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The Conifers (Pinophyta)
... Conifer plant species are found dominantly in the major terrestrial landscapes. However, conifers have less species diversity which accounts for less than 0.3% of the species diversity from the earth's plant species [1]. Ethiopia has eight natural vegetation types based on elevation and climate gradients. ...
The Juniperus procera and Podocarpus falcatus tree species are the only indigenous conifer plants that Ethiopia has and dominantly found in dry Afromontane forests of the country. However, dry Afromontane forests are threatened by climate change. The objective of this study is to analyze the effect of climate change on the regenera-tion and dominance of the J. procera and P. falcatus tree species in Ethiopia. The regeneration status classes and importance value index score classes analysis was done along the time series. This study revealed that J. procera had a fair regeneration status, while P. falcatus exhibited an alternate regeneration status between fair and good. Not regenerating regeneration status was recorded in 2006-2010 and 2016-2020 time series for J. procera, while in 2011-2015 and 2021-2023 for P. falcatus. Regarding the importance value index score of the species, J. procera had the top three throughout the all-time series except in 2011-2015 which had the lowest importance value index score, whereas P. falcatus had the top three importance value index score status from 2016 to 2023 time series. Safeguarding these conifer species from the negative effects of climate change relies on the attention of all responsible bodies.
... Gymnosperms are ancient plant groups having their origin in the Permian era, 200e300 million years ago (Gernandt et al., 2011). Among gymnosperms, the position of Taxaceae has been a source of controversy in view of systematics. ...
Endophytes Secondary metabolites Taxol Taxus a b s t r a c t Endophytes are the plant microorganisms that flourish inside plants (endosphere) and support the growth under normal and challenging environmental circumstances. Besides biological activities, microbial endophytes are important for their contribution in adaptation and survival of the host plants under stressed environments. While various species of Taxus have been globally recognized mainly due to their anticancer property, emphasis has also been on isolation of taxol producing endophytes in view of the taxonomic (endan-gered) status of the species. Furthermore, Taxus associated endophytes are also being recognized for the biological activities other than taxol production. The present study reviews the diversity of Taxus associated endophytes along with their biological activities. Available literature on Taxus associated endophytes revealed that T. chinensis has received maximum attention (19.5 %), followed by T. wallichiana (18.5 %), T. baccata (16.4 %), T. cuspi-data (11.3 %), and T. mairei (10.3 %); with a minimum number of reports accounted for T. globose (1.0 %), and T. celebica (2.0 %). Most fungal endophytes have been identified as asco-mycetes. Basidiomycetous endophytes have been reported in a limited number of studies. No endophytes have yet been identified from three species, namely T. controta (West Hima-layan yew), T. floridana (Florida yew), and T. canadensis (Canadian yew). A total of 70 diverse endophytic species have been reported from different Taxus species. Fusarium sp. (25.2 %), Aspergillus sp. (17.6 %), Alternaria sp. (11.3 %), Penicillium sp. and Cladosporium sp. (10.0 %) are the five dominant genera. Furthermore, 59.6 % of studies from the reported literature are related to taxol production by fungal endophytes, 9.6 % related to antimicrobial activity, and a combined 15.3 % related to other biological activities, i.e., antifeeding, antimitogenic, antioxidant and cytotoxic activities. Additionally, 3.8 % of fungal endophytes were not studied for any of their biological activities. Only three bacterial endophytes namely Bur-kholderia sp., Enterobacter sp., and Pseudomonas sp., have been recorded from Taxus along with their contribution in plant growth, antagonistic, and antioxidant activities. Isolation.in (A. Pandey). j o u r n a l h o m e p a g e : w w w. e l s e v i e r. c o m / l o c a t e / f b r f u n g a l b i o l o g y r e v i e w s 4 5 (2 0 2 3) 1 0 0 3 0 8
... However, the remaining orthogroups that are represented in only a few species are also of interest for further research. In general, the generated phylogenetic tree in Figure 1 is in agreement with consensual phylogenetic relationships for these species based on traditional markers [20,21]. The OrthoFinder software was used to carry out a comparative analysis of the proteomes of evergreen and deciduous trees. ...
In the course of evolution, both flowering plants and some gymnosperms have developed such an adaptation to winter and unfavorable living conditions as deciduousness. Of particular interest is Siberian larch (Larix sibirica Ledeb.), which is the only species in the pine family (Pinaceae) with a seasonal deciduousness. New generation sequencing technologies make it possible to study this phenomenon at the genomic level and to reveal the genetic mechanisms of leaf and needle aging in angiosperms and gymnosperms. Using a comparative analysis of the genomes of evergreen and deciduous trees, it was found that the genes that control EXORDIUM LIKE 2 (EXL2) and DOR-MANCY-ASSOCIATED PROTEIN 1 (DRM1) proteins are most represented in Siberian larch, while an excess of genes that control proteins acting as immune receptors were found in evergreens. Orthologs from the family of genes that control leucine-rich repeat receptor-like kinases (LRR-RLK) contributed mostly to the distinction between evergreens and deciduous plants.
... Pinus is the largest genus within the gymnosperms and Pinaceae Family, containing more than 100 species . Pine species are predominantly distributed in the Northern Hemisphere, reaching the equator in Asia and being present in the Mediterranean areas of Africa, but a few species are also native to the Southern Hemisphere (Gernandt et al. 2011). They are adapted to very different ecological and environmental conditions, from tropical to boreal climates, and are able to grow in pure stands or mixed with other evergreen or deciduous trees (Plomion et al. 2007). ...
The largest pine tree in the world, sugar pine, also has one the largest genomes ever sequenced in any plant species. The reference genome, transcriptome, and SNP markers developed for the species have been used to support breeding disease resistant trees and answer questions related to genome obesity. These resources also create an opportunity to explore associations between genetic variation and environmental variables. By combining ordination and association techniques such as PCA, MLM, and RDA, we identified markers and genes associated with environmental variation across the Sugar Pine species range. Most of the genes identified by our analysis were associated with precipitation though temperature and continentality were also found to be associated with putatively adaptive genes. The results of the PCA and environmental correlations demonstrated explicit groupings among the environmental variables. Functional annotations for these genes were primarily related to signal transduction and disease resistance, but annotations related to biotic and abiotic stress were also identified. Results further provide insight into the geographic pattern of environmentally correlated genetic variation in the species. These findings may provide important insights to guide management strategies looking to maintain the species through ongoing changes in climate and fire regimes.KeywordsGenotype-environment associationRedundancy analysisSugar pineClimate adaptationgenomics
... Pinus is the largest genus within the gymnosperms and Pinaceae Family, containing more than 100 species (Mullin et al. 2011). Pine species are predominantly distributed in the Northern Hemisphere, reaching the equator in Asia and being present in the Mediterranean areas of Africa, but a few species are also native to the Southern Hemisphere (Gernandt et al. 2011). They are adapted to very different ecological and environmental conditions, from tropical to boreal climates, and are able to grow in pure stands or mixed with other evergreen or deciduous trees (Plomion et al. 2007). ...
Pines are economically important species widely planted across the globe. Therefore, the industry is interested in increasing the efficacy of their breeding programs, which explains the urge to implement new technological solutions to increase breeding efficiency for traditional and novel breeding objectives. Recently, the development of genotyping platforms accessible even for non-model organisms such as Scots and radiata pines has made it possible to evaluate genomic selection for their breeding programs. Genomic studies in both species are limited by the size and complexity of their genomes; therefore, genotyping platforms based on reduced genome representation have been implemented. Genomic selection studies performed within their breeding programs show viability and potential to increase the intensity of genetic progress compared to conventional (i.e., pedigree-based) strategies. Additionally, genomic prediction of traits with challenging or costly phenotyping, such as forest diseases or wood quality and cell wall chemistry, might allow for large-scale screening and selection of individuals with superior traits. This chapter presents a review of the recent research on genomic selection for Scots pine in Sweden, and radiata pine in New Zealand, as well as future perspectives for the implementation of this methodology in their breeding programs.
... Pinus is the largest genus within the gymnosperms and Pinaceae Family, containing more than 100 species . Pine species are predominantly distributed in the Northern Hemisphere, reaching the equator in Asia and being present in the Mediterranean areas of Africa, but a few species are also native to the Southern Hemisphere (Gernandt et al. 2011). They are adapted to very different ecological and environmental conditions, from tropical to boreal climates, and are able to grow in pure stands or mixed with other evergreen or deciduous trees (Plomion et al. 2007). ...
Pinus species are highly suitable for monitoring anthropogenic pollutants, including air contaminants, heavy metals and radionuclides. Scots pine (Pinus sylvestris L.) is one of the most widely distributed conifers in the world, and is characterized by a high sensitivity to environmental pollutants and an increased ability to accumulate pollutants in tissues. Because of its large genome size, this species is extremely sensitive to ionizing radiation, thus considered by the International Commission on Radiological Protection as a reference plant for radiation protection of biota. Current approaches in functional genomics and bioinformatics allow studying the transcriptional profiles of P. sylvestris in radioactively contaminated areas, revealing adaptive responses at a previously unattainable level. In the Chernobyl exclusion zone, where natural populations are under low-dose chronic radiation stress, such responses include direct structural protection of DNA integrity from radiation damage and modulation of reactive oxygen species production. Chronically irradiated pine populations have increased expression of genes encoding heat shock proteins and histones. However, no differential expression of genes related to DNA repair was revealed, while the transcriptional responses pointed to modulation of redox cellular homeostasis. These observations suggest that the response patterns to chronic low-dose and acute high-dose ionizing radiation exposure are partially different. Biomonitoring properties of P. sylvestris and a pipeline for assembling the transcriptome of this non-model species are also discussed.
... Spanning the surface of the Earth for the last 300 million years (Gernandt et al., 2011), conifers had to cope and adapt to diverse local climatic conditions. Extreme climatic events, such as drought episodes, have been an important driver in the shaping of selection and dispersion of adapted genotypes to these conditions as water availability has proven to be a key determinant of survival and reproduction (Allen et al., 2010;Williams, 2009). ...
With climate change, increasingly intense and frequent drought episodes will be affecting water availability for boreal tree species, prompting tree breeders and forest managers to consider adaptation to drought stress as a priority in their reforestation efforts. We used a 19‐year‐old polycross progeny test of the model conifer white spruce (Picea glauca) replicated on two sites affected by distinct drought episodes at different ages to estimate the genetic control and the potential for improvement of drought response in addition to conventional cumulative growth and wood quality traits. Drought response components were measured from dendrochronological signatures matching drought episodes in wood ring increment cores. We found that trees with more vigorous growth during their lifespan resisted better during the current year of a drought episode when the drought had more severe effects. Phenotypic data were also analyzed using genomic prediction (GBLUP) relying on the genomic relationship matrix of multi‐locus gene SNP marker information, and conventional analysis (ABLUP) based on validated pedigree information. The accuracy of predicted breeding values for drought response components was marginally lower than that for conventional traits and comparable between GBLUP and ABLUP. Genetic correlations were generally low and non‐significant between drought response components and conventional traits, except for resistance which was positively correlated to tree height. Heritability estimates for the components of drought response were slightly lower than for conventional traits, but similar single‐trait genetic gains could be obtained. Multi‐trait genomic selection simulations indicated that it was possible to improve simultaneously for all traits on both sites while sacrificing little on gain in tree height. In a context of rapid climate change, our results suggest that with careful phenotypic assessment, drought response may be considered in multi‐trait improvement of white spruce, with accelerated screening of large numbers of candidates and selection at young age with genomic selection.
... Picea is a member of the family Pinaceae, together with other widespread genera such as Pinus, Abies, Larix, and Tsuga. The family is an important component of the order Pinales, also known as Coniferales, the conifers (Gernandt et al. 2011). With approximately 38 extant species (Table 1), Picea is the third most diversified genus of the Pinaceae after Pinus and Abies. ...
Spruce (Picea spp.) species are the dominant component of the circumboreal forest and one of the most reforested species groups in the world. They have become a reference among conifers for fundamental and applied genomics research. This chapter reviews the compelling progress made in the field of spruce population genomics, from the supportive field trials established by tree breeders to the release of complete sequences of their cytoplasmic and nuclear genomes to most recent applications in forestry. Initial efforts focusing on sequencing the spruce gene space resulted in the development of extensive genomic resources such as expressed sequence tags libraries, gene and single nucleotide polymorphism catalogs, genotyping arrays, and high-resolution genetic maps. During the last decade, these resources allowed to gain insights into a variety of topics such as phylogeography and phylogeny, introgression and speciation processes, as well as association mapping. Thanks to the recent advent of high-throughput genotyping and sequencing technologies, population genomics data are now being produced at an exponential rate, which translates into new applications and opportunities in conservation genetics and spruce breeding, such as genomic prediction.
... Currently, it is largely accepted that conifers contain two major clades, Pinaceae and the remaining non-Pinaceae conifers (Conifers II or cupressophytes), in which the first and second largest families are Pinaceae and Podocarpaceae (Knopf et al., 2012). Overall, the cupressophytes include five families, namely the Cupressaceae, Araucariaceae, Sciadopityaceae, Taxaceae, and Podocarpaceae, with approximately 405 species (Gernandt et al., 2011). The gnetophytes contain three families (Gnetaceae, Ephedraceae, and Welwitschiaceae), each of which contains a single genus. ...
Gymnosperms are among the most endangered groups of plant species; they include ginkgo, pines (Conifers I), cupressophytes (Conifers II), cycads, and gnetophytes. The relationships among the five extant gymnosperm groups remain equivocal. We analyzed 167 available gymnosperm plastomes and investigated their diversity and phylogeny. We found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub. and Macrozamia mountperriensis F.M.Bailey had the smallest and largest plastomes, respectively. The inverted repeats (IRs) of the five groups were shown to have evolved through distinctive evolutionary scenarios. The IRs have been lost in all conifers but retained in cycads and gnetophytes. A positive association between simple sequence repeat (SSR) abundance and plastome size was observed, and the SSRs with the most variation were found in Pinaceae. Furthermore, the number of repeats was negatively correlated with IR length; thus, the highest number of repeats was detected in Conifers I and II, in which the IRs had been lost. We constructed a phylogeny based on 29 shared genes from 167 plastomes. With the plastome tree and 13 calibrations, we estimated the tree height between present‐day angiosperms and gymnosperms to be ∼380 million years ago (mya). The placement of Gnetales in the tree agreed with the Gnetales–other gymnosperms hypothesis. The divergence between Ginkgo and cycads was estimated as ∼284 mya; the crown age of the cycads was 251 mya. Our time‐calibrated plastid‐based phylogenomic tree provides a framework for comparative studies of gymnosperm evolution.
Gymnosperms, also termed as Acrogymnospermae, are an assemblage of seed-bearing vascular plants that contain “naked” seeds. Although the early evolutionary history of seed plants is a bit tricky and confusing due to inconclusive fossil evidences, recent molecular phylogenetic studies place extant gymnosperms in a monophyletic group allied to the Magnoliophyta. All major groups of gymnosperms have found usage in the nanofabrication nanoparticles with majority of the studies carried out in the last 10 years. Among the gymnosperms, conifers have been the popular choice in the eco-friendly synthesis of nanoparticles primarily due to the structural and chemical diversity of natural compounds present in different members of this group. Ginkgo, Cycas, and Ephedra have also yielded nanoparticles, while Gnetum has also been utilized to some extent.
There are only a few natural polyploids in gymnosperms. These have been reported in Ephera spp. (Gnetales), and Juniperus chinensis 'Pfitzeriana' (2n = 4x = 44), Fitzroya cupressoides (2n = 4x = 44), and the only hexaploid conifer Sequoia sempervirens (2n = 6x = 66) (Coniferales). Sporadic polyploids and aneuploids occur at a very low frequency in nurseries in conifers, but most of them show growth abnormalities, remain dwarf, and may not reach maturity. One exception is an autotetraploid tree of Larix decidua (2n = 4x = 48) that has survived in a private estate in Denmark. Colchicine-induced polyploids (colchiploids) have been produced in a several genera of conifers, including, Pinus, Picea, and Larix. These colchiploids (Co) were hybridized to untreated diploids to produce C1 and C2 generations to investigate their chromosome behavior. The colchiploids showed a wide range of chromosome variability, ranging from diploids, triploids, and tetraploids, and many were mixoploids. The colchiploids also show growth retardation, remain dwarf, and their future potential applications in forestry remains uncertain. However, genetic variability in the colchiploids still offers prospects for isolating genetically stable new genotypes. Even though polyploidy is rare in extant conifers, is it possible that ancient polyploidy or paleopolyploidy, that is prevalent in angiosperms, has also played a role in the evolution of conifers. In this paper we shall review the current status of polyploidy in gymnosperms.
Mild, moist maritime conditions characterise a region of forest with Pseudotsuga menziesii, Tsuga heterophylla, Thuja plicata, Picea sitchensis and Sequoia sempervirens. These dominant conifers are the largest and longest-lived representatives of their genera, and the forests provide the greatest biomass accumulations of some of the highest productivity levels of any in the world. Disturbance regimes are characterised by infrequent catastropic events, eg fire, at intervals of several hundreds of years. Major forest types are described: Douglas-fir/western hemlock; Sitka spruce/western hemlock; coast redwood; Klamath Mountains mixed evergreen forests (primarily Douglas-fir plus evergreen hardwoods, eg Lithocarpus densiflorus, Quercus chrysolepis, Arbutus menziesii and Castanopsis chrysophylla); and Sierran type mixed conifer forest. Other vegetation types include subalpine forests (with Abies amabilis, A. magnifica var. shastensis, Tsuga heterophylla and T. mertensiana) and parklands. -P.J.Jarvis
Compared with the gigantic diversity of angiosperms (c. 400, 000 species), the gymnosperms, once one of the dominant plant types on Earth, are at present, with c.900 species, a tiny minority. With some 630 species in 70 genera and 8 families, the conifers form the bulk of this remnant diversity, the remainder being mostly cycads plus ephedras, gnetums, Welwitschia and Ginkgo. The conifers, though presently recognised as a monophyletic group in relation to other seed plants, are nevertheless a typical mixture reflecting two phenomena: extinction and radiation. The author recognises three families with but a single genus, one family with a single species, and numerous unispecific genera. This classification reflects extinction of closely allied lineages rather than character accumulation within single taxa. In other families, some genera are prolific in species and many of these are rapidly evolving (e.g., Pinus) and widely spread and successful in certain environments related to severe climatic change (e.g., Juniperus). Such genera display radiation. Conifers, despite their minute diversity in comparison with angiosperms, occupy an enormous range of environments on all continents but Antarctica, where they became extinct. The author presents an overview of this diversity.
Few anatomical details are currently available concerning the processes of gametophyte development and fertilization in members of the conifer family Podocarpaceae. Electron microscope studies of a New Zealand native podocarp, Podocarpus totara, provided ultrastructural details of male and female gamete participation in fertilization, and suggested a mechanism of cytoplasmic inheritance.
Antisera were made in rabbits to seed extracts from 12 different species in 7 different genera of the conifer family Pinaceae. The immunogens were characterized as mainly protein in nature. The Ouchterlony double diffusion technique was used to measure intra- and intergeneric antigenic distances. The antigenic distances were used to calculate the average rate of protein evolution. Protein evolution has proceeded at about the standard rate found in other groups of organisms. By contrast, chromosomal evolution has proceeded very slowly in the Pinaceae. Possibly, the remarkably slow anatomical evolution which is a characteristic feature of Pinaceae is ascribable to their slow chromosomal evolution. Antigenic distances were also used to derive possible phylogenetic relationships. A close relationship between Larix (larch) and Pseudotsuga (Douglas-fir) was inferred.