Recent advances on phylogenomics of gymnosperms and a new classification

Living gymnosperms comprise four major groups:cycads,Ginkgo,conifers,and gnetophytes.Relationships among/within these lineages have not been fully resolved.Next generation sequencing has made available a large number of sequences,including both plastomes and single-copy nuclear genes,for reconstruction of solid phylogenetic trees.Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics.Here,we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms.This new classification includes three classes(Cycadopsida,Ginkgoopsida,and Pinopsida),five subclasses(Cycadidae,Ginkgoidae,Cupressidae,Pinidae,and Gnetidae),eight orders(Cycadales,Ginkgoales,Araucariales,Cupressales,Pinales,Ephedrales,Gnetales,and Welwitschiales),13 families,and 86 genera.We also described six new tribes including Acmopyleae Y.Yang,Austrocedreae Y.Yang,Chamaecyparideae Y.Yang,Microcachrydeae Y.Yang,Papuacedreae Y.Yang,and Prumnopityeae Y.Yang,and made 27 new combinations in the genus Sabina.

Comparative Studies of Tracheary Element Structure of Some Gymnosperms with Angiosperms

Tissues of the pinna and rachis of Cycas diannaensis and pinna, rachis, and root of Cycas taiwaniana, rachis of Cycas szechuanensis, stem of Metasequoia glyptostroboides (Taxodiaceae), stems of Chamaecyparis obtusa (Sieb.et Zucc.) Endl cv. Tetragona (Cupressaceae), and leaves and stems of Michelia alba and Michelia figo and stems of Amygdalus persica (angiosperms) were compared using the scanning electron microscopy. In all species of these gymnosperms, their many tracheary elemnts have perforations in end walls and lateral walls. These structures are the same as vessels of angiosperms;therefore, these tracheary elements are vessel elements. Many types of vessels were found in cycads: pitted vessels in M. glyptostroboides, spiral and pitted vessels in Chamaecyparis obtusa cv. Tetragona. The development and structural characteristics of vessels of cycads, the two other gymnosperms, and the angiosperms were identical. Some characters such as extent of incline of perforation plate in the end wall showed that vessel characters of some angiosperms were more primitive than the cycads or M. glyptostroboides and C. obtusa cv. Tetragona. Many of the vessel elements of the angiosperms were band shaped, without end walls, and had only two lateral walls and other two margins;the end was acuate or with an arc margin;the end of some vessel elements was acute with no perforations, many perforations located only in lateral wall. Such results are rarely reported in previous work. In all species, perforations were seen only in tracheae, and the walls of parenchyma cells only had a thin primary wall and without perforation. Analysis and discussion to the experimental measures which were observed and research of the structure of vessel or tracheid, pointed out that several measures all could be used and the Jeffrey’ method effects were better. Comparing the vessels of cycads, Taxodiaceae and Cupressaceae helps us to understand the mechanism in which these most primitive or more primitive extant gymnosperms were adapted to harsh environments and to understand these species’ evolutionary extent, and has the significance to the studies of plant anatomy, plant systematics and plant evolution.

Evolutionary history shapes variation of wood density of tree species across the world

The effect of evolutionary history on wood density variation may play an important role in shaping variation in wood density,but this has largely not been tested.Using a comprehensive global dataset including 27,297 measurements of wood density from 2621 tree species worldwide,we test the hypothesis that the legacy of evolutionary history plays an important role in driving the variation of wood density among tree species.We assessed phylogenetic signal in different taxonomic(e.g.,angiosperms and gymnosperms)and ecological(e.g.,tropical,temperate,and boreal)groups of tree species,explored the biogeographical and phylogenetic patterns of wood density,and quantified the relative importance of current environmental factors(e.g.,climatic and soil variables)and evolutionary history(i.e.,phylogenetic relatedness among species and lineages)in driving global wood density variation.We found that wood density displayed a significant phylogenetic signal.Wood density differed among different biomes and climatic zones,with higher mean values of wood density in relatively drier regions(highest in subtropical desert).Our study revealed that at a global scale,for angiosperms and gymnosperms combined,phylogeny and species(representing the variance explained by taxonomy and not direct explained by long-term evolution process)explained 84.3%and 7.7%of total wood density variation,respectively,whereas current environment explained 2.7%of total wood density variation when phylogeny and species were taken into account.When angiosperms and gymnosperms were considered separately,the three proportions of explained variation are,respectively,84.2%,7.5%and 6.7%for angiosperms,and 45.7%,21.3%and 18.6%for gymnosperms.Our study shows that evolutionary history outpaced current environmental factors in shaping global variation in wood density.

Gymnosperms on the eve of the terminal Permian mass extinction in North China and their survival strategies

Main characteristics of the Permian redbed gymnosperms in North China have been summarized: dominant peltasperms and conifers, numerous enigmatics such as Gigantonoclea and Psygmophyllum, and abundant precursors of Mesozoic gymnosperms. Furthermore, stresses affecting these plants survival are suggested to be paleoatmospheric CO-2 concentration, water stress, wind and fire activities, and fungal infection. Consequently, a preliminary analysis accounts for the ecological strategies of these gymnosperms to the P-Tr event.

Cytological Mechanism of Cytoplasmic Inheritance in Pinus tabulaeformis: Ⅱ. Transmission of Male and Female Organelles During Fertilization and Proembryo Development

In an earlier report the ultrastructure and nucleoid organelles of male gamete in Pinus tabulaeformis Carr. have been described. Presently, the ultrastructure of the cytoplasm of the egg cell and pollen tube—immediately before fertilization and during cytoplasmic transmission of male gametophyte—has been described for the same species. The fate of parental plastids and mitochondria in the proembryo has also been followed. The mature egg cell contains a large amount of mitochondria, but seems to lack normal plastids. Most plastids have transformed into large inclusions. Apart from the large inclusions, there are abundant small inclusions and other organelles in the egg cell. During fertilization, pollen tube penetrates into the egg cell at the micropylar end and thereafter the contents are released. Plastid and mitochondrion of male origin are lacking near the fusing sperm_egg nuclei. The second sperm nucleus—not involved in karyogamy—remains at a site near the receptive vacuole. This nucleus is surrounded by large amount of male cytoplasm containing mixed organelles from the sperm cell, tube cell, and egg cell. At the free nuclear proembryo stage, organelles of male and female origin are visible in the perinucleus_cytoplasmic zone. Most of the mitochondria have the same morphological features as those in the egg cell. Some of the mitochondria appear to have originated from the sperm and tube cells. Plastids are most likely of male gametophyte origin because they have similar appearance as those of the sperm and tube cell. Large inclusions in the egg cell become vacuole_like. Paternal plastids have been incorporated into the neocytoplasm of the proembryo. In the cellular proembryo, maternal mitochondria are more abundant. Plastids resembling those of the sperm and tube cell are still present. These cytological results clearly show that in P. tabulaeformis, plastids are inherited paternally and mitochondria bipaternally. The cytological mechanism of plastid and mitochondrion inheritance in gymnosperm is discussed.

Development of Plant Embryology in China

The development of plant embryology in China can be roughly divided into three stages: (1) the initial stage, (2) the stage of establishing plant embryology as a branch of plant sciences, and (3) the stage when plant embryology evolves into plant reproductive biology with its vigorous development. It is in the third stage that research work in this field in China has developed rapidly and many of the significant achievements obtained are described in more details in this review. Researches of experimental embryology are not included in this paper.

Distribution and variability of n-alkanes in waxes of conifers

Epicuticular waxes have vital roles in the growth and development of plants and in defense. Conifers have a considerable amount of waxes on their cones and leaves.Here we characterized the n-alkane composition of Iranian conifers, including Juniperus oblonga, J. foetidissima, J.sabina, J. communis subsp. hemisphaerica, J. excelsa,Cupressus sempervirens, Platycladus orientalis from Cupressaceae and Taxus baccata from Taxaceae for the first time using GC-FID analyses. In the waxes, 25 n-alkane homologs with chain lengths ranging from C7 to C32 were identified. Short-chain n-alkanes were dominant in almost all samples with some exceptions. Complementary studies to elucidate complete wax constituents of Iranian conifers and n-alkane distribution pattern as a function of geographical and bioclimatic variables are recommended.

Cytological Mechanism of Cytoplasmic Inheritance in Pinus tabulaeformis: Ⅰ. Ultrastructural Aspects and Nucleoids of the Male Gametes

The cytological mechanism of plastid and mitochondrion inheritance in Pinus is an interesting research topic with only a limited number of published articles. The results indicate that the sperms of Pinus tabulaeformis Carr. contain abundant plastids, mitochondria and organelle DNA. These data provide reliable cytological evidence of paternal plastid and mitochondrion inheritance in Pinus . The results are in line with the confirmed general rule of paternal plastid inheritance in Pinaceae. But whether mitochondria in sperm cells can be transmitted into the embryos is an issue needs further developmental studies. Another important finding is that contrary to earlier classification of the male gamete of Pinaceae into the male nuclei type, the results reveal that male gametes in Pinus tabulaeformis are actually cells. However, the sperm cells are only surrounded by plasma membranes without cell walls. The larger leading sperm cell in a pollen tube section is long in shape, with a large amount of cytoplasm; while the second sperm cell is smaller, round in shape and contains less cytoplasm. Whether this feature of the male gamete type could be considered as a representative characteristic of the family is discussed and further conclusions await more experimental evidences from studies on plants from different species.

Male Cone Evolution in Conifers:Not All That Simple

Despite the simple structure of male conifer cones, there is an enormous variability in cone properties observed upon more careful examination. The diversity ranges from simple cones to compound cones. Moreover, cones can be distinguished according to different spatial distributions on the tree. Simple cones are distributed either as solitary cones or as fascicular or clustered aggregations, while compound cones only exhibit fascicular or clustered aggregations. Here, we demonstrate that these different spatial distribution patterns correlate with distinct leaf types and variable branching frequencies. Furthermore, we provide new insights into the evolution of the sporangiophore, particularly in Taxaceae. Two notably important and fast-evolving characters of conifers are the number of sporangia per sporangiophore and the number of sporangiophores per cone. We demonstrate, across many species and types of cones, how these characters are able to adjust according to the optimal amount of pollen.

Granule-bound and Soluble Starch Synthases in Post-Germination Pinus edulis Seedlings

Seedlings of the gymnosperm, Pinus edulis Engelm., have a distinctive pattern of starch accumulation following germination; however, the enzymes involved in starch synthesis have not been studied in gymnosperm species. In this study, enzymes and starch were extracted from P. edulis seedlings germinated in the dark at room temperature. Granule_bound proteins of 58 kD and 91 kD were recognized by a pea SS Ⅱ antiserum. The 58 kD granule_bound protein was purified and identified as granule_bound starch synthase Ⅰ by alignment of the N_terminal sequence with that of granule_bound starch synthase Ⅰ from several angiosperms. Elution of soluble starch synthase activity from a DEAE_Sepharose column showed two starch synthase activity peaks, indicating at least two isoforms of soluble starch synthases. Primer affinities of soluble starch synthases were investigated. Glycogen from rabbit was the best primer for soluble starch synthase. The enzymological properties of Pinus starch synthases appear to be similar to those reported for angiosperms.

Climate characteristics of the eastern Mongolian Plateau,China during the early Early Cretaceous(145-132 Ma):Palynological evidence from the Tongbomiao Formation in Well Hong-6,Hailar Basin

This study identified two palynological assemblages,namely Bayanhuasporites-Cycadopites-Protoconiferus and Cicatricosisporites-Cedripites-Perinopollenites,in the Tongbomiao Formation in the Hongqi Sag in the Hailar Basin,Inner Mongolia,China for the first time.The former is distributed in the lower part of the Tongbomiao Formation and is characterized by abundant gymnosperm pollen and diverse fern spores.Among them,the gymnosperm pollen is dominated by Paleoconifer(4.98%-31.62%)and Cycadopite(8.55%-25.23%)pollen grains and also includes other pollen grains such as Classopollis,Parcisporites,Erlianpollis,Callialasporites,and Jiaohepollis.The fern spores in the former palynological assemblage contain Bayanhuasporite(0-8.96%),Granulatisporites(0.93%-6.97%),and some important Cretaceous genera,such as Cicatricosisporites,Concavissimisporites,Densoisporites,Hsuisporites,Foraminisporis,and Leptolepidites.The Cicatricosisporites-Cedripites-Perinopollenites palynological assemblage is distributed in the upper part of the Tongbomiao Formation.Gymnosperm(77.30%),Pinaceae(31.9%),and Paleoconiferus(19.02%)pollen predominate this palynological assemblage,and Quadraeculina,Erlianpollis,and Jiaohepollis pollen are also common in this assemblage.The fern spores in this palynological assemblage include abundant Cicatricosisporites(4.29%).Besides,Concavissimisporites,Aequitriradites,and Leptolepidites are also common in this palynological assemblage.No angiosperm pollen has been found in both palynological assemblages.The identification of both palynological assemblages provides important evidence for the biostratigraphic correlation between the Hailar Basin and its adjacent areas.It also enables the reconstructions of the Berriasian-Valanginian(Early Cretaceous)vegetation and the paleoclimate on the eastern Mongolian Plateau during 141-132 Ma.The vegetation reconstructed on the palynological data of the represented by Hailar Basin in eastern Mongolian Plateau(141.6-141.4 Ma),form conifer forest or conifer broad-leaved mixed forest to conifer forest with shrubs and grassland,the climate belongs to warm temperate and warm-subtropicalt,the highest temperature is estimated to reach 35-38℃.Form 132.3 Ma,the vegetation type is conifer forest,and its paleoclimate is sub-humid warm temperate,the highest temperature is estimated to reach 24-29℃.

Molecular Characterization of a Dehydroascorbate Reductase from Pinus bungeana

Dehydroascorbate reductase （DHAR） plays a critical role in the ascorbate-glutathione recycling reaction for most higher plants. To date, studies on DHAR in higher plants have focused largely on Arabidopsis and agricultural plants, and there is virtually no information on the molecular characteristics of DHAR in gymnosperms. The present study reports the cloning and characteristics of a DHAR （PbDHAR） from a pine, Pinus bungeana Zucc. ex Endl. The PbDHAR gene encodes a protein of 215 amino acid residues with a calculated molecular mass of 24.26 kDa. The predicted 3-D structure of PbDHAR showed a typical glutathione S-transferase fold. Reverse transcripUon-polymerase chain reaction revealed that the PbDHAR was a constitutive expression gene in P. bungeana. The expression level of PbDHAR mRNA in P. bungeana seedlings did not show significant change under high temperature stress. The recombinant PbDHAR was overexpressed in Escherichia coil following purification with affinity chromatography. The recombinant PbDHAR exhibited enzymatic activity （19.84 i.mnol/min per mg） and high affinity （a Krn of 0.08 mM） towards the substrates dehydroascorbate （DHA）. Moreover, the recombinant PbDHAR was a thermostable enzyme, and retained 77% of its initial activity at 55℃. The present study is the first to provide a detailed molecular characterization of the DHAR in P. bungeana.

Pliocene taxodiaceous fossil wood from southwestern Ukraine and its palaeoenvironmental implications

Mineralized wood collected from Late Pliocene strata near Gorbki village in the Transcarpathian region of Beregovo Kholmogor’e in southwestern Ukraine was anatomically studied and identified.The wood possesses distinctive anatomical features and has distinct growth rings with an abrupt transition from early-to late-wood.Wood consists of tracheids with 1-3 seriate,dominating bi-seriate,opposite pits on the radial walls and taxodioid crossfield pitting,indentures present.Rays are uni-seriate and 1 to 73 cells high.Ray parenchyma horizontal walls thin and smooth.Axial parenchyma distributed in early-and late-wood and is solitary and diffuse,with end walls nearly smooth or slightly nodular.The combination of features observed in the wood indicates it belongs to the conifer family Taxodiaceae and is most similar to modern Sequoia and assigned to the fossil genus Sequoioxylon.Comparison with species of Sequoioxylon show it is most similar to Sequoioxylon burejense,but ray tracheids were not found in our specimens.We describe the specimens here as Sequoioxylon cf.s.burejense noting this similarity.Extant Sequoia is distributed in the northern California coastal forest eco-region of northern California and southern Oregon in the United States where they usually grow in a unique environment with heavy seasonal precipitation(2500 mm annually),cool coastal air and fog drip.This study supplies magafossil evidence of Sequoioxylon as an element of the Late Pliocene forest community in Ukraine and indicates a climate with heavy seasonal precipitation and fog drip.