clade comprises the genus Nectriasensu stricto including the type species, N. cinnabarina, and 28 additional species. Within the genus Nectria, four subclades exist. One subclade includes species with sporodochial anamorphs and another with synnematous anamorphs. The other two paraphyletic subclades include species that produce abundant stromata in which the large perithecia are immersed, large ascospores, and peculiar anamorphs that form pycnidia or sporodochia either on their natural substrate or in culture. In this study the evolution of species, morphology, and ecology of the three genera, Allantonectria, Nectria, and Pleonectria, are discussed based on the phylogenetic analyses. In addition, descriptions, illustrations, and keys for identification are presented for the 56 species in Allantonectria, Nectria, and Pleonectria.
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Affiliation(s)
- Y Hirooka
- Department of Plant Sciences and Landscape Architecture, 2112 Plant Sciences Building, University of Maryland, College Park, Maryland 20742, USA
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Ibrahim RIH, Sakamoto M, Azuma JI. PCR-RFLP and genetic diversity analysis of cpDNA in some species of the genus Salvia L. ACTA ACUST UNITED AC 2012. [DOI: 10.3199/iscb.7.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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CAI QING, ZHANG DAMING, LIU ZHANLIN, WANG XIAORU. Chromosomal localization of 5S and 18S rDNA in five species of subgenus Strobus and their implications for genome evolution of Pinus. ANNALS OF BOTANY 2006; 97:715-22. [PMID: 16481361 PMCID: PMC2803414 DOI: 10.1093/aob/mcl030] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Studying the genome structure of pines has been hindered by their large genomes and uniform karyotypes. Consequently our understanding of the genome organization and evolutionary changes in different groups of pines is extremely limited. However, techniques are now available that can surmount these difficulties. The purpose of this study was to exploit some of these techniques to characterize the genome differentiation between the two subgenera of Pinus: Pinus and Strobus. METHODS Double-probe fluorescence in-situ hybridization (FISH) was used to localize the 5S and 18S rDNA loci on chromosomes of five species from the subgenus Strobus: P. bungeana, P. koraiensis, P. armandii, P. wallichiana and P. strobus. * KEY RESULTS The rDNA FISH pattern varied considerably among the five species, with P. bungeana being the most distinct. By comparing the results obtained with those of previous rDNA FISH studies of members of the subgenus Pinus, several general features of rDNA loci distribution in the genus Pinus can be discerned: (a) species of subgenus Strobus generally have more rDNA loci than species of subgenus Pinus, correlating with their larger genomes in the subgenus Strobus; (b) there is a clear differentiation in 5S and 18S rDNA loci linkage patterns between the two subgenera; (c) variations in the rDNA FISH pattern correlate with phylogenetic relationships among species within the subgenus; (d) P. bungeana has fewer 18S rDNA sites than other pines investigated to date, but they give intense signals, and may reflect the primary distribution of the 18S-25S rDNA loci in the genus. CONCLUSIONS The stable differentiation in rDNA FISH pattern between the subgenera suggests that chromosomal rearrangements played a role in the splitting of the two subgenera, and transpositional events rather than major structural changes are likely responsible for the variable rDNA distribution patterns among species of the same subgenus with conserved karyotypes.
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Affiliation(s)
- QING CAI
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
| | - DAMING ZHANG
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
| | - ZHAN-LIN LIU
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
| | - XIAO-RU WANG
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
- For correspondence. E-mail
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Syring J, Willyard A, Cronn R, Liston A. Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. AMERICAN JOURNAL OF BOTANY 2005; 92:2086-2100. [PMID: 21646125 DOI: 10.3732/ajb.92.12.2086] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sequence data from nrITS and cpDNA have failed to fully resolve phylogenetic relationships among Pinus species. Four low-copy nuclear genes, developed from the screening of 73 mapped conifer anchor loci, were sequenced from 12 species representing all subsections. Individual loci do not uniformly support either the nrITS or cpDNA hypotheses and in some cases produce unique topologies. Combined analysis of low-copy nuclear loci produces a well-supported subsectional topology of two subgenera, each divided into two sections, congruent with prior hypotheses of deep divergence in Pinus. The placements of P. nelsonii, P. krempfii, and P. contorta have been of continued systematic interest. Results strongly support the placement of P. nelsonii as sister to the remaining members of sect. Parrya, suggest a moderately well-supported and consistent position of P. krempfii as sister to the remaining members of sect. Quinquefoliae, and are ambiguous about the placement of P. contorta. A successful phylogenetic strategy in Pinus will require many low-copy nuclear loci that include a high proportion of silent sites and derive from independent linkage groups. The locus screening and evaluation strategy presented here can be broadly applied to facilitate the development of phylogenetic markers from the increasing number of available genomic resources.
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Affiliation(s)
- John Syring
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
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Grotkopp E, Rejmánek M, Sanderson MJ, Rost TL. EVOLUTION OF GENOME SIZE IN PINES (PINUS) AND ITS LIFE-HISTORY CORRELATES: SUPERTREE ANALYSES. Evolution 2004. [DOI: 10.1554/03-545] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nkongolo KK, Michael P, Gratton WS. Identification and characterization of RAPD markers inferring genetic relationships among Pine species. Genome 2002; 45:51-8. [PMID: 11908668 DOI: 10.1139/g01-121] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Total genomic DNAs were extracted from several populations of pine species and amplified using oligonucleotides of random sequences. Polymorphism in random amplified polymorphic DNA (RAPD) markers was high and sufficient in distinguishing each of the species. Genetic relationships among eight pine species (Pinus sylvestris, Pinus strobus, Pinus rigida, Pinus resinosa, Pinus nigra, Pinus contorta, Pinus monticola, and Pinus banksiana) from different provenances were analyzed. The degree of band sharing was used to evaluate genetic distance between species and to construct a phylogenetic tree. In general, the dendrogram corroborated the description of relationships based on morphological characteristics and crossability, but also provided new insights into pine taxonomy. RAPD markers specific to some pine species were cloned and sequenced. PCR amplifications using pairs of designed specific primers revealed that all the cloned sequences were likely genus specific because they were not found in spruce or larch. True species-specific sequences were identified using designed primers flanking cloned RAPD fragments. The analysis of RAPD fragment sequences confirmed the genetic relationships among species. A 2281-bp RAPD band called PI-Mt-Stb-23 from P. strobus was used as a probe in restriction fragment length polymorphism (RFLP) analysis and produced distinct banding patterns for each species examined, consistent with the highly polymorphic character of DNA-fingerprinting probes.
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Affiliation(s)
- K K Nkongolo
- Department of Biological Sciences, Laurentian University, Sudbury, ON, Canada.
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Ickert-Bond SM. Cuticle Micromorphology of Pinus krempfii Lecomte (Pinaceae) and Additional Species from Southeast Asia. INTERNATIONAL JOURNAL OF PLANT SCIENCES 2000; 161:301-317. [PMID: 10777455 DOI: 10.1086/314243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/1998] [Revised: 10/01/1999] [Indexed: 05/23/2023]
Abstract
Cuticle micromorphology of the unusual Vietnamese pine, Pinus krempfii Lecomte, and three additional endemic southeast Asian species of Pinus L. (Pinaceae) is characterized for the first time. Taxa studied include (1) P. krempfii, typically placed in its own subgenus Ducampopinus (Chevalier) Ferré ex Little & Critchfield; (2) the endemic Vietnamese species Pinus dalatensis Ferré and (3) the southeast Asian species Pinus kwantungensis Chun ex Tsiang, both of subgenus Strobus; and (4) the widespread Asian species Pinus kesiya Royle ex Gordon of subgenus Pinus. The current and previous studies demonstrate that the genus Pinus and its subgenera are delimited by unique combinations of cuticular characters, although some of these characters may occur individually in other conifers. Cuticular micromorphology supports taxonomic assignment of P. krempfii to subgenus Strobus rather than to its own subgenus, a result that is also indicated by other anatomical studies and recent molecular studies. Sectional affinities of P. krempfii are usually with Parrya, subsection Krempfianae. An alternative classification of P. krempfii with subsection Gerardianae can be supported by micromorphological characters including broad cuticular bridges between stomata, details of the intercellular flanges of the epidermal cells, and usually an amphistomatic stomatal distribution. Features of other Asian species studied are consistent with their taxonomic assignments. The study demonstrates the utility of cuticle micromorphology to taxonomic delimitation within the family Pinaceae.
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Abstract
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.
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Affiliation(s)
- A Karhu
- Department of Biology, University of Oulu, Finland
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Wolff RL, Pédrono F, Pasquier E, Marpeau AM. General characteristics of Pinus spp. seed fatty acid compositions, and importance of delta5-olefinic acids in the taxonomy and phylogeny of the genus. Lipids 2000; 35:1-22. [PMID: 10695919 DOI: 10.1007/s11745-000-0489-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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.
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Affiliation(s)
- R L Wolff
- ISTAB, Université Bordeaux 1, Talence, France.
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12
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Jackson JF, Adams DC, Jackson UB. Allometry of Constitutive Defense: A Model and a Comparative Test with Tree Bark and Fire Regime. Am Nat 1999; 153:614-632. [DOI: 10.1086/303201] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Wu J, Krutovskii KV, Strauss SH. Abundant mitochondrial genome diversity, population differentiation and convergent evolution in pines. Genetics 1998; 150:1605-14. [PMID: 9832536 PMCID: PMC1460421 DOI: 10.1093/genetics/150.4.1605] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- J Wu
- Department of Forest Science, Oregon State University, Corvallis, Oregon 97331-7501, USA
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Tsumura Y, Yoshimura K, Tomaru N, Ohba K. Molecular phytogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:1222-36. [PMID: 24170050 DOI: 10.1007/bf00220933] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/1995] [Accepted: 05/26/1995] [Indexed: 05/12/2023]
Abstract
We investigated the molecular phylogeny of conifers using restriction endonuclease fragment length polymorphism of six polymerase chain reaction-amplified chloroplast genes - frxC, rbcL, psbA, psbD, trnK, and 16S. We detected 227 total site changes among species, representing 23, 26, 38, 48, 67, and 25 site changes in frxC, psbA, psbD, rbcL, trnK and 16S, respectively. The mean nucleotide substitution was 10.75% (SD 0.573) among species in five families. Forty maximally parsimonious trees were obtained using the Wagner parsimony method, and a 50% majority-rule consensus tree was obtained from them. Data analysis produced similar basic patterns when both the Wagner parsimony and the neighbor-joining methods were applied, and the main lineages were clearly separated. Taxaceae and Cephalotaxaceae species were used as the out-groups when applying Wagner parsimony methods. With the Wagner method, the consistency index was 0.510, the retention index was 0.879, and tree length was 435 steps. Our results indicated that Cupressaceae and Taxodiaceae are closely related families and that Sciadopitys verticillata is the basal lineage of Cupressaceae and Taxodiaceae. The neighbor-joining tree is similar to the 50% majority-rule consensus of the 40 Wagner parsimony trees except for the position of Keteleeria daversifolia, the Picea and Cedrus group, and the divergence within Cupressaceae.
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Affiliation(s)
- Y Tsumura
- Bio-resources Technology Division, Forestry and Forest Products Research Institute, Kukizaki, 305, Ibaraki, Japan
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Strauss SH, Hong YP, Hipkins VD. High levels of population differentiation for mitochondrial DNA haplotypes inPinus radiata, muricata, andattenuata. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1993; 86:605-611. [PMID: 24193710 DOI: 10.1007/bf00838716] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/1992] [Accepted: 12/09/1992] [Indexed: 06/02/2023]
Abstract
We analyzed mitochondrial (mt) DNA restriction fragment length polymorphisms (RFLPs) associated with cytochrome oxidase, subunit I (coxI)-related gene sequences in 268 trees derived from 19 natural populations of three species of pines from California (USA): Monterey pine (Pinus radiata D. Don), bishop pine (P. Muricata D. Don), and knobcone pine (P. attenuata Lemm.). Total genomic DNA was digested with four restriction endonucleases and probed with a 750-bp fragment of the mitochondrialcoxI gene amplified fromP. attenuata via the polymerase chain reaction (PCR). ThecoxI gene is repeated at least 4 times in some populations, and all variants that we observed resulted from complex rearrangements rather than from point mutations. There was limited intrapopulation variation, but strong differentiation among populations. When applied to haplotype frequencies, Nei's gene diversity within populations (Hs) averaged 7% (±3), and Gst varied from 75% forP. Radiata to 96% forP. muricata. The high degree of population differentiation for mtDNA suggests that it can be a powerful marker of population differences, but its rapid rate of structural evolution appears to result from recombination among a limited number of repetitive elements-giving frequent homoplasious fragment phenotypes. The phylogenetic trees disagreed with results from chloroplast DNA, nuclear gene, and morphological studies.
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Affiliation(s)
- S H Strauss
- Department of Forest Science, FSL 020, Oregon State University, 97331-7501, Corvallis, OR, USA
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